bluuebunny/crossref_metadata_2025 huggingface dataset:
Thickness-dependent evolution of piezoresponses and a/c domains in [101]-oriented PbTiO3 ferroelectric films
Authors: Feng Y. P. , Tang Y. L. , Zhu Y. L. , Zou M. J. , Wang Y. J. , Ma X. L.
Published: December 2020

It is known that high-index perovskite ferroelectric thin films exhibit giant permittivity, piezoelectric response, and a particular switching behavior. However, the fine domain configuration in high-index ferroelectric films is not yet clarified, which triggers difficulties to further modulate their electric properties. In this work, we focus on the tetragonal PbTiO3 thin films with thicknesses of 20, 40, 55, and 70 nm deposited on a [101]-oriented KTaO3 substrate. By using piezoresponse force microscopy and state-of-the-art scanning transmission electron microscopy, the stripe a/c domains with alternately wide c and narrow a domains are observed in all these PbTiO3 films. The periodic stripe a/c domains with {101} domain walls extend along the in-plane [111¯] or [11¯1¯] direction, which almost completely relaxes the misfit strain between the PbTiO3 films and the KTaO3 substrate. The domain width decreases as the film thickness is reduced following the square root dependence. This results in an increase of ferroelastic a/c domain walls and promotes the enhancement of the piezoresponse amplitude for the thinner PbTiO3 films. In addition, the piezoresponse amplitude of a 20 nm PbTiO3 film is comparable to that of a 40 nm PbTiO3 film, which indicates that the piezoelectric response of ferroelectric films may saturate at a certain film thickness and scarcely increase even after the film thickness reduces further. These results clarify the domain configurations of [101]-oriented PbTiO3 thin films and provide useful information for understanding the relationship between microstructures and piezoelectric properties in ferroelectric films.
Tunable multifunctional fish-bone elastic metasurface for the wavefront manipulation of the transmitted in-plane waves
Authors: Yuan Si-Min , Chen A-Li , Cao Liyun , Zhang Hua-Wei , Fan Shi-Wang , Assouar Badreddine , Wang Yue-Sheng
Published: December 2020

In this work, a tunable fish-bone elastic metasurface is used to manipulate in-plane waves, which are more complex than flexural or out-of-plane waves because of the coupling of P- and SV-waves. First, refracted generalized Snell's law (GSL) for a mixed in-plane wave is deduced, which is also testified by the numerical results. Then, according to the GSL, elastic metasurfaces are designed to realize multifunctions such as directional refraction and wave focusing for different working frequencies. Critical refraction is discussed for the directional refraction, and the behavior of the SV-wave is predicted when the P-wave is designed to focus at any point by the metasurface.
On the conservative property of particle-based Fokker–Planck method for rarefied gas flows
Authors: Jiang Yazhong , Wen Chih-Yung
Published: December 2020

The Fokker–Planck-type approximation of the full Boltzmann equation has aroused intense research interest due to its potential for the stochastic particle simulation of rarefied gas flows. The ellipsoidal statistical Fokker–Planck (ES-FP) model treats the evolution of molecular velocity as a continuous stochastic process, and it satisfies the basic requirements for a proper gas-kinetic model including the H-theorem and an adjustable Prandtl number. The ES-FP model can be numerically implemented with computational particles in a Monte Carlo manner. Two different particle ES-FP schemes are presented. The first scheme utilizes the exact stochastic integral solution of the Langevin equations corresponding to the ES-FP equation and couples free-molecular moves and intermolecular collisions. The second scheme is designed to enforce the conservation of momentum and energy during the numerical simulation based on the decoupled algorithm and the analysis of the specific conditions for the conservative property. Numerical tests are conducted to demonstrate the performances of different schemes. In the simulation of a homogeneous gas system, the ES-FP scheme without enforcement of conservation leads to unphysical variation in the momentum and loss in energy, whereas the conservative ES-FP scheme strictly maintains the momentum and energy of the system. For the Mach 6 flows over the leading edge of a flat plate and over a round-nosed blunt body, the non-conservative ES-FP scheme underestimates the shock angle and the shock standoff distance, makes inaccurate predictions of aerodynamic force and heating, and produces low-temperature anomalies in front of the shock waves. In comparison with the results given by the direct simulation Monte Carlo method, the results of the conservative ES-FP simulations show satisfactory accuracy for the flow fields as well as the distributions of pressure, friction, and heat flux on the wall surfaces.
Temperature characteristics of high-current UWBG enhancement and depletion mode AlGaN-channel MOSHFETs
Authors: Mollah Shahab , Gaevski Mikhail , Hussain Kamal , Mamun Abdullah , Chandrashekhar MVS , Simin Grigory , Khan Asif
Published: December 2020

