bluuebunny/crossref_metadata_2025 huggingface dataset:
Crossover from normal to relaxor ferroelectric in Sr0.25Ba0.75(Nb1−xTax)2O6 ceramics with tungsten bronze structure
Authors: Yang Zi Jin , Liu Xiao Qiang , Zhu Xiao Li , Chen Xiang Ming
Published: September 2020

The crossover from normal to relaxor ferroelectrics in Sr0.25Ba0.75(Nb1−xTax)2O6 (x = 0, 0.1, 0.25, and 0.5) ceramics was determined together with the structure evolution. A single-phase tungsten bronze structure in space group P4bm (x = 0 and 0.1) or P4/mbm (x = 0.25 and 0.5) was obtained in the entire composition range. The lattice parameter a increased, while c, tetragonality c/a, and cell volume decreased with increasing x. Meanwhile, the dielectric maximum temperature Tm went down and the dielectric peak exhibited an enhanced diffused nature with a stronger frequency dispersion, where the saturated P–E loop (x = 0 and 0.1) transformed to a slim relaxor loop (x = 0.25) and finally to the linear one (x = 0.5). Raman spectra results revealed the reduced covalence between the B-site cation and the oxygen ion as a result of Ta-substitution. The coexistence of Nb5+ and Ta5+, which possessed the distinct covalence with the oxygen ion, played the key role in the structural variation and crossover from normal to relaxor ferroelectrics in the present system.
The effect of surface roughness on laser-induced stress wave propagation
Authors: Boyd James D. , Grady Martha E.
Published: September 2020

We investigate laser-induced acoustic wave propagation through smooth and roughened titanium-coated glass substrates. Acoustic waves are generated in a controlled manner via the laser spallation technique. Surface displacements are measured during stress wave loading by the alignment of a Michelson-type interferometer. A reflective coverslip panel facilitates capture of surface displacements during loading of as-received smooth and roughened specimens. Through interferometric experiments, we extract the substrate stress profile at each laser fluence (energy per area). The shape and amplitude of the substrate stress profile are analyzed at each laser fluence. Peak substrate stress is averaged and compared between smooth specimens with the reflective panel and rough specimens with the reflective panel. The reflective panel is necessary because the surface roughness of the rough specimens precludes in situ interferometry. Through these experiments, we determine that the surface roughness employed has no significant effect on substrate stress propagation and smooth substrates are an appropriate surrogate to determine stress wave loading amplitude of roughened surfaces less than 1.2 μm average roughness (Ra). No significant difference was observed when comparing the average peak amplitude and loading slope in the stress wave profile for the smooth and rough configurations at each fluence.
Coherent superconducting qubits from a subtractive junction fabrication process
Authors: Stehli Alexander , Brehm Jan David , Wolz Tim , Baity Paul , Danilin Sergey , Seferai Valentino , Rotzinger Hannes , Ustinov Alexey V. , Weides Martin
Published: September 2020

Josephson tunnel junctions are the centerpiece of almost any superconducting electronic circuit, including qubits. Typically, the junctions for qubits are fabricated using shadow evaporation techniques to reduce dielectric loss contributions from the superconducting film interfaces. In recent years, however, sub-micrometer scale overlap junctions have started to attract attention. Compared to shadow mask techniques, neither an angle dependent deposition nor free-standing bridges or overlaps are needed, which are significant limitations for wafer-scale processing. This comes at the cost of breaking the vacuum during fabrication, but simplifies integration in multi-layered circuits and implementation of vastly different junction sizes and enables fabrication on a larger scale in an industrially standardized process. In this work, we demonstrate the feasibility of a subtractive process for the fabrication of overlap junctions. In an array of test contacts, we find low aging of the average normal state resistance of only 1.6% over 6 months. We evaluate the coherence properties of the junctions by employing them in superconducting transmon qubits. In time domain experiments, we find that both, the qubit life- and coherence time of our best device, are, on average, greater than 20 μs. Finally, we discuss potential improvements to our technique. This work paves the way toward a more standardized process flow with advanced materials and growth processes, and constitutes an important step for the large scale fabrication of superconducting quantum circuits.
Cavity quantum electro-dynamics with solid-state emitters in aperiodic nano-photonic spiral devices
Authors: Trojak Oliver J. , Gorsky Sean , Sgrignuoli Fabrizio , Pinheiro Felipe A. , Park Suk-In , Song Jin Dong , Dal Negro Luca , Sapienza Luca
Published: September 2020

Integrated quantum devices are at the basis of the realization of scalable, high-performance quantum technology, including quantum computers and quantum communication schemes, where single photons are emitted, guided, manipulated, and detected on a chip. Engineered nano-devices enable the efficient confinement of light and, ultimately, the control of the spontaneous emission dynamics of single emitters, which is crucial for cavity quantum electrodynamics experiments and for the development of classical and quantum light sources. Here, we report on the demonstration of enhanced light-matter interaction and Purcell effects on a chip, based on bio-inspired aperiodic devices fabricated in gallium arsenide. Indium arsenide single quantum dots are used as internal light sources to image, by means of micro-photoluminescence spectroscopy, the optical modes supported by photonic membranes with Vogel-spiral geometry. These emitters are also used to probe the density of optical states, modified by the aperiodic devices, by means of time-resolved spectroscopy. Our results show cavity quantum electrodynamics effects providing strong modifications of the spontaneous emission decay of single optical transitions. In particular, thanks to the significant modification of the density of optical states demonstrated in Vogel-spiral photonic structures, we show control of the decay lifetime of single emitters with a dynamic range reaching 20, thus opening the path to the implementation of aperiodic geometries in active classical and quantum devices.
The Great Lakes are filled to their brims, with no signs of receding
Authors: Kramer David
Published: September 2020

