bluuebunny/crossref_metadata_2025 huggingface dataset:
Crystal potentials and dispersion forces in additive approximation
Authors: Kyarov A Kh , Savintsev A P
Published: July 2020

On the basis of the additive approximation model, a formula for determining the van der Waals constant was obtained and the possibility of correctly describing the long-range part of the interaction potential of solidified inert gases crystals was indicated. Using the modified Lennard-Jones potential and experimental data on the dissociation energy and the equilibrium radius, the dispersion constants of systems of inert gas pairs and an alkali metal–inert gas are determined. The results of the calculations are in general agreement with the experiment.
Structure properties of warm dense hydrogen
Authors: Sartan R A
Published: July 2020

The warm dense hydrogen is studied by the ab initio molecular dynamics in the region of the fluid–fluid phase transition. A method for calculating the properties such as concentration and lifetime of H2 molecules is developed. As warm dense hydrogen passes the transition, the concentration of H2 molecules decreases smoothly, while the lifetime changes abruptly by several orders.
Shear viscosity of n-pentane from diffusivity based molecular dynamics methods
Authors: Kondratyuk N D , Orekhov M A
Published: July 2020

The molecular dynamics methods for calculation of shear viscosity based on liquid diffusivity are tested against the classical Green–Kubo relation for n-pentane at 330 K and 0.601 g/cm3. The D-based method is shown to be as accurate as calculation of viscosity from the Green–Kubo formalism for pentane liquid. Stokes–Einstein relation is also in agreement with simulation results. However, it has much bigger uncertainty. The results of the simulation are in agreement with experimental data.
Influence of chemical composition of the surface layer on the nucleation of plasticity in CoCrFeMnNi high-entropy alloys
Authors: Korchuganov A V , Lutsenko I S , Zolnikov K P
Published: July 2020

The role of segregation of chemical elements upon free surfaces in the peculiarities of the plastic deformation mechanisms of thin films of the high-entropy CoCrFeMnNi alloy was clarified using a combined simulation of the Metropolis Monte Carlo and molecular dynamics. Irrespectively of surface orientation and stoichiometric composition of alloy Mn escapes to free surface and Fe goes to the bulk of the films. Ni also enriches the (111) surface while Co content is reduced. It is shown that for different compositions segregation reduces or decreases the elastic limit of the samples. In Co10Cr10Fe30Mn30Ni20 for all considered free surfaces, segregation equally influences the type and volume fraction of the formed defects. In Co30Cr30Fe10Mn10Ni20, they may remain the same or the mechanism of plastic deformation may change drastically in samples with segregation depending on the orientation of the free surface. Despite the redistribution of the volume fractions of various type defects, in general, the main mechanism for the development of plasticity in samples both before and after segregation is the growth of the hcp-bands. Change of defect structure in samples with surface segregation compared to samples with random distribution of elements is not necessary related to change of elastic limit.
Interaction of edge dislocation with copper atoms in an aluminum crystal
Authors: Fomin E V , Krasnikov V S
Published: July 2020

In this work, the interaction of the moving edge dislocation with obstacles in form of copper atoms is studied using the molecular dynamics simulations. The samples are aluminum monocrystals of 52 × 60 × 15 nm3 with axes oriented along directions [110], [111], [112]. The structure of copper solid solution is reproduced with following procedure: aluminum atoms are randomly selected and replaced by copper atoms. The concentration of copper atoms varies from 0.25% to 1%. The dislocation movement occurs under action of shear deformation. It is found that zones with a low concentration of copper atoms only slow down dislocation in an aluminum matrix, and the zones with a high local concentration of copper atoms not only produces stronger resistance to dislocation movement, but also they cause the change in the slip plane of the dislocation segment. When a significant part of a dislocation line moves to a neighboring slip plane, the complete transition of the dislocation to this slip plane can occur. It is also noted that such transitions of dislocation segments from one slip plane to another are accompanied by the formation of vacancies. Also the maximum value of the shear stress σxy
is estimated-its value is approximately 250 MPa.
Adhesion energy of ethane–graphite interface: Atomistic study
Authors: Iakovlev E S , Zhilyaev P A , Akhatov I Sh
Published: July 2020

Adhesion energy is an important characteristic of interfacial interactions. Usually one apply notion of adhesion energy to solid–solid interfaces, but it also could be extended to gas–solid and liquid–solid interfaces. In later case phenomenon of adsorption is closely related to the adhesion energy. In this work we apply molecular dynamics method to calculate the specific adhesion energy for gas and liquid ethane on a graphite substrate. Influence of temperature and density on the value of the specific adhesion energy is investigated. Langmuir adsorption model is applied to interpret results and establish connection between notions of adsorption heat and specific adhesion energy. Appearance of multilayer adsorption is detected for higher densities. Developed model and numerical approach to calculate adhesion energy and surface coverage can be applied for different types of the adsorbate and the substrate.
Bending vibrations of free and microdroplet-loaded graphene in the framework of the molecular dynamics method
Authors: Khokonov A Kh , Akhmatov Z A
Published: July 2020

