bluuebunny/crossref_metadata_2025 huggingface dataset:
Plate Fixation for Unstable Displaced Distal Radius Fractures in Children
Authors: van Egmond Jeroen C. , Selles Caroline A. , Cleffken Berry I. , Roukema Gert R. , van der Vlies Kees H. , Schep Niels W.L.
Published: May 2019

Background Distal radius fractures in children are normally treated by plaster immobilization. For displaced unstable distal radius fractures, closed reduction and Kirschner wire (k-wire) fixation can be performed. Disadvantages of k-wire fixation are the need for postoperative plaster treatment for several weeks, which may induce stiffness, and the risks of complications such as tendon irritation and pin-track infections. More invasive volar plate fixation is less popular, although this allows for direct mobilization and enhances anatomical reduction.

Purpose To present the functional outcomes of pediatric patients treated with volar plate fixation for unstable displaced distal radius fractures.

Patients and Methods A retrospective cohort study of all consecutive pediatric patients between September 2010 and July 2017 was performed. A total of 26 patients with a median age of 12.5 years were included. The primary objective was functional outcome determined by the Patient-Rated Wrist Evaluation (PRWE) questionnaire. Secondary objectives were range of motion, grip strength, radiological parameters, complications, and incidence of plate removal.

Results Median PRWE score was 3 after a median follow-up of 29 months. Range of motion and grip strength did not differ significantly between the injured and uninjured wrists. No wound infections were found. Plate removal was performed in 15 patients (58%).

Conclusion Volar plate fixation for unstable displaced distal radius fractures in children provides good functional and radiological outcomes with minor complications.

Level of evidence This is a Level IV cohort study.
Invariant tori for two-dimensional nonlinear Schrödinger equations with large forcing terms
Authors: Geng Jiansheng , Xue Shuaishuai
Published: May 2019

We prove an infinite dimensional Kolmogorov–Arnold–Moser theorem. As an application, we use the theorem to study the two-dimensional forced nonlinear Schrödinger equation with periodic boundary conditions, and we emphasize that the forced term is not small perturbation. We obtain a Whitney smooth family of small-amplitude quasiperiodic solutions which are partially hyperbolic.
Single- and double-resonant enhancement of second-harmonic generation in asymmetric AlGaN/GaN/AlGaN quantum well heterostructures
Authors: Saidi Imen
Published: May 2019

The second-harmonic generation susceptibility is theoretically investigated based on the compact density-matrix formalism in two- and three-level AlGaN/GaN systems. The electronic states and their related wave functions were calculated by solving self-consistently the Schrödinger–Poisson equations within the effective mass and Hartree approximations. The presence of spontaneous and piezoelectric polarizations is taken into account in the modeling part. It was revealed from the relevant results that (i) the second-order susceptibility shows a multiple peak structure due to intersubband and their corresponding virtual transitions, (ii) the use of a back doping as well as the optimization of the layer widths in delta-doped AlGaN/GaN asymmetric quantum wells improved considerably the second-harmonic susceptibility, and (iii) the three-level AlGaN/GaN system is the most efficient structure, which generates the second-harmonic with a significant intensity up to 4.36 × 10−5 mV−1. Numerical results of the present work could lay the basis for research in AlGaN-related optoelectronic device applications.
Existence of conformal symmetries in locally rotationally symmetric spacetimes: Some covariant results
Authors: Singh Sayuri , Goswami Rituparno , Maharaj Sunil D.
Published: May 2019

In this paper, we investigate conformal symmetries in Locally Rotationally Symmetric (LRS) spacetimes using a semitetrad covariant formalism. We establish that a general LRS spacetime, with simultaneous rotation and spatial twist, must contain a conformal Killing vector in the plane spanned by the fluid flow lines and the preferred spatial direction. If this conformal vector is Killing, then these spacetimes are just tilted solutions of class I or class III. We then transparently show the existence of more general conformal Killing vectors and establish covariant relations between different geometric quantities in these spacetimes. We also prove that a null Killing horizon can exist in these spacetimes when they are simultaneously rotating and twisting and the heat flux attains an extremal value. Our results compliment the earlier work of van den Bergh.
Fluctuation-dissipation in active matter
Authors: Burkholder Eric W. , Brady John F.
Published: May 2019

In a colloidal suspension at equilibrium, the diffusive motion of a tracer particle due to random thermal fluctuations from the solvent is related to the particle’s response to an applied external force, provided this force is weak compared to the thermal restoring forces in the solvent. This is known as the fluctuation-dissipation theorem (FDT) and is expressed via the Stokes-Einstein-Sutherland (SES) relation D = kBT/ζ, where D is the particle’s self-diffusivity (fluctuation), ζ is the drag on the particle (dissipation), and kBT is the thermal Boltzmann energy. Active suspensions are widely studied precisely because they are far from equilibrium—they can generate significant nonthermal internal stresses, which can break the detailed balance and time-reversal symmetry—and thus cannot be assumed to obey the FDT a priori. We derive a general relationship between diffusivity and mobility in generic colloidal suspensions (not restricted to near equilibrium) using generalized Taylor dispersion theory and derive specific conditions on particle motion required for the FDT to hold. Even in the simplest system of active Brownian particles (ABPs), these conditions may not be satisfied. Nevertheless, it is still possible to quantify deviations from the FDT and express them in terms of an effective SES relation that accounts for the ABPs conversion of chemical into kinetic energy.
First-principles study of interfacial magnetoelectric coupling in Fe3Ga/BaTiO3/Fe3Ga heterostructure
Authors: Zhong Gaokuo , Zou Daifeng , Xie Shuhong , Li Jiangyu
Published: May 2019