Experts see the fingerprints of climate change on the lakes’ record high water levels.
Long-term variability of the mean sea level pressure field over the Black Sea
Authors: Islek Fulya , Yuksel Yalcin , Sahin Cihan
Published: September 2020

This paper aims to evaluate spatiotemporal variability of the mean sea level pressure trends over the Black Sea using the gridded 40-year (1979-2018) reanalysis mean sea level pressure data from two different datasets. These datasets are the European Centre for Medium-Range Weather Forecasts ERA-Interim with a spatial resolution of 0.25° and temporal resolution of six hours, and the National Centers for Environmental Prediction/Climate Forecast System Reanalysis with a spatial resolution of 0.5° and temporal resolution of one hour. Data from both databases show that the mean sea level pressure tends to decrease towards the recent years over the entire Black Sea. The long-term averages of mean sea level pressure reflect the spatial variability over the Black Sea with much lower pressures in the eastern part of the Black Sea than that on the western side. The long-term variation is more intense in the eastern part of the Black Sea. Sea Level Anomaly over the Black Sea, spanning 26 years between 1993 and 2018, was analyzed using satellite altimetry data. It was found that there is a high Sea Level Anomaly where the mean sea level pressure is low, described by an inverted barometer response. The 39-year long Sea Surface Temperature Anomaly data (1981-2018) indicate the rising tendency in sea surface temperature towards recent years in the entire Black Sea. An inverse relationship is found between North Atlantic Oscillation index and sea surface temperature anomaly. On a seasonal scale, mean sea level pressure in winter (high-pressure system) is larger than that in summer (low-pressure system). Our analyses show that mean sea level pressure tends to decrease, sea surface temperature anomaly and sea surface temperature anomaly tends to increase in recent years over the Black Sea.
Data fusion of terrestrial laser scanner and remotely piloted aircraft systems points clouds for monitoring the coastal protection systems
Authors: Saponaro M. , Pratola L. , Capolupo A. , Saponieri A. , Damiani L. , Fratino U. , Tarantino E.
Published: September 2020

Frequently exposed to natural agents such as waves, wind, tides, storm activity, seasonal changes and anthropogenic agents, coastal areas are tangibly high energy environments and therefore subject to considerable dynamics. In order to mitigate and reduce the impacts on these areas, different types of coastal protection systems can be implemented. Rockwalls and breakwaters are the most ordinary structures and even if used precisely for coastal protection, these flexible structures can in turn be damaged or ineffective over time. Therefore, like the monitoring of coastal areas in terms of execution frequency and accuracy, the measurement of changes over time of these structures, in particular after significant events, can allow to carry out an economic maintenance service before a serious occurrence and costly damage. However, given the rapid evolution of the preservation state of coastal areas and protection structures, it is therefore essential to plan an equally frequent, practical and accurate structural-coastal monitoring. On the other hand, their accessibility can sometimes be dangerous or uncomfortable such as to compromise operations in the field. In this work, the application of two close-range detection techniques competitor, i.e. from the Terrestrial Laser Scanner and from Remote Piloted Aircraft Systems, aimed at the generation of three-dimensional reconstructions of a protection structure, was analyzed. By performing a cloud-to-cloud comparison, interesting considerations have been obtained on the precision that can be achieved and on the technical limits deriving from the two methodologies. Considering the economy and practicality of use, if used correctly, a Remote Piloted Aircraft Systems supported by a suitable geo-referencing and an optimized data processing, can produce accurate and coherent 3D reconstructions as those derivable from the Terrestrial Laser Scanner. Finally, the results obtained by merging the point clouds generated from the two different techniques were evaluated in order to identify any advantages in the structural maintenance of the systems.
Inflammasomes: Exosomal miRNAs loaded for action
Authors: Matikainen Sampsa , Nyman Tuula A. , Cypryk Wojciech
Published: September 2020

Inflammasomes are multiprotein complexes of the innate immune system. Their activation leads to robust secretion of exosomes. In this issue, Wozniak et al. (2020. J. Cell Biol. https://doi.org/10.1083/jcb.201912074) reveal a connection between inflammasome-mediated cleavage of Rab-interacting lysosomal protein (RILP) and sequence-specific loading of miRNAs into exosomes.
Streamer propagation along a profiled dielectric surface
Authors: Meyer H K H , Marskar R , Gjemdal H , Mauseth F
Published: September 2020