Molecular dynamic (MD) modeling revealed that takes place swing up of transverse vibrations of graphene atoms with their transition to bending vibrations of membrane type. The amplitudes of such oscillations can reach large values, which considerably exceed the interatomic distances already for samples of micron sizes and amount to 10−2 from the length of the sample. The results of MD simulation were compared with the characteristic vibrational frequencies of graphene in the approximation of the tensioned membrane. The behavior of the graphene membrane during it loading with a liquid metal microdroplet has been considered also. Contact angles and relative stretching of the membrane outside and under the drop allow us to calculate the surface tension of the drop.
Determination of the effective emissivity distribution of a heated specimen using tandem acousto-optical tunable filter
Authors: Mantrova Yu V , Zinin P V , Bykov A A , Bulatov K M
Published: July 2020

We present the first experimental demonstration of a new imaging system for in-situ measurement the two-dimensional distribution of the effective emissivity and temperature of a heated specimen. In this work, we use the model of a gray body, assuming that the emissivity is constant over the entire wavelength range from 600 to 800 nm. Data acquisition was done using the laser heating (LH) system developed at the STC UI RAS. The LH system allows us to reach extremely high temperatures up to 6000 K at high pressures. The main component of the system is an imaging tandem acousto-optical tunable filter synchronized with a video camera. The maximal error of the emissivity measurement of the tungsten sample was found to be 13%, whereas the maximal error of the temperature measurements did not exceed 2%. An influence of different factors on the error of the emissivity determination is also discussed.
Experimental setup for determining the surface tension of highly curved interfaces by static and dynamic methods
Authors: Sergeev I N , Khokonov A Kh , Akhmatov Z A
Published: July 2020

Experimental devices and techniques for determining surface and interface tensions microdroplets of low-melting metals bordering with vacuum, liquid mediums and solid substrates have been described. Dynamic method is discussed for the gallium microliter sessile droplet immersed in water and a static method is considered for the tin microdroplet pending on a conical tip of a cantilever needle.
Simulation of the filtration process of hydrocarbon binary fluid with retrograde properties
Authors: Molchanov D A
Published: July 2020

This paper presents the results of the experimental studies of filtration modes of gas-condensate fluid using a binary mixture of methane–n-butane. It is shown that there is a possibility to obtain both the normal two-phase filtration mode and the self-oscillatory mode depending on the filtration conditions and the composition of the model mixture.
Flow bifurcation transitions of inelastic shear thinning fluids in a channel with sudden contraction and expansion
Authors: Roshchin D E , Kravchenko I V , Patlazhan S A
Published: July 2020

The bifurcation transitions from the symmetric to asymmetric flow regimes in shear thinning fluids in a channel with sudden contraction and expansion were studied by means of numerical simulations. On the example of the Carreau–Yasuda model, the bifurcation diagrams of shear thinning fluids with different viscosity flow curves were revealed along the critical Reynolds numbers of the bifurcation transitions. It was found that increase in variations of viscosity with shear rate leads to a noticeable decrease in critical Reynolds number and increase in dimensions of the angular vortices as compared to Newtonian fluids. The obtained results indicate the enhancement of flow instability of shear thinning fluids in channels with the variable cross-sections.
Microfibers formation in two-phase fluid flowing in a channel with the abrupt constriction: Numerical modeling
Authors: Kravchenko I V , Patlazhan S A , Sultanov V G
Published: July 2020

Numerical modeling was used to study the patterns of droplet deformation in two-phase Newtonian fluids flowing through a three-dimensional rectangular microchannel with a sharp narrowing. The elongation of single droplets of different viscosities was investigated in different channel zones. Calculations were carried out for different confinement parameter—the ratio of droplet diameter to the gap thickness. The increase in this parameter was shown to lead to the substantial increase in the droplet relative elongation. The effect of coalescence to microfiber formation in flowing emulsion was considered.
Numerical simulation of the fiber spinning with the viscoelastic Giesekus constitutive model
Authors: Kravchenko I V , Vagner S A , Sultanov V G
Published: July 2020

The numerical simulation of the first stage of fiber-spinning process was performed. The single-mode Giesekus model was used for polymer fiber stress calculations. Fiber profiles, longitudinal velocity, tensile stress and apparent elongational viscosity were analyzed depending on the stretch speed and the degree of anisotropy of the polymer.
Influence of an electric field on Rydberg nD states of cold lithium atoms
Authors: Bronin S Ya , Bobrov A A , Fomichev D E , Saakyan S A , Sautenkov V A , Zelener B B , Zelener B V
Published: July 2020

Influence of a weak electric field on the coherent Rydberg resonances was studied on two-photon transitions 2S–nD by recording the resonance fluorescence of lithium atoms in a magneto-optical trap. It was observed that an isolated spectral line 2P–nD transferred to the spectral band width growing with a principal number n (or an electric field E). It was shown that the frequency tuning of a resonant radiation on the left (right) edge of the band allows to create a gas of Rydberg atoms with fixed and large dipole moments d ∝ ea
0
n
2 (e is the elementary charge, a
0 is the Bohr radius), oriented against (along) the electric field. The radiation frequency was tuned on the center of the band would produced atomic states with zero dipole moments, but with a big contribution of states with maximum angular momentum quantum number l ~ n.
Numerical study of energy loss rate of fast proton in cold dense electron gas in strong magnetic field
Authors: Bobrov A A
Published: July 2020