Electrically controlled magnetism is highly desirable for future magnetic memories and spintronic devices. In this work, magnetoelectric (ME) coupling at the interfaces in the Fe3Ga/BaTiO3/Fe3Ga heterostructure is investigated by using first-principles calculations. It is found that the ME coupling in the Fe3Ga/BaTiO3/Fe3Ga heterostructure originates from interfacial bonding, which results in a changed magnetization of interfacial atoms when the ferroelectric layer reverses its polarization direction. The results of electronic density of states indicate that the induced magnetization arises from the changed hybridization state among the d-orbitals of interfacial Fe and Ti atoms. The ME coefficient of the Fe3Ga/BaTiO3 bilayer structure is estimated to be 4.13 × 10−7 μB m/V from the change of magnetic moment induced by polarization reversal, providing a theoretical guidance on further development of multiferroic heterostructures for potential multifunctional device applications.
Approaching a burning plasma on the NIF
Authors: Hurricane O. A. , Springer P. T. , Patel P. K. , Callahan D. A. , Baker K. , Casey D. T. , Divol L. , Döppner T. , Hinkel D. E. , Hohenberger M. , Berzak Hopkins L. F. , Jarrott C. , Kritcher A. , Le Pape S. , Maclaren S. , Masse L. , Pak A. , Ralph J. , Thomas C. , Volegov P. , Zylstra A.
Published: May 2019

The locus of National Ignition Facility (NIF) inertial confinement fusion (ICF) implosion data, in hot-spot burn-average areal density (ρR) and Brysk temperature (T) space, is shown and illustrates that several implosions are nearing a burning plasma state, where α-heating is the dominant source of plasma heating. A formula for diagnosing a burning plasma using measured/inferred data from ICF implosion experiments is given with the underlying derivation. Plotting ICF implosion performance against inferred hot-spot energy illustrates the key need to maximize the delivery of energy to an implosion hot-spot. A very compact analytical equation for α-heating is given, which shows that fundamentally, α-heating provides a discrete “boost” to pVγ of an implosion hot-spot. It is then shown numerically that the analytical expression for the amplification of pVγ is simply related to yield amplification and to other more famous metrics used for inferring yield amplification in experiments. Interestingly, the argument of the pVγ boost equation appears to provide a fundamental ignition condition that implicitly includes the effects of asymmetry, and it also exposes the origin of why there is uncertainty in defining single ignition criteria. The resulting analysis of NIF implosion data indicates that an increase in burn-average hot-spot temperature will be needed in order to ignite, and the strategy being pursued to achieve this goal is outlined.
Self-dual gravity via Hitchin’s equations
Authors: Chacón Erick , García-Compeán Hugo
Published: May 2019

In this work, half-flat metrics are obtained from Hitchin’s equations. The SU(∞) Hitchin’s equations are obtained, and as a consequence of them, the Husain-Park equation is found. Certain solutions of Hitchin’s equations with gauge group SU(2) associated with Liouville, sinh-Gordon, and Painlevé III equations are used to find solutions of the SU(∞) Hitchin’s equations. This is achieved via the Moyal deformation of Hitchin’s equations. From these solutions, Hamiltonian vector fields are determined, which in turn are used to construct the half-flat metrics. Following an approach of Dunajski, Mason, and Woodhouse, it is also possible to construct half-flat metrics on M×CP1, where M is R2 or S2.
Comparison of a 2D nonlocal transport model to ECRH experiments in LHD
Authors: Maggs J. E. , Morales G. J.
Published: May 2019

A recently developed model of nonlocal transport in two dimensions (2D), the “iterative method” [J. E. Maggs and G. J. Morales, Phys. Rev. E 99, 013307 (2019)], is applied to the published results of ECRH experiments [Takahashi et al. AIP Conf. Proc. 1580, 145 (2014)] performed in the Large Helical Device. It is found from the temperature profiles obtained from the 2D model that the sharply peaked electron temperature profiles observed in such experiments, and previously associated with local transport and “internal transport barriers” or Core Electron-Root Confinement, are also consistent with nonlocal transport. It is shown that the iterative method is suited to handling both scenarios.
Quantum-classical path integral with a harmonic treatment of the back-reaction
Authors: Wang Fei , Makri Nancy
Published: May 2019

The quantum-classical path integral (QCPI) provides a rigorous methodology for simulating condensed phase processes when a fully quantum mechanical description of a small subsystem is necessary. While full QCPI calculations have been shown to be feasible on parallel computing platforms, the large number of trajectory calculations required leads to computational cost that significantly exceeds that of classical molecular dynamics calculations. This paper describes the harmonic back-reaction (HBR) approximation to the QCPI expression, which reduces dramatically the computational cost by requiring a single classical trajectory from each initial condition. Test calculations on a model of strongly anharmonic oscillators show that the HBR treatment quantitatively reproduces the full QCPI results. The HBR-QCPI algorithm is applicable to a variety of condensed phase and biological systems with effort only somewhat greater than that of molecular dynamics simulations.
Towards surface diffusion potential mapping on atomic length scale
Authors: Villarreal Renan , Kirkham Christopher J. , Scarfato Alessandro , Bowler David R. , Renner Christoph
Published: May 2019