We investigate the propagation of positive streamers along a profiled dielectric surface in air at atmospheric pressure. Results from experiments and two-dimensional planar low-temperature plasma fluid simulations are presented and analysed. The test object consists of a disk-shaped high voltage electrode and a dielectric slab with 0.5 mm deep corrugations. The corrugated surface has a 47% larger surface area than the smooth reference surface. The experiments and simulations are performed at voltage levels that lead to either gap-bridging or arrested streamers. In both experiments and simulations, the streamers take a longer time to reach the ground electrode when propagating along the profiled surface than along the smooth reference surface. Also, arrested streamers stop closer to the high voltage electrode when a profiled surface is used. Streamers propagate closely along the surface profile in the simulations, which suggests that the observed surface profile effect is mainly a result of elongated streamer channels. Compared to the streamers propagating along the smooth surface, the elongated streamers on the profiled surface have less residual voltage at the streamer front to drive the streamer advancement.
Dissociative electron attachment cross sections for ro-vibrationally excited NO molecule and N
−
anion formation
Authors: Laporta V , Schneider I F , Tennyson J
Published: September 2020

Motivated by the huge need for data for non-equilibrium plasma modeling, a theoretical investigation of dissociative electron attachment to the NO molecule is performed. The calculations presented here are based on the local-complex-potential approach, taking into account five NO− resonances. Three specific channels of the process are studied, including the production of excited nitrogen atoms N(2D) and of its anions N−. Interpretation of the existing experimental data and their comparison with our theoretical result are given. A full set of ro-vibrationally-resolved cross sections and the corresponding rate coefficients are reported. In particular, a relatively large cross sections for N− ion formation at low energy of the incident electron and for vibrationally excited NO target are predicted. Finally, molecular rotation effects are discussed.
Plasma activation of N2, CH4and CO2: an assessment of the vibrational non-equilibrium time window
Authors: van de Steeg A W , Butterworth T , van den Bekerom D C M , Silva A F , van de Sanden M C M , van Rooij G J
Published: September 2020

Vibrational excitation potentially enhances the energy efficiency of plasma dissociation of stable molecules and may open new routes for energy storage and process electrification. Electron, vibrational and rotational temperatures were measured byin situThomson and Raman scattering in order to assess the opportunities and limitations of the essential vibration-translation non-equilibria in N2, CO2and CH4plasma. Electron temperatures of 1.1–2.8 eV were measured in N2and CH4. These are used to confirm predominant energy transfer to vibrations after an initial phase of significant electronic excitation and ionization. The vibrational temperatures initially exceed rotational temperatures by almost 8000 K in N2, by 900 K in CO2, and by 300 K in CH4. Equilibration is observed at the 0.1 ms timescale. Based on the vibrational temperatures, the vibrational loss rates for different channels are estimated. In N2, vibrational quenching via N atoms is identified as the dominant equilibration mechanism. Atomic nitrogen population reaches a mole fraction of more than 1%, as inferred from the afterglow emission decay, and explains a gas heating rate of 25 Kμs−1. CH4equilibration at 1200 K is predominantly caused by vibrational-translational relaxation in CH4–CH4collisions. As for CO2, vibrational-translational relaxation via parent molecules is responsible for a large fraction of the observed heating, whereas product-mediated VT relaxation is not significantly contributing. It is suggested that electronic excitation, followed by dissociation or quenching contributes to the remaining heat generation. In conclusion, the time window to profit from vibrational excitation under the present conditions is limiting practical application.
Conceptual design and multifield coupling behavior of magnetically propelled fish-like swimmers
Authors: Gao Wei , Wang Xingzhe
Published: September 2020

Composites reinforced with ferromagnetic particles have been widely used in various engineering areas and have been extensively attracted more attention for the past decade because of their magnetic dependent properties can be dramatically altered by applying a magnetic field. In this study, a conceptual model based on the soft composites filled with magnetoactive particles was proposed, and the numerical research of magneto-fluid-solid coupling behaviours for a soft biomimetic robot fish driven magnetically was carried out. Under the action of magnetic field, the magnetic sensitive materials distributed in specific parts of the robot fish body will deform and cause the whole body of the fish swinging, to flap the liquid and generate forward thrust, resulting in pushing the fish forward. The corresponding multifield coupling equations for the mechanism and responses of magnetically propelled fish-like swimmers were developed and simulated numerically using the COMSOL multiphysics software. The effects of the tail length, the modulus of magnetic sensitive materials and spatial arrangement feature on the swimming ability of the fish-like structure were analyzed in detail. The relevant results are expected to provide a theoretical guidance for the potential applications of such biomimetic devices in intelligent far-field driving, drug delivery and other fields.
Hand Gesture Recognition of Double-Channel EMG Signals Based on Sample Entropy and PSO-SVM
Authors: Zhang He , Su Mengwei
Published: September 2020