We present the temperature-dependent electrical characteristics of high-current depletion (D-mode) and barrier-recessed enhancement-mode (E-mode) ultrawide bandgap (UWBG) AlxGa1−xN channel insulated gate heterojunction field-effect transistors fabricated on the same wafer. The key motivation is the higher Baliga figure of merit for devices with the UWBG AlGaN channel and their strong potential for use in high-power, high-temperature harsh environmental applications. Over a temperature range of 125 °C, the VTH shifted in the opposite direction for D- and E-mode devices with a rate of +13.5 mV/K and −23 mV/K, respectively, giving an overall shift of +1.7 V and −2.9 V. This was attributed to changes in the fixed and trapped charge densities in the dielectric and at the dielectric–AlGaN barrier interface. A single deep sub-bandgap trap level was sufficient to explain the threshold shifts in both devices. The effective channel mobility in the E-mode devices was argued to be limited by charge scattering, arising from the same charges introduced during barrier recessing that shifted VTH.
A Python implementation in graphic processing unit of a lattice Boltzmann model for unstable three-dimensional flows in immersed permeable media
Authors: Boroni Gustavo , Silin Nicolás , Clausse Alejandro
Published: December 2020

The implementation of a lattice Boltzmann model for three-dimensional permeable media with localized drag forces is presented. The model was previously introduced for two-dimensional geometries and follows the basics of the immersed boundary method. Permeable flows are much less stable than their counterparts in porous media and generally produce large coherent flow structures, such as vortex lines, rolls, and wakes. In addition, in permeable media, the small-scale geometry often needs to be represented to a high degree of detail in order to capture certain transport phenomena, such as micro-convection or pollination. Hence, both calculation speed and memory requirements are under strain. The present model was implemented in a graphic processing unit showing excellent performance in the calculation of stable and unstable flows in a rectangular channel partially obstructed by an array of parallel wires. In particular, the model is able to deal with small and medium spatial scales without losing the heterogeneous nature of permeable flows in the homogenization process. The algorithm to manage memory issues is described in detail, and the results of the test case for stable and unstable conditions show the capability of the method to simulate these types of flows.
Wide spectrum multi-sub-band modulation of excitons and defect state emission simultaneously in surface oxidized CdS micro/nano-wires
Authors: Peng Yuehua , Zheng Qi , Yin Yanling , Zhao Zhuang , Zhong Manyi , Zhou Weichang , Tang Dongsheng
Published: December 2020

Strong optical confinement and light–matter interaction within semiconductor nanostructures are crucial to modulate the emission property. A fundamental understanding of these interesting phenomena is important to scientific and industrial communities. In this paper, we synthesized the surface oxidized CdS micro/nano-wires by post-oxidation of CdS micro/nano-wires at 475 °C and investigated systematically their novel emission properties. Scanning electron microscopy, energy dispersive x-ray spectrometry, and Raman spectroscopy confirmed the formation of the oxidized surface without changing the structure and morphology of CdS micro/nano-wires greatly. In situ micro-photoluminescence showed the continuous modulation of multi-sub-band emission of both near bandgap and defect state simultaneously with an ultra-broad spectrum range from 490 nm to 750 nm. According to the excitation wavelength-, excitation power-, and temperature-dependent PL spectra, the sub-band near bandgap emission originated from strong light–matter interaction such as photon–exciton coupling, while the whispering gallery mode (WGM) micro-cavity played an important role in the sub-band emission of the defect state. The spatial-resolved mapping of emission modes confirmed the sub-band near bandgap and defect WGM micro-cavity emission from the core and oxidized surface of CdS micro-wires, respectively. The multi-exponential lifetime dynamics further indicated the complex recombination process of both near bandgap and defect state emission. These results are different from the one-step synthesized CdS@CdO core/shell micro-wires and reveal an interesting exciton–photon coupling with enhanced optical cavity confinement in the post-treated CdS micro/nano-wires, representing the rational tailoring of surface/interface relevant properties to control the light emission for application in nanophotonic devices.
Calorimetry of DyxY3−xAl5O12 garnet solid solutions in magnetic field
Authors: Lezova I. E. , Charnaya E. V. , Shevchenko E. V. , Khazanov E. N. , Taranov A. V.
Published: December 2020

We report the caloric and magnetocaloric properties of the DyxY3−xAl5O12 garnet single crystals (x = 0, 0.15, 0.5, 1, 1.5, 2.25, 3) studied within a large temperature range at magnetic fields up to 70 kOe. Heat capacity at zero field revealed that the Schottky anomalies ascribed to magnetic splitting the ground Kramers doublet of Dy3+ ions induced by neighbor ions. The low-temperature heat capacity was fitted by a sum of the Debye and Schottky contributions. The antiferromagnetic transition above 1.9 K was observed only for the pure dysprosium aluminum garnet. The shifts of the Schottky anomalies in magnetic fields agreed with strong anisotropy of the g-factor of Dy3+ ions in the c-sites. The Dy3+ ions in the non-stoichiometric positions caused additional weak anomalies in the heat capacity. The heat capacity for the garnet with x = 1 demonstrated strong clustering for this particular composition. The results obtained showed that the measurements of the heat capacity in magnetic field can be used to get information on substitutional disorder and non-stoichiometry in solid solutions. The magnetic entropy was evaluated for the dysprosium-comprising garnets. The pronounced magnitude of the magnetic entropy owing to the Schottky anomalies shows the applicability of the mixed dysprosium yttrium garnets to adiabatic refrigerators.
Root length is proxy for high-throughput screening of waterlogging tolerance in Urochloa spp. grasses
Authors: de la Cruz Jiménez Juan , Cardoso Juan A. , Kotula Lukasz , Veneklaas Erik J. , Pedersen Ole , Colmer Timothy D.
Published: December 2020