The surface diffusion potential landscape plays an essential role in a number of physical and chemical processes such as self-assembly and catalysis. Diffusion energy barriers can be calculated theoretically for simple systems, but there is currently no experimental technique to systematically measure them on the relevant atomic length scale. Here, we introduce an atomic force microscopy based method to semiquantitatively map the surface diffusion potential on an atomic length scale. In this proof of concept experiment, we show that the atomic force microscope damping signal at constant frequency-shift can be linked to nonconservative processes associated with the lowering of energy barriers and compared with calculated single-atom diffusion energy barriers.
Numerical investigation of piston-modal wave resonance in the narrow gap formed by a box in front of a wall
Authors: Jiang Sheng-chao , Bai Wei , Tang Guoqiang
Published: May 2019

Piston-modal wave resonance between a ship section and a bottom mounted terminal is studied by employing a numerical wave flume based on OpenFOAM® package. A systematic investigation on the piston-modal behavior is performed to characterize the influence of fluid viscosity and flow rotation. Around the resonant frequency, the fluid viscosity and flow rotation not only dissipate the wave amplitude in the narrow gap, but also increase the wave amplitude in the upstream of the box. The dynamic mechanism behind the phenomenon is found to be the interaction between the energy dissipation induced by the fluid vortical flow and energy transformation associated with free surface motion. The increased incident wave amplitude can cause the normalized wave amplitudes and wave forces to deviate more from the potential flow results, while the variation of reflection coefficient is dependent on box-wall geometries. All of these phenomena imply a more significant effect of fluid viscosity and flow rotation with the increase of incident wave amplitude, but the energy dissipation is not the only factor in piston-modal resonance.
The effects of cool ion temperature on fast ion-acoustic soliton stopbands in a plasma with two positive ion species
Authors: Maharaj S. K. , Bharuthram R.
Published: May 2019

The existence of stopbands was reported for the very first time in a study of fast ion-acoustic solitons by Nsengiyumva et al. [Phys. Plasmas 21, 102301 (2014)] in a plasma with cold ions, warm (adiabatic) ions, and Boltzmann electrons. We recall that a stopband is a range of speeds (Mach numbers) for which solitons cannot propagate. In this paper, we investigate the effect of the temperature of the cooler ions on stopbands. It is found that the Mach number range for the stopbands and the range of cool ion densities over which the stopbands occur become narrower with increasing temperature of the cooler ions, until the stopbands vanish at an upper limiting value. The extension of the model to include nonthermal effects for the electrons reveals that the range of cool ion temperatures which favors the existence of stopbands becomes wider for a kappa electron distribution, but narrower when the electrons are Cairns distributed for increasing strength of the nonthermal coefficient.
Relativistic and QED effects on NMR magnetic shielding constant of neutral and ionized atoms and diatomic molecules
Authors: Kozioł Karol , Aucar I. Agustín , Aucar Gustavo A.
Published: May 2019

We show here results of four-component calculations of nuclear magnetic resonance σ for atoms with 10 ≤ Z ≤ 86 and their ions, within the polarization propagator formalism at its random phase level of approach, and the first estimation of quantum electrodynamic (QED) effects and Breit interactions of those atomic systems by using two theoretical effective models. We also show QED corrections to σ(X) in simple diatomic HX and X2 (X = Br, I, At) molecules. We found that the Z dependence of QED corrections in bound-state many-electron systems is proportional to Z5, which is higher than its dependence in H-like systems. The analysis of relativistic ee (or paramagneticlike) and pp (or diamagneticlike) terms of σ exposes two different patterns: the pp contribution arises from virtual electron-positron pair creation/annihilation and the ee contribution is mainly given by 1s → ns and 2s → ns excitations. The QED effects on shieldings have a negative sign, and their magnitude is larger than 1% of the relativistic effects for high-Z atoms such as Hg and Rn, and up to 0.6% of its total four-component value for neutral Rn. Furthermore, percentual contributions of QED effects to the total shielding are larger for ionized than for neutral atoms. In a molecule, the contribution of QED effects to σ(X) is determined by its highest-Z atoms, being up to −0.6% of its total σ value for astatine compounds. It is found that QED effects grow faster than relativistic effects with Z.
Multi-stream instability of a single long electron bunch in a storage ring
Authors: Beaudoin B. L. , Haber I. , Kishek R. A. , Koeth T. W. , Antonsen T. M.
Published: May 2019

A multistream instability is observed experimentally during the longitudinal expansion of an electron beam in a storage ring. The instability is observed when the beam expands in length to several times the circumference of the ring so that portions of the beam overlap. While portions of the beam overlap in physical space, they form multiple streams and remain separate in velocity space. The streams become unstable as their number increases and their separation in velocity decreases. An analytical theory predicts the onset of the instability, in agreement with simulations and measurements, over a wide range of peak line-charge densities (10.3 pC/m–1.8 nC/m) and bunch lengths. This work extends previous calculations to include the dynamic nonlinear elongation of the bunch, with a given initial length, and defines an onset criterion for the filament velocity separation for the beam to be unstable.
Optimizing Ag-Pt core-shell nanostructures for solar energy conversion, plasmonic photocatalysis, and photothermal catalysis
Authors: Chen Yun , Zhai Yanni , Deng Liren , Wang Ningning , Mao Yihui , Yang Jinglong , Huang Yu
Published: May 2019

