bluuebunny/crossref_metadata_2025 huggingface dataset:
Inhaled Treprostinil-Prodrug Lipid Nanoparticle Formulations Provide Long-Acting Pulmonary Vasodilation
Authors: Leifer Franziska , Konicek Donna , Chen Kuan-Ju , Plaunt Adam , Salvail Dany , Laurent Charles , Corboz Michel , Li Zhili , Chapman Richard , Perkins Walter , S. Malinin Vladimir
Published: May 2018

Treprostinil (TRE), a prostanoid analogue approved in the USA for the treatment of pulmonary arterial hypertension, requires continuous infusion or multiple dosing sessions per day for inhaled and oral routes of administration due to its short half-life. The inhaled drug is known to induce adverse systemic and local effects including headache, nausea, cough, and throat irritation which may be due at least in part to transiently high drug concentrations in the lungs and plasma immediately following administration [1]. To ameliorate these side effects and reduce dosing frequency we designed an inhaled slow-release TRE formulation. TRE was chemically modified to be an alkyl prodrug (TPD) which was then packaged into a lipid nanoparticle (LNP) carrier. Preclinical screening in a rat model of hypoxia-induced pulmonary vasoconstriction led to selection of a 16-carbon alkyl ester derivative of TRE. The TPD-LNP demonstrated approximately 10-fold lower TRE plasma Cmax compared to inhaled TRE solution while maintaining an extended vasodilatory effect. The favorable PK profile is attributed to gradual dissociation of TPD from the LNP and subsequent conversion to TRE. Together, this sustained presentation of TRE to the lungs and plasma is consistent with a once- or twice-daily dosing schedule in the absence of high Cmax-associated adverse events which could provide patients with an improved treprostinil therapy.
Evidence of Kittel type behaviour of the permittivity of a nanostructured high sensitivity piezoelectric
Authors: Balčiūnas Sergejus , Ivanov Maksim , Grigalaitis Robertas , Banys Juras , Amorín Harvey , Castro Alicia , Algueró Miguel
Published: May 2018

The broadband dielectric properties of high sensitivity piezoelectric 0.36BiScO3-0.64PbTiO3 ceramics with average grain sizes from 1.6 μm down to 26 nm were investigated in the 100–500 K temperature range. The grain size dependence of the dielectric permittivity was analysed within the effective medium approximation. It was found that the generalised core-shell (or brick wall) model correctly explains the size dependence down to the nanoscale. For the first time, the grain bulk and boundary properties were obtained without making any assumptions of values of the parameters or simplifications. Two contributions to dielectric permittivity of the grain bulk are described. The first is the size-independent one, which follows the Curie-Weiss law. The second one is shown to plausibly follow the Kittel's law. This seems to suggest the unexpected persistence of mobile ferroelectric domains at the nanoscale (26 nm grains). Alternative explanations are discussed.
High-pressure chemistry of hydrocarbons relevant to planetary interiors and inertial confinement fusion
Authors: Kraus D. , Hartley N. J. , Frydrych S. , Schuster A. K. , Rohatsch K. , Rödel M. , Cowan T. E. , Brown S. , Cunningham E. , van Driel T. , Fletcher L. B. , Galtier E. , Gamboa E. J. , Laso Garcia A. , Gericke D. O. , Granados E. , Heimann P. A. , Lee H. J. , MacDonald M. J. , MacKinnon A. J. , McBride E. E. , Nam I. , Neumayer P. , Pak A. , Pelka A. , Prencipe I. , Ravasio A. , Redmer R. , Saunders A. M. , Schölmerich M. , Schörner M. , Sun P. , Turner S. J. , Zettl A. , Falcone R. W. , Glenzer S. H. , Döppner T. , Vorberger J.
Published: May 2018

Diamond formation in polystyrene (C8H8)n, which is laser-compressed and heated to conditions around 150 GPa and 5000 K, has recently been demonstrated in the laboratory [Kraus et al., Nat. Astron. 1, 606–611 (2017)]. Here, we show an extended analysis and comparison to first-principles simulations of the acquired data and their implications for planetary physics and inertial confinement fusion. Moreover, we discuss the advanced diagnostic capabilities of adding high-quality small angle X-ray scattering and spectrally resolved X-ray scattering to the platform, which shows great prospects of precisely studying the kinetics of chemical reactions in dense plasma environments at pressures exceeding 100 GPa.
Collective variable discovery and enhanced sampling using autoencoders: Innovations in network architecture and error function design
Authors: Chen Wei , Tan Aik Rui , Ferguson Andrew L.
Published: May 2018

