bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving the technology of aluminothermic rail welding based on software simulation
Authors: Galay M S , Ilinykh A S
Published: August 2021

One of the modern methods of connecting railway rails when creating a continuous welded track is thermite welding. The gap between the rails, into which the metal is poured, is 25 mm. However, when repairing rails on the way, it may not be enough to eliminate the defective rail section. Therefore, an increase in the welding gap up to 50 mm is considered a promising direction in the development of thermite welding of rails. T his study presents the results of modeling the process of rail welding by the thermite method using the NovaFlow& Solid CV software package. The purpose of the study was to assess the change in the length of the weld zone and heat-affected zone with an increase in the welding gap from 25 to 50 mm. The results of the simulation are thermograms reflecting the distribution of heat from the weld zone into the rails. These thermograms were used to determine the boundaries of the welded seam and the heat-affected zone. It was found that the use of a welding gap of 50 mm, instead of 25 mm, leads to the increase in the length of the welded seam by 1.3—1.6 times.
Simulations for Pulsating Breakups of a Nano Taylor Cone
Authors: Nie Qichun , Chen Hao , Li Siqi , Gao Xianxian , An Qiaoru , Fang Haisheng
Published: August 2021

In this paper, a Taylor cone model in the nanoscale is configured using the many-body dissipative particle dynamics method. The sharpening process of the Taylor cone and the breakup process at different electric field intensities and different charge concentrations are systematically investigated. Under a strong electric field, the hemispherical droplet is sharpened over time and evolves into a conic one. Then the conic cusp emits a thin jet. Finally, the cone shrinks into a semi-sphere after jet breaking. These deformation processes occur several times until no charges are emitted from the conic cusp. It is found that the electric field force is responsible for jet emitting, while the Coulombic force causes a jet breakup. With the rising of the intensity of the electric field, the breakup times also increase. However, the breakup times decrease with the rising of the charge concentration. It indicates that a conductive liquid with low electrical conductivities and subjected to a strong electric field is more prone to undergo pulsating breakups.
Modeling and Data Analysis of Spillover Effect on Time Series Fluctuation
Authors: Peng Zhikai , Ke Jinchuan , Liu Chuge , Zhang Tong
Published: August 2021

This paper explores the two-way risk spillover effect between fin-tech innovation and the real economy, applying the time-varying Copula-CoVaR method and quantitatively analyzing the two-way risk spillover effect and risk spillover asymmetry. The research results show that the yield sequence of fin-tech innovation and real economy is asymmetric when risk impact, the impact of bad news is stronger than good news, and there is dynamic linkage effect and positive correlation between fin-tech innovation and the real economy. In addition, there are significant two-way risk spillover effects, namely, risk events in one market can cause increased risk in the other market, but this pair of risk spillover effect is not completely symmetrical.
Simulation Research on Wind Storage Joint Control of Wind Turbine Based on VSG
Authors: Wang Pengcheng , Fu Xiaojin
Published: August 2021

The fluctuation of wind energy has an impact on the stability of active power output and system frequency, resulting in the decline of power quality. In addition, the large-scale wind power generation which is connected to the power grid reduces the inertia of system. The use of VSG control can effectively deal with the lack of inertia response ability of traditional synchronous generators. In the state of large-scale distributed wind power generation connected to the power grid, the ability of wind turbines to suppress the power oscillation of the system can be enhanced. In order to improve this ability, the VSG control strategy is introduced into the control of network test converter, and the virtual inertia control technology is used to respond to the system frequency modulation. The voltage loop and current loop control strategy are adopted for the Generator side rectifier. Meanwhile, the energy storage control of the battery system is introduced. Realize the regulation of wind power active power. In the MATLAB/Simulink, a combined wind energy storage system is built to verify the correctness of the proposed scheme. Finally, the maximum wind energy tracking, the enhancement of system frequency regulation ability and the stabilization of active power output fluctuation are realized. It can effectively restrain the reduction of economic benefits after long-term operation of wind farm.
Lumped Mass Model for Flexible Cable: A Review
Authors: Chen Xin , Hong Bin , Lin Zhangxi , Hou Jing , Gao Zhendong , Lv Shunya
Published: August 2021

Model of a flexible cable plays a great role in the applications of underwater towing system, mooring line system, etc. A complete mathematical model is a basis to accurately describe the dynamic characteristics of flexible cable. This article presents a state of art comprehensive review of lumped mass model. First, the mathematical principle of the lumped mass model, including geometric simplification, force analysis, and solution, are systematically summarized.Second, the dynamic response of cable under different boundary conditions is introduced, and boundary conditions are categoried. Third, the numerical solution of the lumped mass model are assessed. Finally, based on the application of guide dog robot, the authors discussed the research future and trends. The authors aim to ealize human-robot interaction through a flexible cable.
An Image Retrieving Method Based on Strong Constrained Manifold-embedded Hashing
Authors: Liang Hui , Pu Dongbing , Zhang Libiao , Sun Yingjuan
Published: August 2021