As a promising plasmonic photocatalyst, an Ag-Pt core-shell nanostructure is able to convert sunlight into chemical energy. To fully exploit each function of the constituent materials, a numerical study on the optimal design of the hybrid nanostructures is presented in this work. Ag-Pt is demonstrated to be a good material configuration for the core-shell nanostructure because Ag has strong intrinsic plasmonic responses and a low imaginary dielectric function in the visible region, while Pt is catalytically active and has a large imaginary dielectric function. Considering the hot carrier generation and transfer processes in both plasmonic photocatalysis and photothermal catalysis, the catalytically active sites at the Pt shell can be revealed by high local heating power densities. For the dipole resonance, these sites distribute alternately with the spots where local electric fields are greatly enhanced. The former are along the “equatorial belt” of the nanoparticle, while the latter are in the two polar regions. It is then found that the high-efficiency hot carrier generation is related to multiple factors, including at least an ultrathin shell and a core of high aspect ratio with sharp tips. The physics behind these factors is further addressed.
Thin Ti adhesion layer breaks bottleneck to hot hole relaxation in Au films
Authors: Zhou Xin , Tokina Marina V. , Tomko John A. , Braun Jeffrey L. , Hopkins Patrick E. , Prezhdo Oleg V.
Published: May 2019

Slow relaxation of highly excited (hot) charge carriers can be used to increase efficiencies of solar cells and related devices as it allows hot carriers to be extracted and utilized before they relax and lose energy. Using a combination of real-time density functional theory and nonadiabatic molecular dynamics, we demonstrate that nonradiative relaxation of excited holes in an Au film slows down 30-fold as holes relax across the energy range −2 to −1.5 eV below the Fermi level. This effect arises due to sharp decreases in density of states (DOS) and reduced hole-phonon coupling in this energy range. Furthermore, to improve adhesion, a thin film of transition metal, such as Ti, is often inserted between the noble metal layer and its underlying substrate; we demonstrate that this adhesion layer completely eliminates the hot-hole bottleneck because it significantly, 7-fold per atom, increases the DOS in the critical energy region between −1.5 eV and the Fermi level, and because Ti atoms are 4-times lighter than Au atoms, high frequency phonons are introduced and increase the charge-phonon coupling. The detailed ab initio analysis of the charge-phonon scattering emphasizes the nonequilibrium nature of the relaxation processes and provides important insights into the energy flow in metal films. The study suggests that energy losses to heat can be greatly reduced by judicious selection of adhesion layers that do not involve light atoms and have relatively low DOS in the relevant energy range. Inversely, narrow Ti adhesion layers assist heat dissipation needed in electronics applications.
Exact subsystem time-dependent density-functional theory
Authors: Tölle Johannes , Böckers Michael , Neugebauer Johannes
Published: May 2019

In this communication, we show that coupled subsystem time-dependent density functional theory (subsystem TDDFT) [J. Neugebauer, J. Chem. Phys. 126, 134116 (2007)] in combination with projection-based embedding (PbE) is an exact subsystem theory in the sense that supermolecular TDDFT excitation energies can exactly be restored. A correct handling of the kernel contribution due to the enforced orthogonality is crucial in this context, which leads to different PbE kernel contributions in the A and B matrices of the general TDDFT eigenvalue problem. Although this formalism has been proposed before [D. V. Chulhai and L. Jensen, Phys. Chem. Chem. Phys. 18, 21032 (2016)], the symmetric eigenvalue problem used in that work implicitly introduces an approximation concerning this kernel contribution. We show that our treatment numerically exactly reproduces supermolecular results for the previously investigated helium dimer and for the fluoroethane molecule as a more challenging case with a partitioning of a covalent bond. We also demonstrate that the symmetric approximation can lead to significant deviations, including a wrong ordering of electronic transitions.
Applying causal models to explore the mechanism of action of simvastatin in progressive multiple sclerosis
Authors: Eshaghi Arman , Kievit Rogier A. , Prados Ferran , Sudre Carole H. , Nicholas Jennifer , Cardoso M. Jorge , Chan Dennis , Nicholas Richard , Ourselin Sebastien , Greenwood John , Thompson Alan J. , Alexander Daniel C. , Barkhof Frederik , Chataway Jeremy , Ciccarelli Olga
Published: May 2019