Considering wearable device requirements, such as injury-free, comfortable and light, a new method based on sample entropy and PSO-SVM for double-channel EMG signals recognition is proposed. First, the signal is segmented by using a non-overlapping adjacent sliding window. And the sample entropy of the valid information after signal in each window is decomposed by EMD is fast calculated to obtain a feature vector. Then the paper improved the PSO algorithm from two aspects. On the one hand, using a dynamic topology improved the impact of “premature” by replacing the global optimal value with neighborhood optimal value. On the other hand, in order to increase the probability of particles jumping out of local optimum, according to the principle of partition crossover, reset the particles that are trapped in local optimum. Next, the multi-window fusion decision result of the adaptive weight voting is used to identify the gesture. Finally, five methods are used to classify the five combined fingers movements about pinch gestures and compare with each other. The experimental results show that the algorithm (IPSO-SVM-WMV) combined sample entropy has strong robustness, real-time and anti-interference ability in double-channel EMGs signal recognition and the classification accuracy is better than PSO-SVM.
Music Style Transfer with Vocals Based on CycleGAN
Authors: Ye Hongliang , Zhu Wanning
Published: September 2020

In recent years, with the development of generative adversarial networks (GAN), the application of generative adversarial networks has gradually matured. An important application area for generating adversarial networks is called neural style transfer. In recent years, neural style transfer has played a major role in the field of image applications. However, it performed poorly in the music field. In addition, algorithms in the field of music style transfer have poor effect on the style transfer of music with vocals. Therefore, this paper extracts the CQT features and Mel spectrogram features of music, and then uses CycleGAN to transfer the styles of the CQT features and Mel spectrogram mapping pictures, and finally realizes the style transfer of music. On the classifier we trained, the average style transfer rate of music that meets our requirements reached 94.07%.
Research on Military Radio Fault Diagnosis Method Based on Fuzzy Neural Network
Authors: Wang Pan , Guo Wenpu , Yan Luhong
Published: September 2020

In view of the complexity, correlation and fuzziness of military radio faults, a fault diagnosis strategy combining fuzzy neural network with expert system is proposed, and the fault diagnosis method based on T-S fuzzy neural network is mainly studied. The fuzzy neural network model was established by MATLAB R2017a, and the simulation experiment was carried out. The experimental results show that the T-S fuzzy neural network model has good generalization ability, fault tolerance ability and self-adaptability, can quickly locate fault causes, greatly improve the diagnostic efficiency, and can be used in fault diagnosis of military radios.
Optimization and Application of GM(1,1) Model Based on Adams Formula
Authors: Shen Yan , Song Xingyu , Wang Xuesong , Han Shuai
Published: September 2020

Model of GM(1,1) uses the least square method to solve the parameters and the parameter value is one of the main sources of errors in the model of GM(1,1) prediction. In order to improve accuracy of the GM(1,1) prediction model, we construct an improved methods for parameter identification of the optimized models of GM(1,1) based on the fifth and sixth-order Adams implicit formula is proposed. At the same time, the optimized models of GM(1,1) is analysed and compared. Use data of the number of employees in the tertiary industry nationwide from 2014 to 2016 as the testing standard to verify the prediction effect of the improved GM(1,1) model. Numeral examples show that the improved GM(1,1) model has good applicability and effectively improves the prediction accuracy of the traditional model.
Voice Control System Based on Zynq FPGA
Authors: Liu Weili
Published: September 2020

In this paper, a speech recognition system is designed and the relevant hard-ware environment is built through Zynq FPGA AX7020 platform. In this system, the feature extraction of speech signals is based on MFCC (mel-frequency cepstrum coefficients). The algorithm in this system includes Pre-emphasis, Framing and Windowing, FFT, MFCC Parameter Calculation, VED Endpoint Detection and DTW Operations processes commonly used in speech system design. In this paper, the speech recognition algorithm is implemented on Zynq FPGA platform and also simulated in Matlab. At the same time, audio module AN831 is adopted in the hardware part to realize the sound acquisition function. Through the comparison of experimental data, it is found that the average recognition rate in Matlab simulation is 86.67%, while in Zynq FPGA platform test, the recognition rate is 80.67%. Using Zynq FPGA AX7020 as a platform to realize speech recognition, the recognition rate is higher than the traditional speech recognition technology.
Deep Belief Net-Based Fault Diagnosis of Flight Control System Sensors
Authors: Guo Yingnan , Ning Wenhui , Wan Fangyi
Published: September 2020

The present study implements a model based on the deep belief net (DBN) into the sensor fault diagnosis of the flight control system. The principle of DBN system identification was adopted to simulate and establish a nonlinear observer of the unmanned aerial vehicle (UAV) for the online estimation of sensors’ output, which identified the fault type by analyzing the residuals of estimated data and the actual output. After the fault detection is completed, the measured value of the faulty sensor is isolated and replaced by the observer-generated value, in order to ensure the UAV normal flight. The proposed DBN model uses the data of normal flight control system sensors as training samples for offline training. A flight control digital simulation system was established to select the optimal DBN model via comparative test runs. Eventually, the common faults of sensors were analyzed and diagnosed online. The results obtained strongly indicate that the proposed method ensures a rapid and accurate diagnostics and isolation of faults, as well as provides a proper signal reconstruction.
Urbanisation’s contribution to climate warming in Great Britain
Authors: Bassett R , Young P J , Blair G S , Cai X-M , Chapman L
Published: September 2020