C4 perennial Urochloa spp. grasses are widely planted in extensive areas in the tropics. These areas are continuously facing waterlogging events, which limits plant growth and production. However, no commercial cultivar combining excellent waterlogging tolerance with superior biomass production and nutritional quality is available. The objective of this study was to identify root traits that can be used for selecting waterlogging tolerant species of Urochloa. Root respiration, root morphological, architectural and anatomical traits were evaluated in eight contrasting Urochloa spp. genotypes grown under aerated or deoxygenated stagnant solutions. Moreover, modelling of internal aeration was used to relate differences in root traits and root growth in waterlogged soils. Increased aerenchyma formation in roots, reduced stele area and development of a fully suberised exodermis are characteristics improving internal aeration of roots and therefore determining waterlogging tolerance in these C4 forage grasses. Waterlogging-tolerant genotypes had steeper root angles and greater root lengths than the waterlogging-sensitive genotypes. In stagnant conditions, waterlogging-tolerant genotypes had a greater proportion of aerenchyma and reduced stele area in root cross-sections, had deeper roots, steeper root angle and larger root biomass, which in turn, allowed for greater shoot biomass. Total root length had the strongest positive influence on shoot dry mass and can therefore be used as proxy for selecting waterlogging tolerant Urochloa genotypes.
Assessment of silver eel (Anguilla anguilla) route selection at a water-regulating weir using an acoustic camera
Authors: Lenihan Eamonn S. , McCarthy T. Kieran , Lawton Colin
Published: December 2020

Riverine dams and weirs present silver eels with multiple migration routes during their downstream migrations. In relation to dams, understanding route selection is important for estimating silver eel escapement, especially where mortality rates vary among routes. On the lower River Shannon, Ireland, a water-regulating weir presents silver eels with two potential migration routes, the natural river channel and a headrace canal leading to a hydropower station. Route selection at the weir was investigated using a dual-frequency identification sonar (DIDSON) and replicated mark–recapture experiments. The proportion of eels migrating via the headrace canal was strongly related to the proportion of total flow diverted to that route (R2=0.827, P<0.001), suggesting that eel route selection was passive. The active swimming speeds of eels (median=0.16m s−1), observed with the acoustic camera, did not greatly exceed water velocity and further suggested that eels were largely carried by the current. Knowledge of the relationship among flow, water velocity and eel route selection highlighted the potential to strategically alter hydropower-generating protocols to maximise silver eel passage via safer routes, and enhance survival.
Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription
Authors: Rosen Grace A. , Baek Inwha , Friedman Larry J. , Joo Yoo Jin , Buratowski Stephen , Gelles Jeff
Published: December 2020

Significance

The synthesis of a eukaryotic messenger RNA molecule involves the association of RNA polymerase and dozens of accessory proteins on DNA. We used differently colored fluorescent dyes to tag DNA, RNA polymerase II, and the elongation factor Spt4/5 in yeast nuclear extract and then observed the assembly and dynamics of individual molecules of the proteins with single DNA molecules by microscopy. The observations quantitatively define an overall pathway by which transcription complexes form and evolve during activator-dependent transcription. They also suggest how Spt4/5 dynamics might promote efficient RNA production.
Quantum simulation investigation of work-function variation in nanowire tunnel FETs
Authors: Guan Yunhe , Carrillo-Nuñez Hamilton , Georgiev Vihar P , Asenov Asen , Liang Feng , Li Zunchao , Chen Haifeng
Published: December 2020

The variability induced by the work-function variation (WFV) in p-type ultra-scaled nanowire tunnel FET (TFET) has been studied by using the Non-Equilibrium Green’s Function module implemented in University of Glasgow quantum transport simulator called NESS. To provide a thorough insight into the influence of WFV, we have simulated 250 atomistically different nanowire TFETs and the obtained results are compared to nanowire MOSFETs first. Our statistical simulations reveal that the threshold voltage (V
th) variations of MOSFETs and TFETs are comparable, whereas the on-current (I
on) and off-current (I
off) variations of TFETs are smaller and higher, respectively in comparison to the MOSFET. Based on the results of the simulations, we have provided a physical insight into the variations of the I
on and I
off currents. Then, we compared the nanowire and Fin TFETs structures with different oxide thickness in terms of the WFV-induced variability. The results show that WFV has a strongest impact on the I
off, and moderate effect on the I
on and V
th in nanowire TFET with smaller oxide thickness. Lastly, it is found that compared with the random discrete dopants, WFV is a relatively weaker variability source in ultra-scaled nanowire TFETs, especially from the point of view of I
on variation.
Layer thickness influenced irradiation effects of proton beam on MoS2 field effect transistors
Authors: Huang Xin-nan , Shi Jing-yuan , Yao Yao , Peng Song-ang , Zhang Da-yong , Jin Zhi
Published: December 2020