Understanding the mode of action of drugs is a challenge with conventional methods in clinical trials. Here, we aimed to explore whether simvastatin effects on brain atrophy and disability in secondary progressive multiple sclerosis (SPMS) are mediated by reducing cholesterol or are independent of cholesterol. We applied structural equation models to the MS-STAT trial in which 140 patients with SPMS were randomized to receive placebo or simvastatin. At baseline, after 1 and 2 years, patients underwent brain magnetic resonance imaging; their cognitive and physical disability were assessed on the block design test and Expanded Disability Status Scale (EDSS), and serum total cholesterol levels were measured. We calculated the percentage brain volume change (brain atrophy). We compared two models to select the most likely one: a cholesterol-dependent model with a cholesterol-independent model. The cholesterol-independent model was the most likely option. When we deconstructed the total treatment effect into indirect effects, which were mediated by brain atrophy, and direct effects, simvastatin had a direct effect (independent of serum cholesterol) on both the EDSS, which explained 69% of the overall treatment effect on EDSS, and brain atrophy, which, in turn, was responsible for 31% of the total treatment effect on EDSS [β = −0.037; 95% credible interval (CI) = −0.075, −0.010]. This suggests that simvastatin’s beneficial effects in MS are independent of its effect on lowering peripheral cholesterol levels, implicating a role for upstream intermediate metabolites of the cholesterol synthesis pathway. Importantly, it demonstrates that computational models can elucidate the causal architecture underlying treatment effects in clinical trials of progressive MS.
Serotonin regulates mitochondrial biogenesis and function in rodent cortical neurons via the 5-HT2Areceptor and SIRT1–PGC-1α axis
Authors: Fanibunda Sashaina E. , Deb Sukrita , Maniyadath Babukrishna , Tiwari Praachi , Ghai Utkarsha , Gupta Samir , Figueiredo Dwight , Weisstaub Noelia , Gingrich Jay A. , Vaidya Ashok D. B. , Kolthur-Seetharam Ullas , Vaidya Vidita A.
Published: May 2019

Significance

Neuronal mitochondria are crucial organelles that regulate bioenergetics and also modulate survival and function under environmental challenges. Here, we show that the neurotransmitter serotonin (5-HT) plays an important role in the making of new mitochondria (mitochondrial biogenesis) in cortical neurons, through the 5-HT2Areceptor and via master regulators of mitochondrial biogenesis, SIRT1 and PGC-1α. Mitochondrial function is also enhanced by 5-HT, increasing cellular respiration and ATP, the energy currency of the cell. We found 5-HT reduces cellular reactive oxygen species and exerts potent neuroprotective action in neurons challenged with stress, an effect that requires SIRT1. These findings highlight a role for the mitochondrial effects of 5-HT in the facilitation of stress adaptation and identify drug targets to ameliorate mitochondrial dysfunction in neurons.
Suppressor screening reveals common kleisin–hinge interaction in condensin and cohesin, but different modes of regulation
Authors: Xu Xingya , Yanagida Mitsuhiro
Published: May 2019

Cohesin and condensin play fundamental roles in sister chromatid cohesion and chromosome segregation, respectively. Both consist of heterodimeric structural maintenance of chromosomes (SMC) subunits, which possess a head (containing ATPase) and a hinge, intervened by long coiled coils. Non-SMC subunits (Cnd1, Cnd2, and Cnd3 for condensin; Rad21, Psc3, and Mis4 for cohesin) bind to the SMC heads. Here, we report a large number of spontaneous extragenic suppressors for fission yeast condensin and cohesin mutants, and their sites were determined by whole-genome sequencing. Mutants of condensin’s non-SMC subunits were rescued by impairing the SUMOylation pathway. Indeed, SUMOylation of Cnd2, Cnd3, and Cut3 occurs in midmitosis, and Cnd3 K870 SUMOylation functionally opposes Cnd subunits. In contrast, cohesin mutants
rad21
and
psc3
were rescued by loss of the RNA elimination pathway (Erh1, Mmi1, and Red1), and loader mutant
mis4
was rescued by loss of Hrp1-mediated chromatin remodeling. In addition, distinct regulations were discovered for condensin and cohesin hinge mutants. Mutations in the N-terminal helix bundle [containing a helix–turn–helix (HTH) motif] of kleisin subunits (Cnd2 and Rad21) rescue virtually identical hinge interface mutations in cohesin and condensin, respectively. These mutations may regulate kleisin’s interaction with the coiled coil at the SMC head, thereby revealing a common, but previously unknown, suppression mechanism between the hinge and the kleisin N domain, which is required for successful chromosome segregation. We propose that in both condensin and cohesin, the head (or kleisin) and hinge may interact and collaboratively regulate the resulting coiled coils to hold and release chromosomal DNAs.
Refining effect of nitrogen on M7C3 carbides in hypereutectic Fe–25Cr–4C–0.5Ti–0.5Nb hardface coatings
Authors: Wang Jibo , Xing Xiaolei , Zhou Yefei , Qi Xiaowen , Yang Qingxiang
Published: May 2019

Hypereutectic Fe–Cr–C–Ti–Nb coatings with N additives were developed by surface-hardening welding (hardfacing). The experimental results showed that the primary M7C3 carbides were refined by the N additives in the coatings. Based on the micro-morphologies of M7C3 and (Ti,Nb)(C,N), the (Ti,Nb)(C,N) was present inside the primary M7C3 carbides, and they were tightly combined. The mismatch between the (010) crystal plane of M7C3 and the (110) crystal plane of (Ti,Nb)(C,N) was 6.15%, which indicated that (Ti,Nb)(C,N) was moderately effective as a heterogeneous nucleus of M7C3 carbides. Therefore, the preferentially precipitated (Ti,Nb)(C,N) in the Fe–Cr–C–Ti–Nb coating was the heterogeneous nucleus of the primary M7C3 carbides and thereby refined the primary M7C3 carbides.
Photoluminescence properties of ultrathin CsPbCl3 nanowires on mica substrate
Authors: Gao Yan , Zhao Liyun , Shang Qiuyu , Li Chun , Liu Zhen , Li Qi , Wang Xina , Zhang Qing
Published: May 2019