Urbanisation is changing the climate of the world we live in. In Great Britain (GB) 5.8% of the total land area is covered by artificial surfaces, increasing from 4.3% in 1975. Aside from associated loss of farmland, biodiversity and a range of ecosystem services, changing to urban form warms the Earth’s surface: the urban heat island (UHI) effect. Standard estimates of temperature changes do not account for urbanisation (i.e. use of rural-only stations or removal of urban bias in observations), meaning that anthropogenic modifications to the land surface may be causing the surface-level atmosphere to warm quicker than those estimates suggest. Using observations from a high-density urban monitoring network, we show that locally this warming (instantaneously) may be over 8 °C. Based on the relationships between UHI intensity, urban fraction and wind speed in this network, we create a statistical model and use it to estimate the current daily-mean urban warming across GB to be 0.04 °C [0.02 °C –0.06 °C]. Despite this climate contribution appearing small (94% of GB’s land cover for the time-being is still rural), we show that half of GB’s population currently live in areas with average daily-mean warming ∼0.4 °C. Under heatwave conditions our high estimates show 40% of GB’s population may experience over a 1 °C daily-mean UHI. Furthermore, simply due to urbanisation (1975–2014) we estimate GB is warming at a rate equivalent and in addition to 3.4% [1.9%–5.0%] of the observed surface-level warming calculated from background stations. In the fastest urbanising region, South East GB, we find that these warming rates are up to three times faster. The methodology is straightforward and can be readily extended to other countries or updated as future land cover data becomes available.
Dual drug delivery system based on pH-sensitive silk fibroin/alginate nanoparticles entrapped in PNIPAM hydrogel for treating severe infected burn wound
Authors: Rezaei Fatemeh , Damoogh Sheyda , Reis Rui L , Kundu Subhas C , Mottaghitalab Fatemeh , Farokhi Mehdi
Published: September 2020

Herein, the pH-sensitive vancomycin (VANCO) loaded silk fibroin-sodium alginate nanoparticles (NPs) embedded in poly(N-isopropylacrylamide) (PNIPAM) hydrogel containing epidermal growth factor (EGF) are introduced for treating chronic burn wound infections. The hybrid system was developed to control the release rates of an antibiotic and growth factor for optimal treatment of burn infections. VANCO had a pH responsive release behavior from the nanoparticle (NP) and showed higher release rate in an alkaline pH compared to the neutral pH during 10 d. About 30% of EGF was also released from the hydrogel within 20 d. The released VANCO and EGF preserved their bioactivity more than ∼ 80%. The suitable physico-chemical properties and cellular behaviors of PNIPAM hydrogel supported the proliferation and growth of the fibroblast cells. Furthermore, the higher re-epithelialization with good wound contraction rate, neovascular formation, and expression of transforming growth factor-beta were observed in S. aureus infected rat burn wound by using the hydrogel containing VANCO and EGF compared with untreated wounds and hydrogel alone. The wound infection was also significantly reduced in the groups treated with the hydrogels containing VANCO. Overall, in vitro and in vivo results suggested that developed hybrid system would be a promising construct to treat severe wound infection.
Smart wing load alleviation through optical fiber sensing, load identification, and deep reinforcement learning
Authors: Wada Daichi , Tamayama Masato , Murayama Hideaki
Published: September 2020

The use of optical fiber sensors has been considered to realize smart structures, which can sense and respond to environments. To develop this concept in aviation, this paper reports on a smart wing framework that senses and responds to the environment to alleviate the wing structural loads. The wing is equipped with optical fiber sensors that measure the strain distributions on the wing surface. Considering the strains, a group of neural networks determine the wing load distributions and angle of attacks. This information is fed into a controller that drives multiple flaps to re-distribute the loads. The controller is trained via a deep reinforcement learning technique. The wind tunnel experiments demonstrated that the proposed closed-loop control could alleviate the bending moment by 56.6% on average over the test duration from the initial state while the total load variations could be maintained within a range of ±5 N for 87.1% of the test duration. The proposed approach was also applicable to another scenario involving variations in the target loads, and the results indicated the generalized applicability of the neural-network-based controller trained via deep reinforcement learning.
Particle Gibbs sampling for Bayesian phylogenetic inference
Authors: Wang Shijia , Wang Liangliang
Published: September 2020

Motivation

The combinatorial sequential Monte Carlo (CSMC) has been demonstrated to be an efficient complementary method to the standard Markov chain Monte Carlo (MCMC) for Bayesian phylogenetic tree inference using biological sequences. It is appealing to combine the CSMC and MCMC in the framework of the particle Gibbs (PG) sampler to jointly estimate the phylogenetic trees and evolutionary parameters. However, the Markov chain of the PG may mix poorly for high dimensional problems (e.g. phylogenetic trees). Some remedies, including the PG with ancestor sampling and the interacting particle MCMC, have been proposed to improve the PG. But they either cannot be applied to or remain inefficient for the combinatorial tree space.

Results

We introduce a novel CSMC method by proposing a more efficient proposal distribution. It also can be combined into the PG sampler framework to infer parameters in the evolutionary model. The new algorithm can be easily parallelized by allocating samples over different computing cores. We validate that the developed CSMC can sample trees more efficiently in various PG samplers via numerical experiments.