Energy loss of a proton propagating through a low-temperature gas of magnetized electrons is studied by molecular dynamics method for the case when proton velocity is much more than electrons thermal velocity. Strong uniform magnetic field is considered when electron Larmor radius is much smaller than distance of closest approach (Coulomb radius). High electron density, and hence small values of the Coulomb logarithm, is considered. The dependence of energy loss on angle between the proton velocity and the magnetic field direction is studied. Results of calculations are compared to Derbenev and Skrinskii theoretical approach to average friction force.
Thermodynamics of complex plasmas with two different sorts of macroions
Authors: Martynova I A , Iosilevskiy I L
Published: July 2020

Three-component electroneutral systems of finite-size classical macroions with two different charge numbers Z
1 ≫ 1 and Z
2 ≫ 1 and point-like oppositely charged microions are analyzed. Free energy of a mixture of two sorts of macroions is estimated within the Wigner–Seitz cells approximation. The non-linear screening effect is taken into account via the Poisson–Boltzmann approximation within the both cells. The equality of microions pressures at the boundary between the co-existing cells with the different sorts of macroions is used as an equilibrium condition. The difference between the total Helmholtz free energy in equilibrium is shown in comparison with the situation when the Wigner–Seitz cells with macroions with the different charges have the same volumes.
Electric field influence on dust particle dynamics in dust vortices
Authors: Izvekova Yu N , Popel S I
Published: July 2020

We study dust vortices called dust devils and dynamics of dust in this structures. Dust devils are well formed relatively short-lived vortices that can appear over well heated surfaces like deserts and are clearly visible due to large amount of dust raised. Dust particles rotating in a flow bump and scrape each other and as a result particles obtain electric charges. Space separation of particles with opposite charges leads to generation of macroscopic electric field. We simulate dust dynamics with taking into account the electric field of the vortex.
Relationship between the dust-acoustic soliton parameters and the Debye radius
Authors: Trukhachev F M , Petrov O F , Vasiliev M M , Tomov A V
Published: July 2020

Based on the analysis of the dusty-acoustic soliton properties, a simple technique for estimating the Debye radius is proposed. It is shown that the Debye radius is approximately equal to 1–1/3 of the width of the soliton density profile, which can be easily determined from the analysis of photographs of a dust cloud.
Dynamics of motion of particles with a modified surface in a dusty plasma monolayer
Authors: Vasiliev M M , Kononov E A , Arkar K , Petrov O F
Published: July 2020

The results of the analysis of the mean square displacement and the trajectories of moving polymer particles with a modified surface in a dusty plasma monolayer under the influence of laser radiation are presented. It has been revealed that the dynamics of particle motion in a monolayer consists of three modes: finite motion within confinement, Brownian motion, and combined directional chaotic motion. The results of the analysis of linear displacement along and across the direction of motion of dust particles at various values of the laser radiation power are presented too. It has been shown experimentally that polymer particles with a modified surface are active Brownian particles and their activity grows with increasing laser radiation power.
About the mechanism of modification of melamine formaldehyde particles in dusty plasmas
Authors: Karasev V Yu , Polischuk V A , Dzlieva E S , Pavlov S I , Gorbenko A P
Published: July 2020

The article presents the previously obtained results of the modification of spherical microparticles of melamine-formaldehyde injected as a dust component of complex plasma formed in stratified glow discharge in neon. Particular attention is paid to changing the particle size depending on the residence time in the plasma. A mechanism is proposed for heating particles by ion flow sustaining a stable charge of their surface. Calculations of the heat balance are presented, confirming the results obtained in the experiment.
Comparison of megaampere channel temperature value measured by different methods at its maximal contraction in high density hydrogen
Authors: Bogomaz A A , Pinchuk M E , Budin A V , Leks A G , Sakan N M
Published: July 2020

Comparison of discharge channel temperature in gaseous hydrogen of high density with current amplitude of ~ 1 MA at initial gas pressure of 5–7 MPa, determined by two methods, was done under stage of its maximal contraction. In the first case determination of the temperature value of 72–73 eV was made by intensity of soft x-ray radiation from the channel for experiments with current amplitude of 1.1–1.5 MA. The estimation of the temperature on the basis of the data received by magnetic probe method and specified electric characteristics of the channel was of ≈ 140 eV for experiment with initial gas pressure of 5 MPa at current amplitude of 0.93 MA. The temperature determination by the last procedure has small accuracy caused by the limitation of the magnetic probe technique in determination of the channel contraction ratio and some assumptions for near-electrode voltage drops calculations by this way. Apparently, the channel temperature in stage of maximal contraction is of ~ 100 eV.
Soft x-ray source based on the point Z-pinch for pulse radiography
Authors: Artyomov A P , Chaikovsky S A , Rousskikh A G , Fedunin A V
Published: July 2020