In recent years hashing methods have attracted considerable attention. The main procedure of manifold hashing methods is to convert the high dimension features into binary codes and then use manifold distance to approximate the original Euclidean distance. However, there still is a problem that how to directly preserve the manifold structure by hashing. Besides, because of information loss, the effect of using existing hashing methods to retrieve images is not ideal when the length of binary code is very short. In order to solve these problems, we proposed a strong constrained manifold-embedded hash (SCDMH), which can not only explore the nonlinear manifold structure of data, but also make full use of the semantic information in the data. Additionally, the objective function we proposed reconstructs the original features of the datasets and the hash representation mutually to preserve the semantic information. Our experimental results on three large benchmark datasets demonstrate that SCDMH outperforms other state-of-the-art baselines.
Upper Boundsand Extreme Results for Conflict-free Vertexconnection Number
Authors: Ji Meng , Li Xueliang , Schiermeyer Ingo
Published: August 2021

A path of a vertex-colored graph is conflict-free path, if there exists a color used only on one of its vertices; a vertex-colored graph is conflict-free vertex-connected, if there is a conflict-free path between each pair of distinct vertices of the graph. For a connected graph G, the minimum number of colors required to make G conflict-free vertex-connected is conflict-free vertex- connection number of G, denoted by vcfc(G). In this paper, we first showed an upper bound of vcfc(G) for the general graph by structural method. And then, we gave a partial solution to the conjecture on the conflict-free vertex-connection number by contradiction, posed by Doan and Schiermeyer in [Conflict-free vertex connection number at most 3 and size of graphs, Discus. Math. Graph Theory].
Maximum Power Tracking of Ocean Energy Generator Based on Active Disturbance Rejection Control
Authors: Li Dalian , Tian Ka , Zhang Fuxi , Wang Shiming , Sun Xinyi
Published: August 2021

In order to make the ocean energy generator system realize the maximum power under various conditions, this paper proposes a control strategy based on linear active disturbance rejection control algorithm. The output power is mainly affected by the spin-speed of the generator in a nonlinear manner, and this phenomenon is originated from the tip speed ratio state of the turbine blades. This tip speed ratio associated maximum power can be achieved through a coupled control system that adjusts the spin-speed of generator elaborately. The state equations of ocean power generation system are transformed into a standard form to fit the linear active disturbance rejection control. Finally, the simulation model of the system is established by using Matlab/Simulink platform, with a series of input signals for different working conditions. The results verify that the maximum power under control can be effectively attained by a quick tracking of the target speed.
Secure Private Comparison of Equality using Quantum Resources
Authors: Wei Tingting , Zhang Cai
Published: August 2021

Private comparison of equality is an essential task in secure multiparty computation. In this paper, we investigate such a task in quantum settings. Particularly, we design a comparison protocol using quantum resources. The protocol allows three users to verify whether the private inputs of three users are identical and preserve their inputs’ privacy without an extra third party who can help the verifying process. The proposed protocol does not require unitary operations for the information encoding, which, to some extent, facilitates the protocol’s implementation. In addition, the Trojan horse attacks are invalid to the proposed protocol as it only employs one-step quantum transmissions. We also show that the presented protocol is secure against some well-known attacks.
Information system for analyzing negative impacts on forests of the border regions
Authors: Zelentsov V A , Potryasaev S A , Semenov A E
Published: August 2021

The article describes the architecture and composition of a software package for the creation of an information system (IS) to be used in the state of natural objects analysis, in particular, forests of the border region of Russia-South-East Finland. Information system development is carried out within the InnoForestView Project of the ENI CBC Program. The project addresses the consequences of three types of negative impacts: forest fires, diseases and insects, and the proximity of roads. It is shown that the use of a service-oriented architecture with the implementation of individual components of IS in the form of web services, as well as the proposed technologies for integrating heterogeneous information resources, including Earth remote sensing data, ensures the fulfillment of the basic requirements for IS, including the possibility of multi-temporal analysis, maximum automation of tasks to be solved, and user friendliness.
Forest monitoring and analysis based on Earth observation data services
Authors: Ponomarenko M R , Zelentsov V A
Published: August 2021