We investigated the influence of the flake thickness for molybdenum disulfide (MoS2) field effect transistors on the effect of a 150 keV high-energy proton beam applied on these devices. The electrical characteristics of the devices with channel thicknesses ranging from monolayer to bulk were measured before and after proton irradiation with a proton fluence of 5 × 1014 cm−2. The subthreshold swing (SS), threshold voltage shift and electron mobility were extracted with the Y-function method after proton irradiation and significant degradation were observed. It is found that, with the increase of layer thickness, mobility degradation and threshold voltage shift both eased, but the SS degradation was insensitive to the MoS2 flake thickness increase. We also demonstrate that the threshold voltage shift is dominated by oxide charges; however, the mobility and SS degradations are mainly affected by the interface traps. Our study will enhance the understanding of the influence of high-energy particles on MoS2-based nano-electronic devices. By increasing the MoS2 flake thickness to a certain extent, one can hopefully find a balance between effectively resisting

V

T
H

shift and achieving high mobility and small SS degradation.
Models for the self-heating evaluation of a gallium nitride-based high electron mobility transistor
Authors: Florovič M , Kováč J , Kováč J , Chvála A , Weis M , Jacquet J-C , Delage S L
Published: December 2020

We propose a novel model approach for temperature evaluation in the channel region of a InAlN/AlN/gallium nitride high electron mobility transistor (HEMT) due to self-heating effects. The heat transfer in a HEMT device has been investigated experimentally by the nearby temperature sensor and compared by theoretical models solved by both numerical and analytical methods. The average temperature of the channel area of almost 160 °C for dissipated power of 2 W was determined using the drain-source current variation analysis. The electrical and thermal behavioral numerical model under quasi-static conditions have been used to describe the HEMT device. In contrast, the one-dimensional thermal model for analytical evaluation has been proposed as an alternative approach. Surprisingly, the experimental results verified not only the validity of precise numerical simulation but also the simplified analytical model that makes it a reliable tool even for complex electronic devices.
Study of contact resistivity of a no-insulation superconducting coil
Authors: Liu Yingzhen , Ou Jing , Gyuraki Roland , Schreiner Fabian , de Sousa Wescley T B , Noe Mathias , Grilli Francesco
Published: December 2020

Previous studies of test coils have demonstrated the high thermal and electrical stability of no-insulation (NI) high temperature superconducting (HTS) coils thanks to the presence of turn-to-turn current paths. These turn-to-turn current paths in a NI coil are significantly influenced by the contact resistivity. In practice, it is very challenging to measure the contact resistivity of a NI coil by direct experiments of short samples, since the contact resistivity of superconducting tapes is influenced by surface roughness and tolerance, stress, temperature etc. A proper simulation model is needed to investigate the contact resistivity of the NI coils with dedicated experiments. Hence, in this paper a distributed circuit model is employed. This model, implemented in Matlab 2018a, considers the local contact resistivity, self and mutual inductance, and HTS resistance, which depends on the supplied current, magnetic field and temperature. To validate the model, experimental results from literature, including sudden discharge, and charge–discharge processes, are employed and the results from simulations are consistent with experimental results. Then the model is used to investigate the equivalent contact resistivity of a 157-turn NI coil. Through the comparison of simulated and experimental results, it is found that the contact resistivity of the NI coil has an inhomogeneous distribution. When the current changes with different speeds, ramping rates or frequency, a different number of turn-to-turn contacts carries radial current. Since the turn-to-turn contacts have different contact resistivity, the equivalent contact resistivity calculated from sudden discharge cannot be used in simulations to reproduce all the experimental data.
A scalable superconducting nanowire memory cell and preliminary array test
Authors: Butters Brenden A , Baghdadi Reza , Onen Murat , Toomey Emily A , Medeiros Owen , Berggren Karl K
Published: December 2020

There has been a demand for a scalable superconducting memory technology for cryogenic computing for some time. This demand has proven difficult to satisfy due to the simultaneous need for high speed operation, low power consumption, and high density, all while maintaining cryogenic and SFQ compatibility. In an effort to satisfy this demand, we have developed a simple memory cell based on our prior work with nanowire-based memories. Due to the memory cell’s reliance on kinetic inductance, the cell can be scaled to almost any size. The cell has been designed specifically such that it can easily form into an array simply by arranging in a 2D pattern. This design eliminated the need for external addressing circuitry. This new cell, when operated in isolation and without the heater, performs very well with predicted bit error rates around 10−17. However, preliminary array tests show that while the memory operates, the predicted error rates rise to 1.5 × 10−3. We believe that this issue is predominantly due to the hTron-channel kinetic inductance dramatically changing upon the application of the row-select heaters. This issue might be addressed by designing the cell to compensate for the change in kinetic inductance when the heater is activated. If this remedy proves to be effective, then this memory would enable the development of compact and scalable memory arrays.
Waveform analysis of a large-area superconducting nanowire single photon detector
Authors: Marvinney Claire E , Lerner Brian E , Puretzky Alexander A , Miller Aaron J , Lawrie Benjamin J
Published: December 2020