This article presents the study of the influence of the cathode material of a plasma injector on the parameters of the x-ray source of a point Z-pinch (PZ-pinch). The experiments were carried out on the compact pulse power radiograph PR-PZP-M1 (210 kA, 220 ns). The new type of the plasma injector based on a ceramic insulator and a composite cathode is developed and tested in the experiments. PZ-pinches based on tin, silver and gold were studied. It was shown that tin is the most applicable material to the PZ-pinch formation in terms of radiography. The PZ-pinch mass optimization has been carried out to obtain the brightest x-ray source with minimum sizes. The achieved x-ray source diameter is 12 ± 3 μm, height is 18 ± 5 μm in the spectral range hν = 1–3 keV.
Radiation energy losses in a single chamber three phase plasma torch with rod electrodes
Authors: Dudnik Yu D , Kovshechnikov V B , Safronov A A , Kuznetsov V E , Shiryaev V N , Vasilieva O B
Published: July 2020

The paper deals with the results of the study of the plasma energy loss in a chamber of the three phase alternating current arc plasma torch at pressures above atmospheric. It is shown that the loss due to radiation takes the main share. A time-averaged estimation of the radiation power per unit length of the arcs and its dependence on pressure was obtained based on the results of calorimetric measurements of the heat flux into the end part of the plasma torch. The dependence of the fraction of energy loss by radiation versus the total loss in the plasma torch chamber depending on the pressure and gas flow rate are presented. The dependence of the efficiency of the plasma torch versus the gas flow rate and pressure is also given. Studies were conducted on a plasma torch over the power range from 50 to 200 kW. The working gas was nitrogen.
Verification of experimental studies of pulsed plasma accelerators
Authors: Shurupov A V , Shurupov M A , Zavalova V E , Mashtakov A V , Kozlov A V , Kozlov A A , Gusev A N , Shurupova N P
Published: July 2020

Explosive-magnetic generators (EMGs) unlike capacitive storages (CSs), as a rule, have growing power. The effective operation of pulsed plasma loads, such as pulsed plasma accelerators (PPAs), plasma foci, plasma breakers, etc, can be provided at realization of the mentioned advantage of EMG as a power source. A technique of laboratory experiments with PPA is presented in this paper. The experiments with PPA powered by CS precede the explosive experiment with EMG. The dependencies of the load operation modes on the start parameters are determined by the analysis of the experimental data. They included the dynamics of the inductance and the position of the current shell inside the PPA. The technique allows reducing the number of expensive explosive experiments and supplements the database of nonlinear dependencies of the load parameters under various amplitudes of the current pulse that is important for mathematical modeling. The technique based on experiments together with the estimations allowed solving the problem of matching of non-linear loads type PPA with EMG. Thus, the productivity of experiments with EMG increases greatly. The developed technique can be adapted to a wide class of nonlinear loads.
Study of the discharge with a liquid cathode with organic impurities
Authors: Chistolinov A V , Yakushin R V , Sargsyan M A , Khromov M A , Perfilieva A V
Published: July 2020

Dynamics of the discharge with a liquid cathode was studied using the method of high-speed visualization. The video data was compared with the emission spectra of the discharge plasma. Electrical parameters of the discharge were measured. The effect of organic impurities in the solution on the discharge parameters was investigated.
Impacts of the Arctic-midlatitude teleconnection on wintertime seasonal climate forecasts
Authors: Jung Euihyun , Jeong Jee-Hoon , Woo Sung-Ho , Kim Baek-Min , Yoon Jin-Ho , Lim Gyu-Ho
Published: July 2020

The impact of the Arctic on midlatitude weather and climate is still in scientific debate. The observation-based analysis, however, shows frequent concurrences of Arctic warming with extreme cold in the midlatitudes, and vice versa. This teleconnection could aid in seasonal climate forecasts for the midlatitudes. This study assessed the forecast skill of Arctic temperature and the Arctic-midlatitude teleconnection patterns in operational seasonal climate forecast models based on their wintertime forecast archives. Further, the impact of the Arctic-midlatitude teleconnection on the midlatitude forecast skill is evaluated. The results revealed that most climate forecast models have the capability to simulate the overall pattern of Arctic-midlatitude teleconnection for both the eastern Eurasian and North American regions. However, this is little converted to practical forecast skill in midlatitude likely due to poor capabilities in forecasting Arctic temperatures. Idealized analysis (assuming a perfect forecast of Arctic temperature) showed that considerable forecasting improvements could be achieved, and further improvements are possible with accurate simulations of the Arctic and its teleconnection patterns. These results highlight the importance of better predictions of the Arctic conditions in seasonal forecasts that are not just limited to their own region but extend to midlatitude weather and climate as well.
Mapping pervasive selective logging in the south-west Brazilian Amazon 2000–2019
Authors: Hethcoat M G , Carreiras J M B , Edwards DP , Bryant R G , Peres C A , Quegan S
Published: July 2020