Auto-associative neural networks (“autoencoders”) present a powerful nonlinear dimensionality reduction technique to mine data-driven collective variables from molecular simulation trajectories. This technique furnishes explicit and differentiable expressions for the nonlinear collective variables, making it ideally suited for integration with enhanced sampling techniques for accelerated exploration of configurational space. In this work, we describe a number of sophistications of the neural network architectures to improve and generalize the process of interleaved collective variable discovery and enhanced sampling. We employ circular network nodes to accommodate periodicities in the collective variables, hierarchical network architectures to rank-order the collective variables, and generalized encoder-decoder architectures to support bespoke error functions for network training to incorporate prior knowledge. We demonstrate our approach in blind collective variable discovery and enhanced sampling of the configurational free energy landscapes of alanine dipeptide and Trp-cage using an open-source plugin developed for the OpenMM molecular simulation package.
Periodic changes in the oxidation states of the center ion in the cobalt-histidine complex induced by the BrO3− – SO32− pH-oscillator
Authors: Kurin-Csörgei Krisztina , Poros Eszter , Csepiova Julianna , Orbán Miklós
Published: May 2018

The coupling of acid-base type pH-dependent equilibria to pH-oscillators expanded significantly the number and type of species which can participate in oscillatory chemical processes. Here, we report a new version of oscillatory phenomena that can appear in coupled oscillators. Oscillations in the oxidation states of the center ion bound in a chelate complex were generated in a combined system, when the participants of the oscillator as dynamical unit and the components of the complex formation interacted with each other through redox reaction. It was demonstrated, when the BrO3− – SO32− pH-oscillator and the Co2+ – histidine complex were mixed in a continuous stirred tank reactor, periodic changes in the pH were accompanied with periodic transitions in the oxidation number of the cobalt ion between +2 and +3. The oscillatory build up and removal of the Co(III)-complex were followed by recording the light absorption at the wavelength characteristic for this species with simultaneous monitoring the pH-oscillations. The dual role of the SO32− ion in the explanation of this observation was pointed out. Its partial and consecutive total oxidations by BrO3− give rise to and maintain sustained pH-oscillations in the combined system and its presence induces the rapid conversion of the Co2+ to a highly inert Co(III)-histidine chelate when the system jumps to and remains in the high pH-state. The oscillatory cycle is completed when the Co(III)-complex is washed out from the reactor and the reagents are replenished by the flow during the time the system spends in the acidic range of pH. The idea, to couple a core oscillator to an equilibrium through a redox reaction that takes place between the constituents of the oscillator and the target species of the linked subsystem, may be generally used to bring about forced oscillations in many other combined chemical systems.
Hot electrons in metal films at low temperatures (Review)
Authors: Shklovskij V. A.
Published: May 2018

This review discusses research completed as a result of the author's cooperation with the Department of Igor Mikhailovich Dimitrenko, from 1975 to 1992. Based on kinetic equations for electron and phonon distribution functions, we theoretically considered hot electrons at low temperatures in metal films deposited on dielectric substrates with high thermal conductivity. We present a brief analysis of the major results related to hot electrons in superconducting films, the problem of heat removal from a sample, the form of a hot electron distribution function when thermalization criterion is not satisfied, the size effect in heat transfer from metal films, the tunneling of hot electrons, as well as the generalization of these results for metals with arbitrary dispersion of electrons and phonons in terms of Eliashberg spectral functions.
The Berezinskii-Kosterlitz-Thouless phase transition in the Josephson medium of a two-level granular high-temperature superconductor YBa2Cu3O7-δ
Authors: Sukhareva T. V. , Finkel V. A.
Published: May 2018

The temperature dependences ρ(T) of the electrical resistivity of the granular high-temperature superconductor YBa2Cu3O7-δ are measured in different transverse external magnetic fields 0 ≤ Hext ≤ 100 Oe for temperatures ranging from the temperature Tρ=0 at which resistivity appears to the critical superconducting transition temperature Tc and transport current densities ranging from 50 to 2000 mA/cm2. The effects of temperature, external magnetic field, and transport current density on the kinetics of phase transitions in both subsystems of the granular HTSC are studied. The possibility of a topological phase transition—a Berezinskii-Kosterlitz-Thouless phase transition in a Josephson medium—is established and the conditions for its occurrence are studied.
Microwave oscillations in superconducting tunnel mesa structures under spin filtration conditions
Authors: Constantinian K. Y. , Ovsyannikov G. A. , Kislinsky Yu. V. , Petrzhik A. M. , Shadrin A. V. , Demidov V. V.
Published: May 2018

The production of microwave oscillations in thin-film tunnel mesa structures consisting of an epitaxial film of cuprate superconductor YBa2Cu3O7-x, a barrier layer of manganite LaMnO3, and an upper superconducting Au/Nb bilayer is studied experimentally. The frequency of the detected microwaves is tuned by the bias voltage and an external magnetic field, and the linewidth is 50 MHz. Conductivity peaks are detected in the mesa structure at voltages corresponding to the niobium gap and a resistance peak at V = 0. When the temperature is lowered to below the critical temperature of niobium, an increase in the resistance peak is observed for zero bias and the tunneling magnetoresistance is 10% for a field H = 0.5 kOe, which can be explained by the effect of the spin-polarized current on the resistive characteristics of the mesa structure. The magnetic characteristics of the manganite spacer in the mesa structures are studied by FMR spectroscopy of Au/LaMnO3/YBa2Cu3O7-x heterostructures.
Transfer of excited state between two qubits in an open waveguide
Authors: Sultanov A. N. , Greenberg Ya. S.
Published: May 2018