Superconducting nanowire single photon detectors (SNSPDs) are typically used as single-mode-fiber-coupled single-pixel detectors, but large area detectors are increasingly critical for applications ranging from microscopy to free-space quantum communications. However, the long meander-line length of such large-area SNSPDs results in a proportionately large kinetic inductance that affects the waveform generated by the device. Here, we explore changes in the rising edge of the readout pulse for a single-pixel large-area SNSPD as a function of the optical spot size on the detector and compare to the rising edge of the dark-count waveform. We observe a bimodal distribution of bright-count rise times and show that the probability of a slow rise time increases in the limit of large spot sizes, indicative of a position sensitive response. Additionally, in the limit of low bias currents, the dark-count readout pulse is most similar to the large spot-size bright-count readout pulse, which suggests that dark counts arise from locations spanning the device. These results are consistent with a simple model of traveling microwave modes excited by single photons incident at varying positions along the length of the nanowire.
Deformed two-dimensional rogue waves in the (2+1)-dimensional Korteweg-de Vries equation*
Authors: Cao Yulei , Hu Peng-Yan , Cheng Yi , He Jingsong
Published: December 2020

Within the (2 + 1)-dimensional Korteweg–de Vries equation framework, new bilinear Bäcklund transformation and Lax pair are presented based on the binary Bell polynomials and gauge transformation. By introducing an arbitrary function ϕ(y), a family of deformed soliton and deformed breather solutions are presented with the improved Hirota’s bilinear method. By choosing the appropriate parameters, their interesting dynamic behaviors are shown in three-dimensional plots. Furthermore, novel rational solutions are generated by taking the limit of the obtained solitons. Additionally, two-dimensional (2D) rogue waves (localized in both space and time) on the soliton plane are presented, we refer to them as deformed 2D rogue waves. The obtained deformed 2D rogue waves can be viewed as a 2D analog of the Peregrine soliton on soliton plane, and its evolution process is analyzed in detail. The deformed 2D rogue wave solutions are constructed successfully, which are closely related to the arbitrary function ϕ(y). This new idea is also applicable to other nonlinear systems.
Energy behavior of Boris algorithm
Authors: Zafar Abdullah , Khan Majid
Published: December 2020

Boris numerical scheme due to its long-time stability, accuracy and conservative properties has been widely applied in many studies of magnetized plasmas. Such algorithms conserve the phase space volume and hence provide accurate charge particle orbits. However, this algorithm does not conserve the energy in some special electromagnetic configurations, particularly for long simulation times. Here, we empirically analyze the energy behavior of Boris algorithm by applying it to a 2D autonomous Hamiltonian. The energy behavior of the Boris method is found to be strongly related to the integrability of our Hamiltonian system. We find that if the invariant tori is preserved under Boris discretization, the energy error can be bounded for an exponentially long time, otherwise the said error will show a linear growth. On the contrary, for a non-integrable Hamiltonian system, a random walk pattern has been observed in the energy error.
Closed form soliton solutions of three nonlinear fractional models through proposed improved Kudryashov method
Authors: Rahman Zillur , Ali M Zulfikar , Roshid Harun-Or
Published: December 2020

We introduce a new integral scheme namely improved Kudryashov method for solving any nonlinear fractional differential model. Specifically, we apply the approach to the nonlinear space–time fractional model leading the wave to spread in electrical transmission lines (s-tfETL), the time fractional complex Schrödinger (tfcS), and the space–time M-fractional Schrödinger–Hirota (s-tM-fSH) models to verify the effectiveness of the proposed approach. The implementing of the introduced new technique based on the models provides us with periodic envelope, exponentially changeable soliton envelope, rational rogue wave, periodic rogue wave, combo periodic-soliton, and combo rational-soliton solutions, which are much interesting phenomena in nonlinear sciences. Thus the results disclose that the proposed technique is very effective and straight-forward, and such solutions of the models are much more fruitful than those from the generalized Kudryashov and the modified Kudryashov methods.
Protein subcellular localization based on deep image features and criterion learning strategy
Authors: Su Ran , He Linlin , Liu Tianling , Liu Xiaofeng , Wei Leyi
Published: December 2020

The spatial distribution of proteome at subcellular levels provides clues for protein functions, thus is important to human biology and medicine. Imaging-based methods are one of the most important approaches for predicting protein subcellular location. Although deep neural networks have shown impressive performance in a number of imaging tasks, its application to protein subcellular localization has not been sufficiently explored. In this study, we developed a deep imaging-based approach to localize the proteins at subcellular levels. Based on deep image features extracted from convolutional neural networks (CNNs), both single-label and multi-label locations can be accurately predicted. Particularly, the multi-label prediction is quite a challenging task. Here we developed a criterion learning strategy to exploit the label–attribute relevancy and label–label relevancy. A criterion that was used to determine the final label set was automatically obtained during the learning procedure. We concluded an optimal CNN architecture that could give the best results. Besides, experiments show that compared with the hand-crafted features, the deep features present more accurate prediction with less features. The implementation for the proposed method is available at https://github.com/RanSuLab/ProteinSubcellularLocation.
Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning
Authors: Stiehler Felix , Steinborn Marvin , Scholz Stephan , Dey Daniela , Weber Andreas P M , Denton Alisandra K
Published: December 2020