Availability and implementation

The implementation of our method and the data underlying this article are available at https://github.com/liangliangwangsfu/phyloPMCMC.

Supplementary information

Supplementary data are available at Bioinformatics online.
COVID-Align: accurate online alignment of hCoV-19 genomes using a profile HMM
Authors: Lemoine Frédéric , Blassel Luc , Voznica Jakub , Gascuel Olivier
Published: September 2020

Motivation

The first cases of the COVID-19 pandemic emerged in December 2019. Until the end of February 2020, the number of available genomes was below 1000 and their multiple alignment was easily achieved using standard approaches. Subsequently, the availability of genomes has grown dramatically. Moreover, some genomes are of low quality with sequencing/assembly errors, making accurate re-alignment of all genomes nearly impossible on a daily basis. A more efficient, yet accurate approach was clearly required to pursue all subsequent bioinformatics analyses of this crucial data.

Results

hCoV-19 genomes are highly conserved, with very few indels and no recombination. This makes the profile HMM approach particularly well suited to align new genomes, add them to an existing alignment and filter problematic ones. Using a core of ∼2500 high quality genomes, we estimated a profile using HMMER, and implemented this profile in COVID-Align, a user-friendly interface to be used online or as standalone via Docker. The alignment of 1000 genomes requires ∼50 minutes on our cluster. Moreover, COVID-Align provides summary statistics, which can be used to determine the sequencing quality and evolutionary novelty of input genomes (e.g. number of new mutations and indels).

Availability and implementation

https://covalign.pasteur.cloud, hub.docker.com/r/evolbioinfo/covid-align.

Supplementary information

Supplementary data are available at Bioinformatics online.
Oxytocin amino acid variation within Neotropical primates: new genetic variants in hormone and receptor sequences and evidence for evolutionary forces driving this unexpected diversity
Authors: Campbell Susanna K , Cortés-Ortiz Liliana
Published: September 2020

Oxytocin is a mammalian neuropeptide hormone that mediates behaviours important to reproduction. Despite almost universal amino acid sequence conservation across most groups of mammals, several unique forms have been reported across Neotropical primates. To explore sequence diversity, we investigated the genes encoding oxytocin and its receptor across the Atelidae, which was known to contain at least three unique oxytocin sequences. Additionally, we included the genus Cebus, within the Cebidae, to further explore the ubiquity of the Pro8 variant in this family. We found a novel amino acid variant (Val3) within the Atelidae radiation, bringing the total number of oxytocin sequences within Neotropical primates to seven. Analyses of physicochemical properties revealed conservative substitutions that are likely tolerated within the selective constraints imposed by receptor binding. Furthermore, we report radical substitutions at the eighth codon and evidence for co-evolution between Pro8 and a ligand-binding region of the oxytocin receptor in the Atelidae, supporting the notion that this variant may affect binding specificity. Overall, we suggest that selective constraint on binding specificity may maintain proper oxytocin function and that the diversification of amino acid sequence is likely due to a variety of processes such as relaxed constraint, neutral mutation, positive selection and coevolution.
Magnetic resonance spectroscopy reveals mitochondrial dysfunction in amyotrophic lateral sclerosis
Authors: Sassani Matilde , Alix James J , McDermott Christopher J , Baster Kathleen , Hoggard Nigel , Wild Jim M , Mortiboys Heather J , Shaw Pamela J , Wilkinson Iain D , Jenkins Thomas M
Published: September 2020

Mitochondrial dysfunction is postulated to be central to amyotrophic lateral sclerosis (ALS) pathophysiology. Evidence comes primarily from disease models and conclusive data to support bioenergetic dysfunction in vivo in patients is currently lacking. This study is the first to assess mitochondrial dysfunction in brain and muscle in individuals living with ALS using 31P-magnetic resonance spectroscopy (MRS), the modality of choice to assess energy metabolism in vivo. We recruited 20 patients and 10 healthy age and gender-matched control subjects in this cross-sectional clinico-radiological study. 31P-MRS was acquired from cerebral motor regions and from tibialis anterior during rest and exercise. Bioenergetic parameter estimates were derived including: ATP, phosphocreatine, inorganic phosphate, adenosine diphosphate, Gibbs free energy of ATP hydrolysis (ΔGATP), phosphomonoesters, phosphodiesters, pH, free magnesium concentration, and muscle dynamic recovery constants. Linear regression was used to test for associations between brain data and clinical parameters (revised amyotrophic functional rating scale, slow vital capacity, and upper motor neuron score) and between muscle data and clinico-neurophysiological measures (motor unit number and size indices, force of contraction, and speed of walking). Evidence for primary dysfunction of mitochondrial oxidative phosphorylation was detected in the brainstem where ΔGATP and phosphocreatine were reduced. Alterations were also detected in skeletal muscle in patients where resting inorganic phosphate, pH, and phosphomonoesters were increased, whereas resting ΔGATP, magnesium, and dynamic phosphocreatine to inorganic phosphate recovery were decreased. Phosphocreatine in brainstem correlated with respiratory dysfunction and disability; in muscle, energy metabolites correlated with motor unit number index, muscle power, and speed of walking. This study provides in vivo evidence for bioenergetic dysfunction in ALS in brain and skeletal muscle, which appears clinically and electrophysiologically relevant. 31P-MRS represents a promising technique to assess the pathophysiology of mitochondrial function in vivo in ALS and a potential tool for future clinical trials targeting bioenergetic dysfunction.
Enacting critical community development through anti-gentrification policy advocacy
Authors: Bolton Claire
Published: September 2020