The probability amplitudes of the processes related to the transfer of the excited state from one qubit to another are calculated using an indirect interaction in an open waveguide. The system consists of two qubits located at an arbitrary distance from each other. The non-Hermitian effective Hamiltonian approach used herein makes it possible to bypass using the Markovchain approximation method. Analytic expressions describing the probability of transfer of the excited state from one qubit to another under different initial states of the system were obtained.
The influence of thermal fluctuations on Coulomb blockade edge in small Josephson junctions with linear growing of voltage
Authors: Askerzade I. N.
Published: May 2018

In this study we carried out the analysis of the thermal fluctuations on Coulomb blockade edge in small Josephson junctions with linear growing of voltage. It was shown that, charge fluctuation is determined by the energy ratio-parameter of small size Josephson junction, temperature and growing rate of voltage.
Frequency-tuned microwave photon counter based on a superconductive quantum interferometer
Authors: Shnyrkov V. I. , Yangcao Wu , Soroka A. A. , Turutanov O. G. , Lyakhno V. Yu.
Published: May 2018

Various types of single-photon counters operating in infrared, ultraviolet, and optical wavelength ranges are successfully used to study electromagnetic fields, analyze radiation sources, and solve problems in quantum informatics. However, their operating principles become ineffective at millimeter band, S-band, and ultra-high frequency bands of wavelengths due to the decrease in quantum energy by 4–5 orders of magnitude. Josephson circuits with discrete Hamiltonians and qubits are a good foundation for the construction of single-photon counters at these frequencies. This paper presents a frequency-tuned microwave photon counter based on a single-junction superconducting quantum interferometer and flux qutrit. The control pulse converts the interferometer into a two-level system for resonance absorption of photons. Decay of the photon-induced excited state changes the magnetic flux in the interferometer, which is measured by a SQUID magnetometer. Schemes for recording the magnetic flux using a DC SQUID or ideal parametric detector, based on a qutrit with high-frequency excitation, are discussed. It is shown that the counter consisting of an interferometer with a Josephson junction and a parametric detector demonstrates high performance and is capable of detecting single photons in a microwave band.
Modulation of kinetic Alfvén waves in an intermediate low-beta magnetoplasma
Authors: Chatterjee Debjani , Misra A. P.
Published: May 2018

We study the amplitude modulation of nonlinear kinetic Alfvén waves (KAWs) in an intermediate low-beta magnetoplasma. Starting from a set of fluid equations coupled to the Maxwell's equations, we derive a coupled set of nonlinear partial differential equations (PDEs) which govern the evolution of KAW envelopes in the plasma. The modulational instability (MI) of such KAW envelopes is then studied by a nonlinear Schrödinger equation derived from the coupled PDEs. It is shown that the KAWs can evolve into bright envelope solitons or can undergo damping depending on whether the characteristic ratio (α) of the Alfvén to ion-acoustic speeds remains above or below a critical value. The parameter α is also found to shift the MI domains around the kxkz plane, where kx (kz) is the KAW number perpendicular (parallel) to the external magnetic field. The growth rate of MI, as well as the frequency shift and the energy transfer rate, are obtained and analyzed. The results can be useful for understanding the existence and formation of bright and dark envelope solitons, or damping of KAW envelopes in space plasmas, e.g., interplanetary space, solar winds, etc.
Edge states in gated bilayer-monolayer graphene ribbons and bilayer domain walls
Authors: Mirzakhani M. , Zarenia M. , Peeters F. M.
Published: May 2018

Using the effective continuum model, the electron energy spectrum of gated bilayer graphene with a step-like region of decoupled graphene layers at the edge of the sample is studied. Different types of coupled-decoupled interfaces are considered, i.e., zigzag (ZZ) and armchair junctions, which result in significant different propagating states. Two non-valley-polarized conducting edge states are observed for ZZ type, which are mainly located around the ZZ-ended graphene layers. Additionally, we investigated both BA-BA and BA-AB domain walls in the gated bilayer graphene within the continuum approximation. Unlike the BA-BA domain wall, which exhibits gapped insulating behaviour, the domain walls surrounded by different stackings of bilayer regions feature valley-polarized edge states. Our findings are consistent with other theoretical calculations, such as from the tight-binding model and first-principles calculations, and agree with experimental observations.
A pressure core ultrasonic test system for on-board analysis of gas hydrate-bearing sediments under in situ pressures
Authors: Yang Lei , Zhou Weihua , Xue Kaihua , Wei Rupeng , Ling Zheng
Published: May 2018