Motivation

Current state-of-the-art tools for the de novo annotation of genes in eukaryotic genomes have to be specifically fitted for each species and still often produce annotations that can be improved much further. The fundamental algorithmic architecture for these tools has remained largely unchanged for about two decades, limiting learning capabilities. Here, we set out to improve the cross-species annotation of genes from DNA sequence alone with the help of deep learning. The goal is to eliminate the dependency on a closely related gene model while also improving the predictive quality in general with a fundamentally new architecture.

Results

We present Helixer, a framework for the development and usage of a cross-species deep learning model that improves significantly on performance and generalizability when compared to more traditional methods. We evaluate our approach by building a single vertebrate model for the base-wise annotation of 186 animal genomes and a separate land plant model for 51 plant genomes. Our predictions are shown to be much less sensitive to the length of the genome than those of a current state-of-the-art tool. We also present two novel post-processing techniques that each worked to further strengthen our annotations and show in-depth results of an RNA-Seq based comparison of our predictions. Our method does not yet produce comprehensive gene models but rather outputs base pair wise probabilities.

Availability and implementation

The source code of this work is available at https://github.com/weberlab-hhu/Helixer under the GNU General Public License v3.0. The trained models are available at https://doi.org/10.5281/zenodo.3974409

Supplementary information

Supplementary data are available at Bioinformatics online.
Development of an HPLC-UV Method to Assay Empagliflozin Tablets and Identification of the Major Photoproduct by Quadrupole Time-of-Flight Mass Spectrometry
Authors: Burin Suelen Leticia , Lourenço Rebeca Lino , Doneda Morgana , Müller Edson Irineu , Paula Fávero Reisdorfer , Adams Andréa Inês Horn
Published: December 2020

Diabetes is a set of metabolic disorders that affect >400 million individuals worldwide. Empagliflozin belongs to the gliflozin class and is used orally to treat type 2 diabetes. In this study, a simple stability-indicating HPLC-UV method was developed to assay empagliflozin tablets and its main photoproduct was identified by high-resolution mass spectrometry. The mobile phase, which was optimized by Central Composite Design, was composed of methanol, acetonitrile and purified water (60:5:35 v/v), at a flow rate of 1 mL min−1. The calibration curve was linear in the range of 5–150 μg mL−1. All the validation parameters were met and the method was specific, even in the presence of degradation products. In the forced degradation study, empagliflozin standard and empagliflozin tablets were submitted to several conditions (acidic, alkaline, neutral and oxidant media, thermal, photolytic and humidity), and empagliflozin showed instability under all these conditions. A degradation product generated after drug exposure to ultraviolet C radiation was isolated and analyzed by quadrupole time-of-flight mass spectrometry, and the results suggested that empagliflozin undergoes decomposition by a dechlorination pathway. In silico toxicity was predicted for the degradation product, which showed a high risk of genotoxicity and hepatotoxicity.
Influence of sea ice dynamics on population energetics of Western Hudson Bay polar bears
Authors: Johnson Amy C , Reimer Jody R , Lunn Nicholas J , Stirling Ian , McGeachy David , Derocher Andrew E
Published: December 2020

The Arctic marine ecosystem has experienced extensive changes in sea ice dynamics, with significant effects on ice-dependent species such as polar bears (Ursus maritimus). We used annual estimates of the numbers of bears onshore in the core summering area, age/sex structure and body condition data to estimate population energy density and storage energy in Western Hudson Bay polar bears from 1985 to 2018. We examined intra-population variation in energetic patterns, temporal energetic trends and the relationship between population energetics and sea ice conditions. Energy metrics for most demographic classes declined over time in relation to earlier sea ice breakup, most significantly for solitary adult females and subadult males, suggesting their greater vulnerability to nutritional stress than other age/sex classes. Temporal declines in population energy metrics were related to earlier breakup and longer lagged open-water periods, suggesting multi-year effects of sea ice decline. The length of the open-water period ranged from 102 to 166 days and increased significantly by 9.9 days/decade over the study period. Total population energy density and storage energy were significantly lower when sea ice breakup occurred earlier and the lagged open-water period was longer. At the earliest breakup and a lagged open-water period of 180 days, population energy density was predicted to be 33% lower than our minimum estimated energy density and population storage energy was predicted to be 40% lower than the minimum estimated storage energy. Consequently, over the study, the total population energy density declined by 53% (mean: 3668 ± 386 MJ kg-1/decade) and total population storage energy declined by 56% (mean: 435900 ± 46770 MJ/decade). This study provides insights into ecological mechanisms linking population responses to sea ice decline and highlights the significance of maintaining long-term research programs.
Fully coupled dynamic simulations of bioprosthetic aortic valves based on an embedded strategy for fluid–structure interaction with contact
Authors: Nestola Maria G C , Zulian Patrick , Gaedke-Merzhäuser Lisa , Krause Rolf
Published: December 2020

Aims

This work aims at presenting a fully coupled approach for the numerical solution of contact problems between multiple elastic structures immersed in a fluid flow. The key features of the computational model are (i) a fully coupled fluid–structure interaction with contact, (ii) the use of a fibre-reinforced material for the leaflets, (iii) a stent, and (iv) a compliant aortic root.