Following Newman and Goetz’s call for ‘a critical turn in community development practice and research’ and Fursova’s call for ‘community development as a critical practice aimed at advancing the commons’, this paper argues for a critical community development praxis around gentrification that emphasizes anti-displacement policy. It is more important than ever to look beyond market-friendly strategies and the site of the neighbourhood to shape municipal policy in favour of the ‘right to stay put’. As city governments begin to take the loss of affordable housing in urban centers more seriously, community developers can use vital, localized knowledge to strengthen legislative outcomes. I use a case study of a faith-based community development conference circuit to highlight and analyse the limitations of market-based community development and the promising possibilities of anti-displacement policy advocacy.
The iminosugars celgosivir, castanospermine and UV-4 inhibit SARS-CoV-2 replication
Authors: Clarke Elizabeth C , Nofchissey Robert A , Ye Chunyan , Bradfute Steven B
Published: September 2020

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic poses an unprecedented challenge for health care and the global economy. Repurposing drugs that have shown promise in inhibiting other viral infections could allow for more rapid dispensation of urgently needed therapeutics. The Spike protein of SARS-CoV-2 is extensively glycosylated with 22 occupied N glycan sites and is required for viral entry. In other glycosylated viral proteins, glycosylation is required for interaction with calnexin and chaperone-mediated folding in the endoplasmic reticulum, and prevention of this interaction leads to unfolded viral proteins and thus inhibits viral replication. As such, we investigated two iminosugars, celgosivir, a prodrug of castanospermine, and UV-4, or N-(9-methoxynonyl)-1-deoxynojirimycin, a deoxynojirimycin derivative. Iminosugars are known inhibitors of the α-glucosidase I and II enzymes and were effective at inhibiting authentic SARS-CoV-2 viral replication in a cell culture system. Celgosivir prevented SARS-CoV-2-induced cell death and reduced viral replication and Spike protein levels in a dose-dependent manner in culture with Vero E6 cells. Castanospermine, the active form of celgosivir, was also able to inhibit SARS-CoV-2, confirming the canonical castanospermine mechanism of action of celgosivir. The monocyclic UV-4 also prevented SARS-CoV-2-induced death and reduced viral replication after 24 h of treatment, although the reduction in viral copies was lost after 48 h. Our findings suggest that iminosugars should be urgently investigated as potential SARS-CoV-2 inhibitors.
Vegetarian diets during pregnancy, and maternal and neonatal outcomes
Authors: Yisahak Samrawit F , Hinkle Stefanie N , Mumford Sunni L , Li Mengying , Andriessen Victoria C , Grantz Katherine L , Zhang Cuilin , Grewal Jagteshwar
Published: September 2020

Background

Vegetarian diets are becoming increasingly popular in the USA. Limited research has examined the health consequences of vegetarian diets during pregnancy. We comprehensively examined associations of vegetarianism during pregnancy with maternal and neonatal outcomes.

Methods

We used data from the Eunice Kennedy Shriver National Institute of Child Health and Human Development’s Fetal Growth Studies–Singletons, a prospective multi-site cohort of 1948 low-risk pregnant women of four races/ethnicities (White, Black, Hispanic, Asian/Pacific Islander) in the USA (2009–2013). Vegetarianism was self-reported and also defined based on dietary patterns measured using a self-administered first-trimester food-frequency questionnaire (full [lacto-ovo and vegan], pesco-, semi- and non-vegetarians). Neonatal outcomes included birthweight and neonatal anthropometric measures, small for gestational age, small for gestational age with neonatal morbidity and preterm delivery. Maternal outcomes included gestational weight gain, gestational diabetes, hypertensive disorders of pregnancy and gestational anaemia.

Results

Ninety-nine (6.2%) women self-reported being vegetarian. The diet-based definition identified 32 (2.0%) full vegetarians, 7 (0.6%) pesco-vegetarians and 301 (17.6%) semi-vegetarians. Neonates of diet-based full vegetarians had higher odds of being small for gestational age [adjusted odds ratio (ORadj) = 2.51, 95% confidence interval: 1.01, 6.21], but not of being small for gestational age with a postnatal morbidity. Full vegetarians had marginally increased the odds of inadequate second-trimester gestational weight gain (ORadj = 2.24, 95% confidence interval: 0.95, 5.27).

Conclusion

Vegetarian diets during pregnancy were associated with constitutionally smaller neonatal size, potentially via the mothers’ reduced gestational weight gain. Notably, vegetarianism was not associated with small-for-gestational-age-related morbidities or other adverse maternal outcomes.
Protein foods from animal sources, incident cardiovascular disease and all-cause mortality: a substitution analysis
Authors: Zhong Victor W , Allen Norrina B , Greenland Philip , Carnethon Mercedes R , Ning Hongyan , Wilkins John T , Lloyd-Jones Donald M , Van Horn Linda
Published: September 2020

Background

Protein-rich foods are major parts of the human diet and are highly heterogeneous in nutrient composition and health effects. Designing healthy diets for disease prevention requires careful consideration of substituting unhealthier protein foods with healthier protein foods.