The enormous potential as an alternative energy resource has made natural gas hydrates a material of intense research interest. Their exploration and sample characterization require a quick and effective analysis of the hydrate-bearing cores recovered under in situ pressures. Here a novel Pressure Core Ultrasonic Test System (PCUTS) for on-board analysis of sediment cores containing gas hydrates at in situ pressures is presented. The PCUTS is designed to be compatible with an on-board pressure core transfer device and a long gravity-piston pressure-retained corer. It provides several advantages over laboratory core analysis including quick and non-destructive detection, in situ and successive acoustic property acquisition, and remission of sample storage and transportation. The design of the unique assembly units to ensure the in situ detection is demonstrated, involving the U-type protecting jackets, transducer precession device, and pressure stabilization system. The in situ P-wave velocity measurements make the detection of gas hydrate existence in the sediments possible on-board. Performance tests have verified the feasibility and sensitivity of the ultrasonic test unit, showing the dependence of P-wave velocity on gas hydrate saturation. The PCUTS has been successfully applied for analysis of natural samples containing gas hydrates recovered from the South China Sea. It is indicated that on-board P-wave measurements could provide a quick and effective understanding of the hydrate occurrence in natural samples, which can assist further resource exploration, assessment, and subsequent detailed core analysis.
Small violations of Bell inequalities for multipartite pure random states
Authors: Drumond Raphael C. , Duarte Cristhiano , Oliveira Roberto I.
Published: May 2018

For any finite number of parts, measurements, and outcomes in a Bell scenario, we estimate the probability of random N-qudit pure states to substantially violate any Bell inequality with uniformly bounded coefficients. We prove that under some conditions on the local dimension, the probability to find any significant amount of violation goes to zero exponentially fast as the number of parts goes to infinity. In addition, we also prove that if the number of parts is at least 3, this probability also goes to zero as the local Hilbert space dimension goes to infinity.
Performance enhancement of nonlinear asymmetric bistable energy harvesting from harmonic, random and human motion excitations
Authors: Wang Wei , Cao Junyi , Bowen Chris R. , Inman Daniel J. , Lin Jing
Published: May 2018

Numerical and experimental investigations of nonlinear bistable energy harvesters (BEHs) with asymmetric potential functions are presented under various excitations for performance enhancement. Basin of attraction under harmonic excitation indicates that asymmetric potentials in BEHs have a negative effect on the power output. Therefore, a proper bias angle is introduced to the asymmetric potential BEHs for performance enhancement. Numerical and experimental results show that the power output is actually improved in a certain bias angle range under harmonic and random excitations. Furthermore, experiments under human motion excitation demonstrate that the asymmetric potential BEHs could perfectly combine with the asymmetric motion of lower-limb to improve the performance.
Laser induced phase transition in epitaxial FeRh layers studied by pump-probe valence band photoemission
Authors: Pressacco Federico , Uhlíř Vojtěch , Gatti Matteo , Nicolaou Alessandro , Bendounan Azzedine , Arregi Jon Ander , Patel Sheena K. K. , Fullerton Eric E. , Krizmancic Damjan , Sirotti Fausto
Published: May 2018

We use time-resolved X-ray photoelectron spectroscopy to probe the electronic and magnetization dynamics in FeRh films after ultrafast laser excitations. We present experimental and theoretical results which investigate the electronic structure of FeRh during the first-order phase transition, identifying a clear signature of the magnetic phase. We find that a spin polarized feature at the Fermi edge is a fingerprint of the magnetic status of the system that is independent of the long-range ferromagnetic alignment of the magnetic domains. We use this feature to follow the phase transition induced by a laser pulse in a pump-probe experiment and find that the magnetic transition occurs in less than 50 ps and reaches its maximum in 100 ps.
Beating pattern in radiation-induced oscillatory magnetoresistance in 2DES: Coupling of plasmon-like and acoustic phonon modes
Authors: Iñarrea J.
Published: May 2018

We present a microscopic theory on the observation of a beating pattern in the radiation-induced magnetoresistance oscillations at a very low magnetic field. We consider that such a beating pattern develops as a result of the coupling between two oscillatory components: the first is a system of electron Landau states being harmonically driven by radiation. The second is a lattice oscillation, i.e., an acoustic phonon mode. We analyze the dependence of the beating pattern on temperature, radiation frequency, and power. We conclude that the beating pattern is an evidence of the radiation-driven nature of the irradiated Landau states that makes them behave as a collective plasma oscillation at the radiation frequency. Thus, the frequency of such plasmons could be tuned from microwave to terahertz in the same nanodevice with an apparent technological application.
Distribution law of temperature changes during methane adsorption and desorption in coal using infrared thermography technology
Authors: Zhao Dong , Chen Hao , An Jiangfei , Zhou Dong , Feng Zengchao
Published: May 2018

Gas adsorption and desorption is a thermodynamic process that takes place within coal as temperature changes and that is related to methane (CH4) storage. As infrared thermographic technology has been applied in this context to measure surface temperature changes, the aim of this research was to further elucidate the distribution law underlying this process as well as the thermal effects induced by heat adsorption and desorption in coal. Specimens of two different coal ranks were used in this study, and the surface temperature changes seen in the latter were detected. A contour line map was then drawn on the basis of initial results enabling a distribution law of temperature changes for samples. The results show that different regions of coal sample surfaces exhibit different heating rates during the adsorption process, but they all depends on gas storage capacity to a certain extent. It proposes a correlation coefficient that expresses the relationship between temperature change and gas adsorption capacity that could also be used to evaluate the feasibility of coalbed CH4 extraction in the field. And finally, this study is deduced a method to reveal the actual adsorption capacity of coal or CH4 reservoirs in in situ coal seams.
Photocarrier extraction in GaAsSb/GaAsN type-II QW superlattice solar cells
Authors: Aeberhard U. , Gonzalo A. , Ulloa J. M.
Published: May 2018