Fabricating high-quality cesium lead chloride (CsPbCl3) perovskite nanowires (NWs) with dimension below 10 nm is not only of interests in fundamental physics, but also holds the great promise for optoelectronic applications. Herein, ultrathin CsPbCl3 NWs with height of ~7 nm, have been achieved via vapor phase deposition method. Power and temperature-dependent photoluminescence (PL) spectroscopy is performed to explore the emission properties of the CsPbCl3 NWs. Strong free exciton recombination is observed at ~3.02 eV as the temperature (T) is 78−294 K with binding energy of ~ 37.5 meV. With the decreasing of T, the PL peaks exhibit a first blueshift by 2 meV for T ~ 294−190 K and then a redshift by 4 meV for T ~ 190−78 K. The exciton–optical phonon interaction plays a major role in the linewidth broadening of the PL spectra with average optical phonon energy of ~48.0 meV and the interaction coefficient of 203.9 meV. These findings advance the fabrication of low dimensional CsPbCl3 perovskite and provide insights into the photophysics of the CsPbCl3 perovskite.
Assessing the cumulative adverse effects of offshore wind energy development on seabird foraging guilds along the East Coast of the United States
Authors: Goodale M Wing , Milman Anita , Griffin Curtice R
Published: May 2019

Offshore wind farms are rapidly being permitted along the East Coast of the US, and with subsequent development could cumulatively affect seabird populations. Yet, the seabird guilds most likely at risk of cumulative effects have not been identified. Assessments of cumulative effects must first calculate the cumulative exposure of seabirds to areas suitable for offshore wind farms and then estimate how exposure will affect populations. This paper addresses this first need, and quantifies how three different wind farm siting scenarios could cumulatively expose seven seabird foraging guilds. The coastal bottom gleaner guild (sea ducks) would be exposed at similar rates regardless of siting decision, while other coastal guilds would be exposed at a higher rate when projects are built in shallow areas and close to shore rather than in high-wind areas. The pelagic seabird guild would be exposed at high rates when projects are built in high-wind areas. There was no single offshore wind siting scenario that reduced the cumulative exposure for all guilds. Based upon these findings, we identify the foraging guilds most likely to be cumulatively exposed and propose an approach for siting and mitigation that may reduce cumulative exposure for all guilds.
Counting cusped hyperbolic 3-manifolds that bound geometrically
Authors: Kolpakov Alexander , Riolo Stefano
Published: May 2019

We show that the number of isometry classes of cusped hyperbolic

3
3

-manifolds that bound geometrically grows at least super-exponentially with their volume, both in the arithmetic and non-arithmetic settings.
Testing isomorphism of graded algebras
Authors: Brooksbank Peter , O’Brien E. , Wilson James
Published: May 2019

We present a new algorithm to decide isomorphism between finite graded algebras. For a broad class of nilpotent Lie algebras, we demonstrate that it runs in time polynomial in the order of the input algebras. We introduce heuristics that often dramatically improve the performance of the algorithm and report on an implementation in Magma.
Bayesian metabolic flux analysis reveals intracellular flux couplings
Authors: Heinonen Markus , Osmala Maria , Mannerström Henrik , Wallenius Janne , Kaski Samuel , Rousu Juho , Lähdesmäki Harri
Published: May 2019

Motivation

Metabolic flux balance analysis (FBA) is a standard tool in analyzing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place model assumptions on fluxes due to the convenience of formulating the problem as a linear programing model, while many methods do not consider the inherent uncertainty in flux estimates.

Results

We introduce a novel paradigm of Bayesian metabolic flux analysis that models the reactions of the whole genome-scale cellular system in probabilistic terms, and can infer the full flux vector distribution of genome-scale metabolic systems based on exchange and intracellular (e.g. 13C) flux measurements, steady-state assumptions, and objective function assumptions. The Bayesian model couples all fluxes jointly together in a simple truncated multivariate posterior distribution, which reveals informative flux couplings. Our model is a plug-in replacement to conventional metabolic balance methods, such as FBA. Our experiments indicate that we can characterize the genome-scale flux covariances, reveal flux couplings, and determine more intracellular unobserved fluxes in Clostridium acetobutylicum from 13C data than flux variability analysis.

Availability and implementation

The COBRA compatible software is available at github.com/markusheinonen/bamfa.

Supplementary information

Supplementary data are available at Bioinformatics online.
FunDMDeep-m6A: identification and prioritization of functional differential m6A methylation genes
Authors: Zhang Song-Yao , Zhang Shao-Wu , Fan Xiao-Nan , Zhang Teng , Meng Jia , Huang Yufei
Published: May 2019

Motivation

As the most abundant mammalian mRNA methylation, N6-methyladenosine (m6A) exists in >25% of human mRNAs and is involved in regulating many different aspects of mRNA metabolism, stem cell differentiation and diseases like cancer. However, our current knowledge about dynamic changes of m6A levels and how the change of m6A levels for a specific gene can play a role in certain biological processes like stem cell differentiation and diseases like cancer is largely elusive.