Methods

This was a pooled analysis of six prospective cohort studies of 29 682 US participants. Data were collected in 1985–2016. Adjusted hazard ratios (HRs) and 30-year absolute risk differences (ARDs) were calculated for the associations between simultaneous substitution of one or more animal protein foods with other animal or plant protein foods at various amounts, and incident cardiovascular disease (CVD) and all-cause mortality.

Results

Substituting eggs, processed meat, unprocessed red meat or poultry with nuts, whole grains, legumes or fish was associated with lower risks of incident CVD and all-cause mortality. According to different substitution amounts (varying from one serving per week to one serving per day) and different numbers of protein foods being simultaneously substituted (varying from one to four), estimates ranged between 1%: HR, 0.99 [95% confidence interval (CI), 0.98–1.00], and 54%: HR, 0.46 (0.35–0.60), lower risks on the relative scale and between 0.3%: ARD, -0.29% (-0.48% to -0.05%), and 14.0%: ARD, -13.96% (-17.29% to -9.96%) lower risks on the absolute scale.

Conclusions

Nuts, whole grains, legumes and fish appeared to be healthier protein sources than eggs, processed meat, unprocessed red meat and poultry for preventing incident CVD and premature death. The magnitude of lower risk for incident CVD and all-cause mortality was driven by amount and number of animal protein foods substituted.
Effects of Psychotropics on the Microbiome in Patients With Depression and Anxiety: Considerations in a Naturalistic Clinical Setting
Authors: Tomizawa Yoshihiro , Kurokawa Shunya , Ishii Daiki , Miyaho Katsuma , Ishii Chiharu , Sanada Kenji , Fukuda Shinji , Mimura Masaru , Kishimoto Taishiro
Published: September 2020

Background

The antibacterial effects of psychotropics may be part of their pharmacological effects when treating depression. However, limited studies have focused on gut microbiota in relation to prescribed medication.

Method

We longitudinally investigated the relationship between patients’ prescribed medications and intestinal bacterial diversity in a naturalistic treatment course for patients with major depressive disorders and anxiety disorders. Patients were recruited and their stool was collected at 3 time points during their usual psychiatric treatments. Gut microbiota were analyzed using 16S rRNA gene sequencing. We examined the impact of psychotropics (i.e., antidepressants, anxiolytics, antipsychotics) on their gut microbial diversity and functions.

Results

We collected 246 stool samples from 40 patients. Despite no differences in microbial diversity between medication groups at the baseline, over the course of treatment, phylogenic diversity whole-tree diversity decreased in patients on antipsychotics compared with patients without (P = .027), and beta diversity followed this trend. Based on a fixed-effect model, antipsychotics predicted microbial diversity; the higher doses correlated with less diversity based on the Shannon index and phylogenic diversity whole tree (estimate = −0.00254, SE = 0.000595, P < .0001; estimate = −0.02644, SE = 0.00833, P = .002, respectively).

Conclusion

Antipsychotics may play a role in decreasing the alpha diversity of the gut microbiome among patients with depression and anxiety, and our results indicate a relationship with medication dosage. Future studies are warranted and should consider patients’ types and doses of antipsychotics in order to further elucidate the mechanisms of gut-brain interactions in psychiatric disorders.
Human Polyomavirus 6 Detected in Cases of Eosinophilic Pustular Folliculitis
Authors: Hashida Yumiko , Higuchi Tomonori , Nakajima Saeko , Nakajima Kimiko , Ujihara Takako , Kabashima Kenji , Sano Shigetoshi , Daibata Masanori
Published: September 2020

Background

Human polyomaviruses (HPyVs) have been associated with several cutaneous inflammatory conditions. More investigation is needed to identify further presentations of cutaneous pathology associated with HPyVs. Our aim was to investigate the possible association of skin-tropic HPyVs with folliculitis, particularly eosinophilic pustular folliculitis (EPF).

Methods

This study included 55 Japanese patients, comprising 13 patients with EPF and 42 patients with suppurative folliculitis. HPyV DNAs were detected by quantitative polymerase chain reaction. Expression of viral antigen and geographically related viral genotypes were also assessed.

Results

Human polyomavirus 6 (HPyV6) DNA was found in 9 of 13 (69%) patients with EPF, a rate significantly higher than that found in suppurative folliculitis (1/42; 2%). Of the 7 HPyV6 DNA–positive EPF specimens analyzed, 4 were positive for HPyV6 small tumor antigen. All the HPyV6 strains detected in this study were of the Asian/Japanese genotype.

Conclusions

The predominant detection of HPyV6 DNA and the expression of viral antigen suggest a possible association between HPyV6 infection and EPF in a subset of patients. Worldwide studies are warranted to determine whether Asian/Japanese genotype HPyV6 is associated preferentially with the incidence and pathogenesis of this eosinophil-related skin disease that has an ethnic predilection for the East Asian population.