Photocarrier transport and extraction in GaAsSb/GaAsN type-II quantum well superlattices are investigated by means of inelastic quantum transport calculations based on the non-equilibrium Green's function formalism. Evaluation of the local density of states and the spectral current flow enables the identification of different regimes for carrier localization, transport, and extraction as a function of configurational parameters. These include the number of periods, the thicknesses of the individual layers in one period, the built-in electric field, and the temperature of operation. The results for the carrier extraction efficiency are related to experimental data for different symmetric GaAsSb/GaAsN type-II quantum well superlattice solar cell devices and provide a qualitative explanation for the experimentally observed dependence of photovoltaic device performance on the period thickness.
Detection of anisotropy in the electron velocity distribution produced by electron cyclotron resonance heating using the polarization of helium atom emission lines
Authors: Teramoto Tatsuya , Shikama Taiichi , Ueda Akira , Hasuo Masahiro
Published: May 2018

The anisotropy in the electron velocity distribution (EVD) was measured using the polarization of two helium atom emission lines, 21P–31D (668 nm) and 23P–33D (588 nm), in a helium electron cyclotron resonance (ECR) discharge plasma. A small polarization degree of less than 4% was measured by adopting a temporal modulation technique. It was found that the polarization originated locally from around the ECR layer and that the anisotropic component of the EVD produced by ECR heating had an average kinetic energy of approximately 40 eV.
The fate of arsenic in groundwater discharged to the Meghna River, Bangladesh
Authors: Berube Michelle , Jewell Katrina , Myers Kimberly D. , Knappett Peter S. K. , Shuai Pin , Hossain Abrar , Lipsi Mehtaz , Hossain Sadam , Hossain Alamgir , Aitkenhead-Peterson Jacqueline , Ahmed Kazi M. , Datta Saugata
Published: May 2018

Environmental contextArsenic contamination of groundwater is a major environmental problem in many areas of the world. In south-east Asia, iron-rich reducing groundwater mixes with oxidising river water in hyporheic zones, precipitating iron oxides. These oxides can act as a natural reactive barrier capable of accumulating elevated solid-phase concentrations of arsenic.
AbstractShallow, anoxic aquifers within the Ganges–Brahmaputra–Meghna Delta (GBMD) commonly contain elevated concentrations of arsenic (As), iron (Fe) and manganese (Mn). Highly enriched solid-phase concentrations of these elements have been observed within sediments lining the banks of the Meghna River. This zone has been described as a Natural Reactive Barrier (NRB). The impact of hydrological processes on NRB formation, such as transient river levels, which drive mixing between rivers and aquifers, is poorly understood. We evaluated the impact of groundwater flow dynamics on hydrobiogeochemical processes that led to the formation of an Fe- and Mn-rich NRB containing enriched As, within a riverbank aquifer along the Meghna River. The NRB dimensions were mapped using four complementary elemental analysis methods on sediment cores: X-ray fluorescence (XRF), aqua regia bulk extraction, and HCl and sodium phosphate leaching. It extended from 1.2 to 2.4 m in depth up to 15 m from the river’s edge. The accumulated As was advected to the NRB from offsite and released locally in response to mixing with aged river water. Nearly all of the As was subsequently deposited within the NRB before discharging to the Meghna. Significant FeII release to the aqueous phase was observed within the NRB. This indicates the NRB is a dynamic zone defined by the interplay between oxidative and reductive processes, causing the NRB to grow and recede in response to rapid and seasonal hydrologic processes. This implies that natural and artificially induced changes in river stages and groundwater-tables will impact where As accumulates and is released to aquifers.
Effective adsorptive removal of 2,4,6-trinitrotoluene and hexahydro-1,3,5-trinitro-1,3,5-triazine by pseudographitic carbon: kinetics, equilibrium and thermodynamics
Authors: Choi Jong-Soo , Koduru Janardhan Reddy , Lingamdinne Lakshmi Prasanna , Yang Jae-Kyu , Chang Yoon-Young
Published: May 2018

Environmental contextExplosive organic compounds such as 2,4,6-trinitrotoluene (TNT) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) are major constituents of ammunition materials. These compounds are of environmental concern because they can have a significant impact on ecosystems and humans. Through investigations of adsorption kinetics, isotherms and thermodynamics, we demonstrate the suitability of pseudographitic carbon for removing TNT and RDX from groundwater, and additionally confirm the viability of the use of pseudographitic carbon through comparison with other adsorbents. Abstract2,4,6-Trinitrotoluene (TNT) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) – common explosives in military munitions – can easily enter groundwater supplies and have an adverse impact on human health. There is great concern about the need to remove these explosives from groundwater, and this study presents pseudographitic carbon (PGC) prepared from edible sugar as a material to remove explosives from contaminated groundwater via adsorption. The purity and physicochemical characteristics of the PGC were characterised using advanced spectroscopic techniques. The adsorption mechanism and its efficiency were investigated in terms of the non-linear adsorption kinetics, isotherms and thermodynamics using TNT and RDX adsorption data. The results of the non-linear modelling indicate that TNT and RDX adsorption was determined by rate-limiting monolayer exothermic adsorption on the homogeneous PGC surface. Ionic strength was studied with various ions, and the results indicate that the adsorption of TNT and RDX was significantly influenced by divalent cations and the carbonate anion. The results of desorption and re-use tests indicate that acetone and acetonitrile are the best desorbing agents. The PGC can be recycled and re-used for up to 3 cycles, with insignificant loss in adsorption efficiency. Finally, the PGC was applied to real spiked groundwater to evaluate its applicability in the field in removing TNT and RDX. The overall results indicate that PGC is a cost-effective and efficient adsorbent that effectively removes the organic explosives from groundwater, thereby reducing risk to humans and the aqueous environment.
A study on tributyltin contamination of marine sediments in the major ports of Fiji
Authors: Maata Matakite , Koshy Kanayathu
Published: May 2018