Tropical forests harbour the highest biodiversity on the planet and are essential to human livelihoods and the global economy. However continued loss and degradation of forested landscapes, coupled with a rapidly rising global population, is placing incredible pressure on forests globally. The United Nations has developed the Reducing Emissions from Deforestation and forest Degradation (REDD +) programme in response to the challenges facing tropical forests and in recognition of the role they can play in climate mitigation. REDD + requires consistent and reliable monitoring of forests, however, national-level methodologies for measuring degradation are often bespoke and, because of an inability to track degradation effectively, the majority of countries combine reporting for deforestation and forest degradation into a single value. Here, we extend a recent analysis that enabled the detection of selective logging at the scale of a logging concession to a regional-scale estimation of selective logging activities. We utilized logging records from across Brazil to train a supervised classification algorithm for detecting logged pixels in Landsat imagery then predicted the extent of logging over a 20 year period throughout Rondônia, Brazil. Approximately one-quarter of the forested lands in Rondônia were cleared between 2000 and 2019. We estimate that 11.0% of the forest area present in 2000 had been selectively logged by 2019, comprising >11 500 km2 of forest. In general, rates of selective logging were twice as high in the first decade relative to the last decade of the period. Our approach is a considerable advance in developing an operationalized selective logging monitoring system capable of detecting subtle forest disturbances over large spatial scales.
Inferring ground-level nitrogen dioxide concentrations at fine spatial resolution applied to the TROPOMI satellite instrument
Authors: Cooper Matthew J , Martin Randall V , McLinden Chris A , Brook Jeffrey R
Published: July 2020

Satellite-based estimates of ground-level nitrogen dioxide (NO2) concentrations are useful for understanding links between air quality and health. A longstanding question has been why prior satellite-derived surface NO2 concentrations are biased low with respect to ground-based measurements. In this work we demonstrate that these biases are due to both the coarse resolution of previous satellite NO2 products and inaccuracies in vertical mixing assumptions used to convert satellite-observed tropospheric columns to surface concentrations. We develop an algorithm that now allows for different mixing assumptions to be used based on observed NO2 conditions. We then apply this algorithm to observations from the TROPOMI satellite instrument, which has been providing NO2 column observations at an unprecedented spatial resolution for over a year. This new product achieves estimates of ground-level NO2 with greater accuracy and higher resolution compared to previous satellite-based estimates from OMI. These comparisons also show that TROPOMI-inferred surface NO2 concentrations from our updated algorithm have higher correlation and lower bias than those found using TROPOMI and the prior algorithm. TROPOMI-inferred estimates of the population exposed to NO2 conditions exceeding health standards are at least three times higher than for OMI-inferred estimates. These developments provide an exciting opportunity for air quality monitoring.
Hydrogen evolution on non-metal oxide catalysts
Authors: Rhatigan Stephen , Michel Marie-Clara , Nolan Michael
Published: July 2020

Water splitting to produce hydrogen gas, using renewably produced electricity (electrocatalysis) or by direct conversion of solar energy (photocatalysis), is a strategy that addresses key environmental and energy challenges. The overall water splitting reaction proceeds as two half reactions, namely the oxygen evolution reaction (OER) and hydrogen evolution reaction (HER), each of which require catalysts specifically tailored to maximize efficiency. The benchmark catalysts for the HER are noble metals. However, their expense and rarity makes them economically unfeasible for large-scale H2 production from water. Consequently, there are considerable efforts to find cheap, abundant materials that can efficiently catalyze the HER. Over the last decade, metal chalcogenides and phosphides have emerged as promising candidates for HER. In this review article, we discuss a selection of the multitude of studies and materials in these two classes of catalyst to give a flavor of the relevant developments and properties of these materials. In addition to the selection of catalyst materials, preparation and structuring are playing a strong role in enhancing HER and overcoming fundamental challenges. The role of modeling in the performance of HER catalysts is also discussed and we end with a short perspective on the key attributes of a good HER catalyst.
RecBic: a fast and accurate algorithm recognizing trend-preserving biclusters
Authors: Liu Xiangyu , Li Di , Liu Juntao , Su Zhengchang , Li Guojun
Published: July 2020

Motivation

Biclustering has emerged as a powerful approach to identifying functional patterns in complex biological data. However, existing tools are limited by their accuracy and efficiency to recognize various kinds of complex biclusters submerged in ever large datasets. We introduce a novel fast and highly accurate algorithm RecBic to identify various forms of complex biclusters in gene expression datasets.

Results

We designed RecBic to identify various trend-preserving biclusters, particularly, those with narrow shapes, i.e. clusters where the number of genes is larger than the number of conditions/samples. Given a gene expression matrix, RecBic starts with a column seed, and grows it into a full-sized bicluster by simply repetitively comparing real numbers. When tested on simulated datasets in which the elements of implanted trend-preserving biclusters and those of the background matrix have the same distribution, RecBic was able to identify the implanted biclusters in a nearly perfect manner, outperforming all the compared salient tools in terms of accuracy and robustness to noise and overlaps between the clusters. Moreover, RecBic also showed superiority in identifying functionally related genes in real gene expression datasets.

Availability and implementation

Code, sample input data and usage instructions are available at the following websites. Code: https://github.com/holyzews/RecBic/tree/master/RecBic/. Data: http://doi.org/10.5281/zenodo.3842717.

Supplementary information

Supplementary data are available at Bioinformatics online.
TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting
Authors: Lexa Matej , Jedlicka Pavel , Vanat Ivan , Cervenansky Michal , Kejnovsky Eduard
Published: July 2020

Motivation

Transposable elements (TEs) in eukaryotes often get inserted into one another, forming sequences that become a complex mixture of full-length elements and their fragments. The reconstruction of full-length elements and the order in which they have been inserted is important for genome and transposon evolution studies. However, the accumulation of mutations and genome rearrangements over evolutionary time makes this process error-prone and decreases the efficiency of software aiming to recover all nested full-length TEs.