Results

To address this, we propose in this paper FunDMDeep-m6A a novel pipeline for identifying context-specific (e.g. disease versus normal, differentiated cells versus stem cells or gene knockdown cells versus wild-type cells) m6A-mediated functional genes. FunDMDeep-m6A includes, at the first step, DMDeep-m6A a novel method based on a deep learning model and a statistical test for identifying differential m6A methylation (DmM) sites from MeRIP-Seq data at a single-base resolution. FunDMDeep-m6A then identifies and prioritizes functional DmM genes (FDmMGenes) by combing the DmM genes (DmMGenes) with differential expression analysis using a network-based method. This proposed network method includes a novel m6A-signaling bridge (MSB) score to quantify the functional significance of DmMGenes by assessing functional interaction of DmMGenes with their signaling pathways using a heat diffusion process in protein-protein interaction (PPI) networks. The test results on 4 context-specific MeRIP-Seq datasets showed that FunDMDeep-m6A can identify more context-specific and functionally significant FDmMGenes than m6A-Driver. The functional enrichment analysis of these genes revealed that m6A targets key genes of many important context-related biological processes including embryonic development, stem cell differentiation, transcription, translation, cell death, cell proliferation and cancer-related pathways. These results demonstrate the power of FunDMDeep-m6A for elucidating m6A regulatory functions and its roles in biological processes and diseases.

Availability and implementation

The R-package for DMDeep-m6A is freely available from https://github.com/NWPU-903PR/DMDeepm6A1.0.

Supplementary information

Supplementary data are available at Bioinformatics online.
A statistical simulator scDesign for rational scRNA-seq experimental design
Authors: Li Wei Vivian , Li Jingyi Jessica
Published: May 2019

Motivation

Single-cell RNA sequencing (scRNA-seq) has revolutionized biological sciences by revealing genome-wide gene expression levels within individual cells. However, a critical challenge faced by researchers is how to optimize the choices of sequencing platforms, sequencing depths and cell numbers in designing scRNA-seq experiments, so as to balance the exploration of the depth and breadth of transcriptome information.

Results

Here we present a flexible and robust simulator, scDesign, the first statistical framework for researchers to quantitatively assess practical scRNA-seq experimental design in the context of differential gene expression analysis. In addition to experimental design, scDesign also assists computational method development by generating high-quality synthetic scRNA-seq datasets under customized experimental settings. In an evaluation based on 17 cell types and 6 different protocols, scDesign outperformed four state-of-the-art scRNA-seq simulation methods and led to rational experimental design. In addition, scDesign demonstrates reproducibility across biological replicates and independent studies. We also discuss the performance of multiple differential expression and dimension reduction methods based on the protocol-dependent scRNA-seq data generated by scDesign. scDesign is expected to be an effective bioinformatic tool that assists rational scRNA-seq experimental design and comparison of scRNA–seq computational methods based on specific research goals.

Availability and implementation

We have implemented our method in the R package scDesign, which is freely available at https://github.com/Vivianstats/scDesign.

Supplementary information

Supplementary data are available at Bioinformatics online.
Representation transfer for differentially private drug sensitivity prediction
Authors: Niinimäki Teppo , Heikkilä Mikko A , Honkela Antti , Kaski Samuel
Published: May 2019

Motivation

Human genomic datasets often contain sensitive information that limits use and sharing of the data. In particular, simple anonymization strategies fail to provide sufficient level of protection for genomic data, because the data are inherently identifiable. Differentially private machine learning can help by guaranteeing that the published results do not leak too much information about any individual data point. Recent research has reached promising results on differentially private drug sensitivity prediction using gene expression data. Differentially private learning with genomic data is challenging because it is more difficult to guarantee privacy in high dimensions. Dimensionality reduction can help, but if the dimension reduction mapping is learned from the data, then it needs to be differentially private too, which can carry a significant privacy cost. Furthermore, the selection of any hyperparameters (such as the target dimensionality) needs to also avoid leaking private information.

Results

We study an approach that uses a large public dataset of similar type to learn a compact representation for differentially private learning. We compare three representation learning methods: variational autoencoders, principal component analysis and random projection. We solve two machine learning tasks on gene expression of cancer cell lines: cancer type classification, and drug sensitivity prediction. The experiments demonstrate significant benefit from all representation learning methods with variational autoencoders providing the most accurate predictions most often. Our results significantly improve over previous state-of-the-art in accuracy of differentially private drug sensitivity prediction.

Availability and implementation

Code used in the experiments is available at https://github.com/DPBayes/dp-representation-transfer.
Enabling Green and Blue Infrastructure to Improve Contributions to Human Well-Being and Equity in Urban Systems
Authors: Andersson Erik , Langemeyer Johannes , Borgström Sara , McPhearson Timon , Haase Dagmar , Kronenberg Jakub , Barton David N , Davis McKenna , Naumann Sandra , Röschel Lina , Baró Francesc
Published: May 2019

The circumstances under which different ecosystem service benefits can be realized differ. The benefits tend to be coproduced and to be enabled by multiple interacting social, ecological, and technological factors, which is particularly evident in cities. As many cities are undergoing rapid change, these factors need to be better understood and accounted for, especially for those most in need of benefits. We propose a framework of three systemic filters that affect the flow of ecosystem service benefits: the interactions among green, blue, and built infrastructures; the regulatory power and governance of institutions; and people's individual and shared perceptions and values. We argue that more fully connecting green and blue infrastructure to its urban systems context and highlighting dynamic interactions among the three filters are key to understanding how and why ecosystem services have variable distribution, continuing inequities in who benefits, and the long-term resilience of the flows of benefits.
Loss of Foxg1 Impairs the Development of Cortical SST-Interneurons Leading to Abnormal Emotional and Social Behaviors
Authors: Chen Dongsheng , Wang Chunlian , Li Meiyi , She Xinyu , Yuan Yonggui , Chen Huanxin , Zhang Weining , Zhao Chunjie
Published: May 2019