Tri-n-butyltin (TBT) compounds are synthetic, multipurpose chemicals, which have been extensively used, in marine antifouling paints. They have been known to be extremely poisonous to mollusc fishery resources (oysters, clams, scallops, etc.). TBT levels in marine sediments from the main ports in Fiji were analysed using the GC/FPD method. The results indicated that these sites were among the worst polluted with TBT in the world. The most contaminated site recorded a TBT concentration of 360 μgg-1. TBT comprised 48-90% of the total organotins measured. Some stringent legislative means are needed to regulate the use of this contaminant in marine anti-fouling paints.
The design of a spatially explicit stochastic model for the simulation of oceanic seed dispersal
Authors: Martín-Herrero Julio , Calviño-Cancela María
Published: May 2018

We propose a stochastic model for analyzing the influence of the physical environment on oceanic seed dispersal. The model requires a description of the spatial configuration of the region and of the dynamics of the physical processes involved (ocean and atmosphere dynamics). The degree of accuracy and resolution of these descriptions will determine the accuracy of the simulations. Parameters to characterize the species of interest will come from empirical knowledge about the species, via
experiments and measurements in the field. Two modeling approaches could be used, a particle model or a density model. We discuss both options and provide some recommendations. The described model could be used to answer questions about the origin of the current spatial distributions of species dispersed by the ocean and to study metapopulation dynamics.
Metastable quasicrystal-induced nucleation in a bulk glass-forming liquid
Authors: Kurtuldu Güven , Shamlaye Karl F. , Löffler Jörg F.
Published: May 2018

Significance

A model alloy, Mg69Zn27Yb4, concurrently forms bulk metallic glass, metastable quasicrystals (QCs), and crystalline approximant phases from the melt. We demonstrate that a transient QC phase nucleates first from the melt and subsequently transforms into an equilibrium approximant phase. This nucleation path is likely to be a general mechanism in metastable QC-forming systems. We observed a metastable-to-stable phase transformation when we deployed fast differential scanning calorimetry using the experimental strategy of interrupted cooling after the onset of crystallization followed by heating at ultrafast rates to “up-quench” the previously frozen structure. This strategy can yield the discovery of hidden transient phases that are key to understanding the crystallization behavior in metallic systems, polymers, biological solutions, and pharmaceutical substances.
Role of CD40 and ADAMTS13 in von Willebrand factor-mediated endothelial cell–platelet–monocyte interaction
Authors: Popa Miruna , Tahir Sibgha , Elrod Julia , Kim Su Hwan , Leuschner Florian , Kessler Thorsten , Bugert Peter , Pohl Ulrich , Wagner Andreas H. , Hecker Markus
Published: May 2018

Significance

In this study we have identified a mechanism that links pathophysiological ADAMTS13 deficiency to innate immunity and hemostasis by facilitating monocyte extravasation as a prerequisite for their subsequent on-site differentiation into proinflammatory macrophages under conditions of both physiological laminar flow and disturbed reduced flow, e.g., as occurs at atherosclerosis predilection sites. Our bioassay approach using patients’ plasma may become a useful diagnostic tool to assess ADAMTS13 activity ex vivo under conditions of near-physiological to atherosclerosis-prone arterial blood flow, which seems to be more relevant than the conventional static FRET-based assay method.
A cellular automaton-finite difference simulation of the ausferritic transformation in ductile iron
Authors: Boccardo A. D. , Dardati P. M. , Godoy L. A.
Published: May 2018

The development of the ausferritic transformation of a ductile iron was analysed using a novel cellular automaton-finite difference model, which considers geometrical details of the microstructure, nucleation of the new phase at graphite nodule surface, contact between growing phases, and carbon diffusion in austenite. The role of nucleation, austenite carbon enrichment, and contact between phases in the different stages of the growth kinetics was studied. Moreover, a parametric study was performed to investigate the influences of graphite nodule size, and austenitizing and austempering temperatures on the required time to end the transformation and final phase fractions. The obtained results are in agreement with experimental data reported in the literature.
Expansive measures versus Lyapunov exponents
Authors: Armijo Alma , Pacifico Maria
Published: May 2018