Results

We created software that uses a greedy recursive algorithm to mine increasingly fragmented copies of full-length LTR retrotransposons in assembled genomes and other sequence data. The software called TE-greedy-nester considers not only sequence similarity but also the structure of elements. This new tool was tested on a set of natural and synthetic sequences and its accuracy was compared to similar software. We found TE-greedy-nester to be superior in a number of parameters, namely computation time and full-length TE recovery in highly nested regions.

Availability and implementation

http://gitlab.fi.muni.cz/lexa/nested.

Supplementary information

Supplementary data are available at Bioinformatics online.
Improving Decision Making in Empiric Antibiotic Selection (IDEAS) for Gram-negative Bacteremia: A Prospective Clinical Implementation Study
Authors: Elligsen Marion , Pinto Ruxandra , Leis Jerome A , Walker Sandra A N , Daneman Nick , MacFadden Derek R
Published: July 2020

Background

Timely selection of adequate empiric antibiotics has become increasingly difficult due to rising resistance rates and the competing desire to apply antimicrobial stewardship (AMS) principles. Individualized clinical prediction models offer the promise of reducing broad-spectrum antibiotic use and preserving/improving adequacy of treatment, but few have been validated in the clinical setting.

Methods

Multivariable models were used to predict the probability of susceptibility for gram-negative (GN) bacteria in bloodstream infections (bacteremia) to ceftriaxone, ciprofloxacin, ceftazidime, piperacillin-tazobactam, and meropenem. The models were combined with existing resistance-prediction methods to generate optimized and individualized suggestions for empiric therapy that were provided to prescribers by an AMS pharmacist. De-escalation of empiric antibiotics and adequacy of therapy were analyzed using a quasi-experimental design comparing two 9-month periods (pre- and postintervention) at a large academic tertiary care institution.

Results

Episodes of bacteremia (n = 182) were identified in the preintervention and postintervention (n = 201) periods. Patients who received the intervention were more likely to have their therapy de-escalated (29 vs 21%; aOR = 1.77; 95% CI, 1.09–2.87; P = .02). The intervention also increased the proportion of patients who were on the narrowest adequate therapy at the time of culture finalization (44% in the control and 55% in the intervention group; aOR = 2.04; 95% CI, 1.27–3.27; P = .003). Time to adequate therapy was similar in the intervention and control groups (5 vs 4 hours; P = .95).

Conclusions

An AMS intervention, based on individualized predictive models for resistance, can influence empiric antibiotic selections for GN bacteremia to facilitate early de-escalation of therapy without compromising adequacy of antibiotic coverage.
Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Prevalence in Blood in a Large School Community Subject to a Coronavirus Disease 2019 Outbreak: A Cross-sectional Study
Authors: Torres Juan Pablo , Piñera Cecilia , De La Maza Verónica , Lagomarcino Anne J , Simian Daniela , Torres Bárbara , Urquidi Cinthya , Valenzuela María Teresa , O’Ryan Miguel
Published: July 2020

Background

A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak affecting 52 people from a large school community in Santiago, Chile, was identified (12 March) 9 days after the first case in the country. We assessed the magnitude of the outbreak and the role students and staff played using self-administered antibody detection tests and a self-administered survey.

Methods

The school was closed on 13 March, and the entire community was placed under quarantine. We implemented a home-delivery, self-administered, immunoglobin (Ig) G/IgM antibody test and survey to a classroom-stratified sample of students and all staff from 4–19 May. We aimed to determine the overall seroprevalence rates by age group, reported symptoms, and contact exposure, and to explore the dynamics of transmission.

Results

The antibody positivity rates were 9.9% (95% confidence interval [CI], 8.2–11.8) for 1009 students and 16.6% (95% CI, 12.1–21.9) for 235 staff. Among students, positivity was associated with a younger age (P = .01), a lower grade level (P = .05), prior real-time polymerase chain reaction (RT-PCR) positivity (P = .03), and a history of contact with a confirmed case (P < .001). Among staff, positivity was higher in teachers (P = .01) and in those previously RT-PCR positive (P < .001). Excluding RT-PCR–positive individuals, antibody positivity was associated with fever in adults and children (P = .02 and P = .002, respectively), abdominal pain in children (P = .001), and chest pain in adults (P = .02). Within antibody-positive individuals, 40% of students and 18% of staff reported no symptoms (P = .01).