FOXG1 syndrome is a severe encephalopathy that exhibit intellectual disability, emotional disorder, and limited social communication. To elucidate the contribution of somatostatin-expressing interneurons (SST-INs) to the cellular basis underlying FOXG1 syndrome, here, by crossing SST-cre with a Foxg1fl/fl line, we selectively ablated Foxg1. Loss of Foxg1 resulted in an obvious reduction in the number of SST-INs, accompanied by an altered ratio of subtypes. Foxg1-deficient SST-INs exhibited decreased membrane excitability and a changed ratio of electrophysiological firing patterns, which subsequently led to an excitatory/inhibitory imbalance. Moreover, cognitive defects, limited social interactions, and depression-like behaviors were detected in Foxg1 cKO mice. Treatment with low-dose of clonazepam effectively alleviated the defects. These results identify a link of SST-IN development to the aberrant emotion, cognition, and social capacities in patients. Our findings identify a novel role of Foxg1 in SST-IN development and put new insights into the cellular basis of FOXG1 syndrome.
Outcome of periodontal–orthodontic treatment in subjects with periodontal disease. Part II: a CBCT study of alveolar bone level changes
Authors: Zasčiurinskienė Eglė , Lund Henrik , Lindsten Rune , Jansson Henrik , Bjerklin Krister
Published: May 2019

Aim

To examine alveolar bone level (ABL) changes before (T1) and after (T2) orthodontic treatment (OT) in subjects with periodontal disease.

Methods

The study included 50 subjects with periodontal disease. All patients received subgingival debridement following baseline examination. Control group patients received final periodontal treatment before the start of OT. For the test group patients final periodontal treatment was performed simultaneous to OT. OT was performed with a straight-wire appliance. Micro-implants or temporary crowns on implants were used for posterior anchorage when needed. ABL measurements of 3821 tooth surfaces were performed on cone beam computed tomography images.

Results

No difference was observed between mean ABL at T1 and T2. ABL remained unchanged on 69 per cent of surfaces. A mean of 15.6 (SD 7.4) per cent of surfaces experienced ABL gain, and a mean of 15.1 (SD 7.5) per cent was found with ABL loss. Small significant median ABL difference was observed on mesial and distal surfaces (P < 0.001). A significant difference was found between median ABL changes on mesial/distal in comparison to buccal/lingual surfaces (P < 0.01). Significantly more buccal (17.9 %) and lingual (18.5 %) surfaces experienced ABL loss when compared with mesial (11.3 %) and distal (12.0 %) surfaces (P < 0.001). Significant difference was found in the median ABL change of intruded (0.5 (IQR 0.94) mm) and non-intruded (−0.4 (IQR 1.07) mm) maxillary incisors (P = 0.04). Significant median ABL gain was found on the lingual surface of maxillary incisors, which were retroclined more than 8.6 degree and intruded more than 1.6 mm.

Conclusions

ABL changes after periodontal–orthodontic treatment in patients with periodontal disease were small. ABL gain was more observed on mesial and distal surfaces and ABL loss on buccal and lingual surfaces. Larger orthodontic movements of maxillary incisors influenced ABL gain.
Growing condition variations and grain prices in Niger and Nigeria
Authors: Hatzenbuehler Patrick L , Abbott Philip C , Abdoulaye Tahirou
Published: May 2019

In this paper, we describe how both the existing degree of price correspondence and tradability are important factors explaining why and the extent to which grain price relationships adjust due to growing condition variations. For a set of maize and millet markets in Niger and Nigeria with different agro-ecological characteristics and strengths of price relationships, we use normalised difference vegetation index (NDVI) data to identify years with weather-related production shocks. We then measure the degree to which price transmission between the commercial hub and reference market in each country in the anomalous weather years varies from that in normal years.
Simulating the effects of wind and snow damage on the optimal management of Norwegian spruce forests
Authors: Díaz-Yáñez Olalla , Arias-Rodil Manuel , Mola-Yudego Blas , González-Olabarria José Ramón , Pukkala Timo
Published: May 2019

Overlooking the risk of wind and snow damage in forest planning may lead to suboptimal management prescriptions. In this study, we analysed the optimal management of an even-aged, spruce-dominated stand in Norway under the risk of snow and wind damage. The management aim was to maximize discounted net revenues of timber production. We used a simulation-optimization system based on models for stand dynamics and damage, using either deterministic or stochastic approach to consider risk. The different approaches to simulating damage resulted in 41 optimization cases. The results show that considering risk leads to earlier cuttings, lower growing stock densities towards the end of the rotations and changes in the number and intensity of thinnings. The inclusion of stochastic damage provided a valid approach for considering the uncertainty associated with the risk of damage. Ignoring the effect of wind and snow damage in the calculations resulted in up to 25 per cent overestimation of the revenues. The results from this study will help to integrate the risk of natural disturbances into forestry decision-making, and provide a better understanding of the implications that snow and wind damage have on optimal forest management.