Methods and results

The computational model takes inspiration from the immersed boundary techniques and allows the numerical simulation of the blood–tissue interaction of bioprosthetic heart valves (BHVs) as well as the contact among the leaflets. First, we present pure mechanical simulations, where blood is neglected, to assess the performance of different material properties and valve designs. Secondly, fully coupled fluid–structure interaction simulations are employed to analyse the combination of haemodynamic and mechanical characteristics. The isotropic leaflet tissue experiences high-stress values compared to the fibre-reinforced material model. Moreover, elongated leaflets show a stress concentration close to the base of the stent. We observe a fully developed flow at the systolic stage of the heartbeat. On the other hand, flow recirculation appears along the aortic wall during diastole.

Conclusion

The presented FSI approach can be used for analysing the mechanical and haemodynamic performance of a BHV. Our study suggests that stresses concentrate in the regions where leaflets are attached to the stent and in the portion of the aortic root where the BHV is placed. The results from this study may inspire new BHV designs that can provide a better stress distribution.
Optimizing cryoballoon pulmonary vein isolation: lessons from >1000 procedures— the Frankfurt approach
Authors: Bordignon Stefano , Chen Shaojie , Bologna Fabrizio , Thohoku Shota , Urbanek Lukas , Willems Franziska , Zanchi Simone , Bianchini Lorenzo , Trolese Luca , Konstantinou Athanasios , Fuernkranz Alexander , Schmidt Boris , Chun Julian K R
Published: December 2020

Aims

Cryoballoon (CB) pulmonary vein isolation (PVI) is an accepted ablation strategy for rhythm control in atrial fibrillation (AF). We describe efficacy and safety in a high volume centre with a long experience in the use of the second-generation CB (CB2).

Methods and results

Consecutive paroxysmal AF (PAF) or persistent AF (persAF) patients undergoing CB2-PVI were enrolled. Procedural data, efficacy, and safety issues were systematically collected. The 28 mm CB2 was used in combination with an inner lumen spiral catheter, a luminal oesophageal temperature (LET) probe was used with a cut-off of 15°C, the phrenic nerve (PN) monitored during septal PVs ablation. Freeze duration was mainly set at 240 s with a bonus application in case of delayed time-to-isolation (TTI > 75 s). A total of 1017 CB2 procedures were analysed (58% male, 66 ± 12 years old, 70% with PAF). 3964 PVs were identified, 99.8% PVs isolated using solely the 28 mm CB. Mean procedure time was 69 ± 25 min, TTI during the first application was recorded in 77% of PVs after a mean of 48 ± 31 s. We recorded 0.2% cardiac tamponade, 4.8% PN injury (1.6% of PN palsy), and 19% of LET < 15°C. Among 725 patients with follow-up data, 84% with PAF and 75% with persAF were in stable SR at 1 year. Shorter freezing duration and longer TTI were procedural predictors for recurrence.

Conclusion

Cryoballoon procedures are fast and associated with a benign safety profile. Shorter TTI and longer freeze durations are associated with sinus rhythm during follow-up.
A single nucleotide polymorphism in an IgA1 protease gene determines Streptococcus pneumoniae adaptation to the middle ear during otitis media
Authors: Tikhomirova Alexandra , Trappetti Claudia , Paton James C , Watson-Haigh Nathan , Wabnitz David , Jervis-Bardy Jake , Jardeleza Camille , Kidd Stephen P
Published: December 2020

Factors facilitating the chronicity of otitis media (OM) in children are, to date, not fully understood. An understanding of molecular factors aiding bacterial persistence within the middle ear during OM could reveal pathways required for disease. This study performed a detailed analysis of Streptococcus pneumoniae populations isolated from the nasopharynx and middle ear of one OM case. Isolates were assessed for growth in vitro and infection in a mouse intranasal challenge model. Whole genome sequencing was performed to compare the nasopharyngeal and middle ear isolates. The middle ear isolate displayed a reduced rate of growth and enhanced potential to transit to the middle ear in a murine model. The middle ear population possessed a single nucleotide polymorphism (SNP) in the IgA1 protease gene igA, predicted to render its product non-functional. Allelic exchange mutagenesis of the igA alleles from the genetic variant middle ear and nasopharyngeal isolates was able to reverse the niche-adaptation phenotype in the murine model. These results indicate the potential role of a SNP in the gene encoding the IgA1 protease, in determining S. pneumoniae adaptation to the middle ear during chronic OM. In contrast, a functional IgA1 protease was associated with increased colonisation of the nasopharynx.
The parabolic p-Laplacian with fractional differentiability
Authors: Breit Dominic , Diening Lars , Storn Johannes , Wichmann Jörn
Published: December 2020