Conclusions

Teachers were more affected during the outbreak and younger children were at a higher risk for infection, likely because index case(s) were teachers and/or parents from the preschool. Self-administered antibody testing, supervised remotely, proved to be a suitable and rapid tool. Our study provides useful information for school reopenings.
Inflammation and cardiovascular diseases: lessons from seminal clinical trials
Authors: Liberale Luca , Montecucco Fabrizio , Schwarz Lena , Lüscher Thomas F , Camici Giovanni G
Published: July 2020

Inflammation has been long regarded as a key contributor to atherosclerosis. Inflammatory cells and soluble mediators play critical roles throughout arterial plaque development and accordingly, targeting inflammatory pathways effectively reduces atherosclerotic burden in animal models of cardiovascular (CV) diseases. Yet, clinical translation often led to inconclusive or even contradictory results. The Canakinumab Anti-inflammatory Thrombosis Outcome Study (CANTOS) followed by the Colchicine Cardiovascular Outcomes Trial (COLCOT) were the first two randomized clinical trials to convincingly demonstrate the effectiveness of specific anti-inflammatory treatments in the field of CV prevention, while other phase III trials—including the Cardiovascular Inflammation Reduction Trial one using methotrexate—were futile. This manuscript reviews the main characteristics and findings of recent anti-inflammatory Phase III trials in cardiology and discusses their similarities and differences in order to get further insights into the contribution of specific inflammatory pathways on CV outcomes. CANTOS and COLCOT demonstrated efficacy of two anti-inflammatory drugs (canakinumab and colchicine, respectively) in the secondary prevention of major adverse CV events (MACE) thus providing the first confirmation of the involvement of a specific inflammatory pathway in human atherosclerotic CV disease (ASCVD). Also, they highlighted the NOD-, LRR-, and pyrin domain-containing protein 3 inflammasome-related pathway as an effective therapeutic target to blunt ASCVD. In contrast, other trials interfering with a number of inflammasome-independent pathways failed to provide benefit. Lastly, all anti-inflammatory trials underscored the importance of balancing the risk of impaired host defence with an increase in infections and the prevention of MACE in CV patients with residual inflammatory risk.
Making Her Time (and Time Again): Feminist Phenomenology and Form in Recent British and Irish Fiction Written by Women
Authors: Gray Madeleine
Published: July 2020

This article reads Ali Smith’s 2014 novel How to Be Both alongside Deborah Levy’s Hot Milk (2016) and Sally Rooney’s Conversations with Friends (2017). Using Lauren Berlant’s conception of neoliberal “crisis subjectivity” and Sara Ahmed’s vision of feminist wonderment as an antidote to the neoliberal “promise of happiness,” it argues that each novel considers what might be salvaged and what might grow from situations in which young women become attuned to their mutual incarceration in neoliberal time’s double bind. It contends that the forced improvisation and feminist reorientation undertaken by the protagonists can be analyzed through the lens of temporality. Finally, it contemplates how the disciplinary-specific modes through which the novels’ protagonists consider temporality might be connected to the specific literary projects of their authors.
Insights into the evolution of symbiosis gene copy number and distribution from a chromosome-scaleLotus japonicusGifu genome sequence
Authors: Kamal Nadia , Mun Terry , Reid Dugald , Lin Jie-Shun , Akyol Turgut Yigit , Sandal Niels , Asp Torben , Hirakawa Hideki , Stougaard Jens , Mayer Klaus F X , Sato Shusei , Andersen Stig Uggerhøj
Published: July 2020

Lotus japonicus is a herbaceous perennial legume that has been used extensively as a genetically tractable model system for deciphering the molecular genetics of symbiotic nitrogen fixation. Our aim is to improve the L. japonicus reference genome sequence, which has so far been based on Sanger and Illumina sequencing reads from the L. japonicus accession MG-20 and contained a large fraction of unanchored contigs. Here, we use long PacBio reads from L. japonicus Gifu combined with Hi-C data and new high-density genetic maps to generate a high-quality chromosome-scale reference genome assembly for L. japonicus. The assembly comprises 554 megabases of which 549 were assigned to six pseudomolecules that appear complete with telomeric repeats at their extremes and large centromeric regions with low gene density. The new L. japonicus Gifu reference genome and associated expression data represent valuable resources for legume functional and comparative genomics. Here, we provide a first example by showing that the symbiotic islands recently described in Medicago truncatula do not appear to be conserved in L. japonicus.
Optimizing Parasitoid and Host Densities for Efficient Rearing of Ontsira mellipes (Hymenoptera: Braconidae) on Asian Longhorned Beetle (Coleoptera: Cerambycidae)
Authors: Wang Xingeng , Aparicio Ellen M , Duan Jian J , Gould Juli , Hoelmer Kim A
Published: July 2020

Ontsira mellipes Ashmead is a gregarious larval ectoparasitoid of woodboring cerambycids. It is native to North America but can readily attack the exotic Asian longhorned beetle, Anoplophora glabripennis (Motschulsky). This study aimed to develop an efficient rearing system for this parasitoid, as a potential novel association biocontrol agent for the beetle, by investigating the effects of different densities of host (two, three, or four larvae) and parasitoid (one, two, three, four, five, six, seven, and eight female wasps) on Ontsira’s parasitization efficiency and reproductive outcomes. Results showed that overall parasitism and total numbers of parasitized hosts or progeny produced increased with host and/or parasitoid densities, but the number of parasitized hosts or progeny produced per female parasitoid decreased with parasitoid density at each given host density. Nonlinear regression indicated a consistent pattern of mutual interference as parasitoid density increased. Additional experiments showed that superparasitism (indirect interference) did not occur probably because the parasitoid detects hosts through vibration cues from host feeding and attacked (thus paralyzed) hosts are no longer detectable. Thus, the interference probably results from direct or exploitative competition. Interestingly, female parasitoids responded to increased parasitoid density with a significant increase in clutch size. Overall, per capita parasitization efficiency or reproductive outcomes were optimized at a low parasitoid–host ratio but with large group size of hosts and parasitoids. Therefore, an optimal combination of exposing three or four parasitoids to four hosts is proposed for efficient mass-rearing of this parasitoid.
Methanotroph populations and CH4 oxidation potentials in high-Arctic peat are altered by herbivory induced vegetation change
Authors: Rainer Edda M , Seppey Christophe V W , Tveit Alexander T , Svenning Mette M
Published: July 2020