In this paper we investigate the relation between measure-expansiveness and hyperbolicity. We prove that non-atomic invariant ergodic measures with all of their Lyapunov exponents positive are positively measure-expansive. We also prove that local diffeomorphisms robustly positively measure-expansive are expanding. Finally, we prove that a

C
1

C^1

-volume-preserving diffeomorphism that cannot be accumulated by positively measure-expansive diffeomorphisms has a dominated splitting.
The Effect of the Conservation Reserve Program on Rural Economies: Deriving a Statistical Verdict from a Null Finding
Authors: Brown Jason P. , Lambert Dayton M. , Wojan Timothy R.
Published: May 2018

This article suggests two methods for deriving a statistical verdict from a null finding, allowing economists to more confidently conclude when “not significant” can be interpreted as “no substantive effect.” The proposed methodologies can be extended to a variety of empirical contexts where size and power matter. The example used to demonstrate the methods is the Economic Research Service's 2004 Report to Congress that was charged with statistically identifying any unintended negative employment consequences of the Conservation Reserve Program (CRP). The report failed to identify a statistically significant negative long‐term effect of the CRP on employment growth, but the authors correctly cautioned that the verdict of “no negative employment effect” was only valid if the econometric test was statistically powerful. We replicate the 2004 analysis and use new methods of statistical inference to resolve the two critical deficiencies that preclude estimation of statistical power: (a) positing a compelling effect size, and (b) providing an estimate of the variability of an unobserved alternative distribution using simulation methods. We conclude that the test used in the report had high power for detecting employment effects of ‐1% or lower resulting from the CRP, equivalent to job losses reducing a conservative estimate of environmental benefits by one‐third.
geck: trio-based comparative benchmarking of variant calls
Authors: Kómár Péter , Kural Deniz
Published: May 2018

Motivation

Classical methods of comparing the accuracies of variant calling pipelines are based on truth sets of variants whose genotypes are previously determined with high confidence. An alternative way of performing benchmarking is based on Mendelian constraints between related individuals. Statistical analysis of Mendelian violations can provide truth set-independent benchmarking information, and enable benchmarking less-studied variants and diverse populations.

Results

We introduce a statistical mixture model for comparing two variant calling pipelines from genotype data they produce after running on individual members of a trio. We determine the accuracy of our model by comparing the precision and recall of GATK Unified Genotyper and Haplotype Caller on the high-confidence SNPs of the NIST Ashkenazim trio and the two independent Platinum Genome trios. We show that our method is able to estimate differential precision and recall between the two pipelines with 10−3 uncertainty.

Availability and implementation

The Python library geck, and usage examples are available at the following URL: https://github.com/sbg/geck, under the GNU General Public License v3.

Supplementary information

Supplementary data are available at Bioinformatics online.
LncRNAnet: long non-coding RNA identification using deep learning
Authors: Baek Junghwan , Lee Byunghan , Kwon Sunyoung , Yoon Sungroh
Published: May 2018

Motivation

Long non-coding RNAs (lncRNAs) are important regulatory elements in biological processes. LncRNAs share similar sequence characteristics with messenger RNAs, but they play completely different roles, thus providing novel insights for biological studies. The development of next-generation sequencing has helped in the discovery of lncRNA transcripts. However, the experimental verification of numerous transcriptomes is time consuming and costly. To alleviate these issues, a computational approach is needed to distinguish lncRNAs from the transcriptomes.

Results

We present a deep learning-based approach, lncRNAnet, to identify lncRNAs that incorporates recurrent neural networks for RNA sequence modeling and convolutional neural networks for detecting stop codons to obtain an open reading frame indicator. lncRNAnet performed clearly better than the other tools for sequences of short lengths, on which most lncRNAs are distributed. In addition, lncRNAnet successfully learned features and showed 7.83%, 5.76%, 5.30% and 3.78% improvements over the alternatives on a human test set in terms of specificity, accuracy, F1-score and area under the curve, respectively.

Availability and implementation

Data and codes are available in http://data.snu.ac.kr/pub/lncRNAnet.
NGL viewer: web-based molecular graphics for large complexes
Authors: Rose Alexander S , Bradley Anthony R , Valasatava Yana , Duarte Jose M , Prlić Andreas , Rose Peter W
Published: May 2018

Motivation

The interactive visualization of very large macromolecular complexes on the web is becoming a challenging problem as experimental techniques advance at an unprecedented rate and deliver structures of increasing size.

Results

We have tackled this problem by developing highly memory-efficient and scalable extensions for the NGL WebGL-based molecular viewer and by using Macromolecular Transmission Format (MMTF), a binary and compressed MMTF. These enable NGL to download and render molecular complexes with millions of atoms interactively on desktop computers and smartphones alike, making it a tool of choice for web-based molecular visualization in research and education.