We study the parabolic $p$-Laplacian system in a bounded domain. We deduce optimal convergence rates for the space–time discretization based on an implicit Euler scheme in time. Our estimates are expressed in terms of Nikolskiǐ spaces and therefore cover situations when the (gradient of the) solution has only fractional derivatives in space and time. The main novelty is that, different to all previous results, we do not assume any coupling condition between the space and time resolutions $h$ and $\tau $. For this we show that the $L^2$-projection is compatible with the quasi-norm. The theoretical error analysis is complemented by numerical experiments.
A Switchable Solvent-Based Liquid Phase Microextraction Method for the Detection of Cadmium in Water Samples with Flame Atomic Absorption Spectrometry
Authors: Aydin Urucu Oya , Aracier Esra Duygu
Published: December 2020

Background

The natural concentration of trace elements in water and soil depends on the geological, geomorphological, and climate characteristics of the region. The rapid increase of technology in recent years has increased concentrations of trace elements in nature.

Objective

Separation and enrichment methods are needed to detect trace amounts of heavy metals that cannot be detected due to the detection limit of the instruments or the matrix effect in samples. Recently, low hazard solvents compatible with green chemistry have been used in preconcentration/separation studies of Cd(II).

Methods

Switchable solvent-based liquid phase microextraction is an environmentally-friendly, simple, and fast procedure for the determination of Cd(II) ions in environmental samples combined with flame atomic absorption spectrometry (FAAS).

Results

The switchable polarity solvent was prepared with N,N-dimethyl-n-octylamine. 2–(5-Bromo-2-pyridylazo)-5-(diethylamino) phenol was used as the complexing agent. Important parameters such as pH, amount of switchable polarity solvent and NaOH, as well as ligand and sample volume, all of which might affect the microextraction efficiency were optimized. Under optimal experimental conditions, linear range was found to be between 5 and 500 µg/L. The limit of detection, preconcentration factor, and relative standard deviation were 0.89 μg/L, 150, and 3.2%, respectively.

Highlights

The accuracy of our method was confirmed by the analysis of certified reference material SPS-WW1 Batch 106 (Waste Waters). The developed procedure was successfully applied to determine the cadmium contents of environmental water samples. We believe that this environmentally-friendly method will be useful in detecting Cd(II) ions in water samples.
An Overview of the Pepper Weevil (Coleoptera: Curculionidae) as a Pest of Greenhouse Peppers
Authors: Fernández D Catalina , VanLaerhoven Sherah L , McCreary Cara , Labbé Roselyne M
Published: December 2020

The pepper weevil (Anthonomus eugenii Cano) is a destructive insect pest of field and greenhouse pepper crops across North America. Its management remains challenging with significant implications for pepper production, despite a documented presence in Central America, Mexico, the United States, and the Caribbean for approximately a century, and recently in Canada. Currently, the main tools and methods applied to manage pepper weevil populations in greenhouse peppers are the implementation of strict biosecurity protocols, diligent monitoring, physical and cultural management techniques, and chemical insecticides when necessary. However, these tools can be costly, labor-intensive, and insufficient, particularly when new outbreaks go undetected for prolonged periods. Additionally, the use of available insecticides is limited due to significant nontarget effects these have on biological control agents used to manage other important greenhouse pepper pests. Recently, research efforts have focused on developing better tools for pepper weevil management to mitigate a rising incidence of insecticide resistance and the spread of weevils into temperate regions, however, multiple constraints remain. Here, we review the current state of knowledge of the pepper weevil and identify information gaps, which future research should address to improve the targeted management of this pest in greenhouse pepper production systems.
Addressing migrants’ well-being during COVID-19: An analysis of Chinese communities’ heritage language schools in Germany
Authors: Wang Zi
Published: December 2020

The coronavirus pandemic and the ensuing lockdown affected social life in every regard. In critical times, the well-being of vulnerable groups is often at stake. Migrants represent a case in point because language barriers and the lack of social networks impede their seeking help from public institutions and information access. In migration policy and research, current attention overwhelmingly focusses on COVID-19’s impact on travel restrictions and healthcare. This article contributes a new perspective by demonstrating how migrants’ well-being needs (understood as emotions and sense of achievement) in education during the COVID-19-induced school closure were addressed by community educational organisations. Focussing on the Chinese community in Germany, data were collected in Chinese heritage language (CHL) schools from three urban areas. This article argues that CHL schools’ reaction to public schools’ closure had a positive impact on their members’ well-being. Such organisations achieved this by expanding their educational programmes during and after the lockdown. These measures ensured continuity in migrant children’s education beyond the realm of heritage language instruction, while enabling migrant parents to seek employment as the economy reopened. Overall, the results of this study underscore the potential of community organisations’ educational programmes in maintaining migrants’ well-being, especially in trying times.