Methane oxidizing bacteria (methanotrophs) within the genus Methylobacter constitute the biological filter for methane (CH4) in many Arctic soils. Multiple Methylobacter strains have been identified in these environments but we seldom know the ecological significance of the different strains. High-Arctic peatlands in Svalbard are heavily influenced by herbivory, leading to reduced vascular plant and root biomass. Here, we have measured potential CH4 oxidation rates and identified the active methantrophs in grazed peat and peat protected from grazing by fencing (exclosures) for 18 years. Grazed peat sustained a higher water table, higher CH4 concentrations and lower oxygen (O2) concentrations than exclosed peat. Correspondingly, the highest CH4 oxidation potentials were closer to the O2 rich surface in the grazed than in the protected peat. A comparison of 16S rRNA genes showed that the majority of methanotrophs in both sites belong to the genus Methylobacter. Further analyses of pmoA transcripts revealed that several Methylobacter OTUs were active in the peat but that different OTUs dominated the grazed peat than the exclosed peat. We conclude that grazing influences soil conditions, the active CH4 filter and that different Methylobacter populations are responsible for CH4 oxidation depending on the environmental conditions.
Participatory learning and action cycles with women’s groups to prevent neonatal death in low-resource settings: A multi-country comparison of cost-effectiveness and affordability
Authors: Pulkki-Brännström Anni-Maria , Haghparast-Bidgoli Hassan , Batura Neha , Colbourn Tim , Azad Kishwar , Banda Florida , Banda Lumbani , Borghi Josephine , Fottrell Edward , Kim Sungwook , Makwenda Charles , Ojha Amit Kumar , Prost Audrey , Rosato Mikey , Shaha Sanjit Kumer , Sinha Rajesh , Costello Anthony , Skordis Jolene
Published: July 2020

WHO recommends participatory learning and action cycles with women’s groups as a cost-effective strategy to reduce neonatal deaths. Coverage is a determinant of intervention effectiveness, but little is known about why cost-effectiveness estimates vary significantly. This article reanalyses primary cost data from six trials in India, Nepal, Bangladesh and Malawi to describe resource use, explore reasons for differences in costs and cost-effectiveness ratios, and model the cost of scale-up. Primary cost data were collated, and costing methods harmonized. Effectiveness was extracted from a meta-analysis and converted to neonatal life-years saved. Cost-effectiveness ratios were calculated from the provider perspective compared with current practice. Associations between unit costs and cost-effectiveness ratios with coverage, scale and intensity were explored. Scale-up costs and outcomes were modelled using local unit costs and the meta-analysis effect estimate for neonatal mortality. Results were expressed in 2016 international dollars. The average cost was $203 (range: $61–$537) per live birth. Start-up costs were large, and spending on staff was the main cost component. The cost per neonatal life-year saved ranged from $135 to $1627. The intervention was highly cost-effective when using income-based thresholds. Variation in cost-effectiveness across trials was strongly correlated with costs. Removing discounting of costs and life-years substantially reduced all cost-effectiveness ratios. The cost of rolling out the intervention to rural populations ranges from 1.2% to 6.3% of government health expenditure in the four countries. Our analyses demonstrate the challenges faced by economic evaluations of community-based interventions evaluated using a cluster randomized controlled trial design. Our results confirm that women’s groups are a cost-effective and potentially affordable strategy for improving birth outcomes among rural populations.
Beyond Description: The Many Facets of Dental Biomechanics
Authors: Crofts S B , Smith S M , Anderson P S L
Published: July 2020

Synopsis

Teeth lie at the interface between an animal and its environment and, with some exceptions, act as a major component of resource procurement through food acquisition and processing. Therefore, the shape of a tooth is closely tied to the type of food being eaten. This tight relationship is of use to biologists describing the natural history of species and given the high instance of tooth preservation in the fossil record, is especially useful for paleontologists. However, correlating gross tooth morphology to diet is only part of the story, and much more can be learned through the study of dental biomechanics. We can explore the mechanics of how teeth work, how different shapes evolved, and the underlying forces that constrain tooth shape. This review aims to provide an overview of the research on dental biomechanics, in both mammalian and non-mammalian teeth, and to synthesize two main approaches to dental biomechanics to develop an integrative framework for classifying and evaluating dental functional morphology. This framework relates food material properties to the dynamics of food processing, in particular how teeth transfer energy to food items, and how these mechanical considerations may have shaped the evolution of tooth morphology. We also review advances in technology and new techniques that have allowed more in-depth studies of tooth form and function.