Availability and implementation

The source code is freely available under the MIT license at github.com/arose/ngl and distributed on NPM (npmjs.com/package/ngl). MMTF-JavaScript encoders and decoders are available at github.com/rcsb/mmtf-javascript.
A graph-embedded deep feedforward network for disease outcome classification and feature selection using gene expression data
Authors: Kong Yunchuan , Yu Tianwei
Published: May 2018

Motivation

Gene expression data represents a unique challenge in predictive model building, because of the small number of samples (n) compared with the huge amount of features (p). This ‘n≪p’ property has hampered application of deep learning techniques for disease outcome classification. Sparse learning by incorporating external gene network information could be a potential solution to this issue. Still, the problem is very challenging because (i) there are tens of thousands of features and only hundreds of training samples, (ii) the scale-free structure of the gene network is unfriendly to the setup of convolutional neural networks.

Results

To address these issues and build a robust classification model, we propose the Graph-Embedded Deep Feedforward Networks (GEDFN), to integrate external relational information of features into the deep neural network architecture. The method is able to achieve sparse connection between network layers to prevent overfitting. To validate the method’s capability, we conducted both simulation experiments and real data analysis using a breast invasive carcinoma RNA-seq dataset and a kidney renal clear cell carcinoma RNA-seq dataset from The Cancer Genome Atlas. The resulting high classification accuracy and easily interpretable feature selection results suggest the method is a useful addition to the current graph-guided classification models and feature selection procedures.

Availability and implementation

The method is available at https://github.com/yunchuankong/GEDFN.

Supplementary information

Supplementary data are available at Bioinformatics online.
TomoEED: fast edge-enhancing denoising of tomographic volumes
Authors: Moreno J J , Martínez-Sánchez A , Martínez J A , Garzón E M , Fernández J J
Published: May 2018

TomoEED is an optimized software tool for fast feature-preserving noise filtering of large 3D tomographic volumes on CPUs and GPUs. The tool is based on the anisotropic nonlinear diffusion method. It has been developed with special emphasis in the reduction of the computational demands by using different strategies, from the algorithmic to the high performance computing perspectives. TomoEED manages to filter large volumes in a matter of minutes in standard computers.

Availability and implementation

TomoEED has been developed in C. It is available for Linux platforms at http://www.cnb.csic.es/%7ejjfernandez/tomoeed.

Supplementary information

Supplementary data are available at Bioinformatics online.
Motif scraper: a cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files
Authors: Roberson Elisha D O
Published: May 2018

Many genomic features are defined not by exact sequence matches, but by degenerate nucleotide motifs that represent multiple compatible matches. While there are databases cataloging genomic features, such as the location of transcription factor motifs, for commonly used model species, identifying the locations of novel motifs, known motifs in non-model genomes, or known motifs in personal whole-genomes is difficult. I designed motif scraper to overcome this limitation, allowing for efficient, multiprocessor motif searches in any FASTA file.

Availability and implementation

The motif scraper package (MIT license) is available via PyPI, and the Python source is available on GitHub at https://github.com/RobersonLab/motif_scraper.
Zero-inflated generalized Dirichlet multinomial regression model for microbiome compositional data analysis
Authors: Tang Zheng-Zheng , Chen Guanhua
Published: May 2018

There is heightened interest in using high-throughput sequencing technologies to quantify abundances of microbial taxa and linking the abundance to human diseases and traits. Proper modeling of multivariate taxon counts is essential to the power of detecting this association. Existing models are limited in handling excessive zero observations in taxon counts and in flexibly accommodating complex correlation structures and dispersion patterns among taxa. In this article, we develop a new probability distribution, zero-inflated generalized Dirichlet multinomial (ZIGDM), that overcomes these limitations in modeling multivariate taxon counts. Based on this distribution, we propose a ZIGDM regression model to link microbial abundances to covariates (e.g. disease status) and develop a fast expectation–maximization algorithm to efficiently estimate parameters in the model. The derived tests enable us to reveal rich patterns of variation in microbial compositions including differential mean and dispersion. The advantages of the proposed methods are demonstrated through simulation studies and an analysis of a gut microbiome dataset.
Strange Duality on Rational Surfaces II: Higher-Rank Cases
Authors: Yuan Yao
Published: May 2018

We study Le Potier’s strange duality conjecture on a rational surface. We focus on the strange duality map $SD_{c_n^r,L}$ that involves the moduli space of rank $r$ sheaves with trivial 1st Chern class and 2nd Chern class $n$, and the moduli space of one-dimensional sheaves with determinant $L$ and Euler characteristic 0. We show there is an exact sequence relating the map $SD_{c_r^r,L}$ to $SD_{c^{r-1}_{r},L}$ and $SD_{c_r^r,L\otimes K_X}$ for all $r\geq 1$ under some conditions on $X$ and $L$ that applies to a large number of cases on $\mathbb{P}^2$ or Hirzebruch surfaces. Also on $\mathbb{P}^2$ we show that for any $r>0$, $SD_{c^r_r,dH}$ is an isomorphism for $d=1,2$, injective for $d=3,$ and moreover $SD_{c_3^3,rH}$ and $SD_{c_3^2,rH}$ are injective. At the end we prove that the map $SD_{c_n^2,L}$ ($n\geq 2$) is an isomorphism for $X=\mathbb{P}^2$ or Fano rational-ruled surfaces and $g_L=3$, and hence so is $SD_{c_3^3,L}$ as a corollary of our main result.