The paper presents an overview of thematic services providing Earth observation based products for forest monitoring. The authors analyzed both global and regional (in particular - Russian) forest services including input satellite data, output thematic products and features of data access. Based on gathered information, the main advantages and limitations of existing services were highlighted. The results of performed research confirm the need to develop the system integrating data from various forest remote monitoring services for the efficient and timely analysis of forests (especially - in cross border regions).
Use of LiDAR technology for quantification and design of park, garden and urban tree structure
Authors: Frolova V , Chernyshenko O , Batarin A
Published: August 2021

It is essential to know the parameters of trees making up a city’s green infrastructure for evaluating the functions of its ecosystems and ecosystem services being provided. Traditional methods of creating tree inventories proved to be slow and costly, while not being able to provide sufficient data for ecosystem services mapping. Laser scanning methods can be used to obtain accurate measurements of tree dimensions, crown size measurements and overall tree structure details. They can be used to analyze large forested areas at a fraction of the time needed to measure each tree individually by hand. The goal of this study was to conduct an approbation of ground-based 3D scanning methods and test their capabilities of obtaining tree parameters for use in green infrastructure inventories. The research is based on scans and analysis of sites of the green fund of Moscow, Russia, during the vegetation periods of the years 2019-2020. LiDAR scanning allows automatic georeferencing of data and creates detailed 3D geometry of tree objects. This enables previously impossible measurements of tree dimensions to be taken and calculated: aboveground biomass and crown area. Such methods can automate the process of creating tree inventory databases, while eliminating subjective bias when recording measurements.
The use of digital filters in the calculation of indicators of natural systems in geomodeling
Authors: Istomin E , Kolbina O , Sidorenko A , Yagotinceva N , Petrov Y
Published: August 2021

The use of digital filters is ubiquitous, but their use for predicting data from natural systems has always caused dubious results. This paper discusses the possibility of using the Kalman filter for predictive activities when processing geodata. Large amounts of accumulated information can open up new horizons for human activities, including when using geospatial data referencing. The results of the study are presented and conclusions are drawn about the possibility of using digital filters in the calculation of natural indicators.
Boosting the efficiency of hydrodynamic impact on a coal-rock massif employing the method of seismic tomography to control massif’s parameter
Authors: Tailakov O V , Makeev M P , Sokolov S V
Published: August 2021

The results of numerical modeling of a fracture system spatial development on a coal-rock massif under the hydrodynamic impact are presented. To set boundary conditions, an array of geophysical data obtained with a seismic survey method for the extraction panel roof was used. The parameters of typical geophones placement schemes in mine workings, sufficient for assessing the efficiency of directional hydraulic fracturing are substantiated. Satisfactory convergence of the results of numerical modeling of fracture systems spatial development with areas possessing different physical and mechanical properties revealed during seismic survey of the extraction panel impacted by hydraulic fracturing are presented.
Operator’s workplace virtualization and approaches assessment of its graphic implementation
Authors: Nikitenko M S , Kizilov S A , Ignatova A Yu , Remizov S V , Natura E S
Published: August 2021

The authors discuss objectives of creation of a virtual operator’s workplace. These objectives are connected with implementation of 3D virtual interface within the framework of hardware/software currently available on the market, and with general workplace ergonomics. A brief description for different approaches to the design and organization of a virtual workspace is given. The task to develop a test virtual “control panel” to study parameters of the virtual cockpit elements is described.
The influence of the pipeline system on the socio-economic development of oil and gas regions
Authors: Provornaya I V , Filimonova I V , Mishenin M V , Dzyuba Yu A , Chebotareva A V
Published: August 2021

In the article on the basis of the cluster, 20 oil and gas regions of Russia are allocated for which the level of pipeline provision is calculated. The group with a low level of transport security included mainly the regions of Eastern Siberia and the Far East. On the example of the ESPO and the “Power of Siberia” it is shown that the construction of pipelines favorably affects the socio-economic development of regions along the routes.
Investigation of the transition layer of the core – shell of ceramic matrix composites based on coal waste
Authors: Stolboushkin A Yu , Fomina O A
Published: August 2021

The study results of the chemical, particle size, and mineral compositions of the raw materials of ceramic samples (coal waste and clay) are presented. A model of the transition layer between the shell and the core of the ceramic matrix composite is provided. The technique for preparing multilayer ceramic samples imitating the phase boundary of a ceramic material of a matrix structure is described. The differentiated studies of the phase composition and microstructure of multilayer ceramic samples are presented. The interaction of the products of the core and the shell in the transition layer in ceramic materials of the matrix structure during firing is established.
The conception of developing unallocated fund of subsoil raw material resources base in the coal mining industry
Authors: Klishin V I , Pissarenko M V , Rogova T B , Shaklein S V
Published: August 2021

Coal mining industry raw material bases analysis of allocated, newly introduced and unsold subsoil reserve fund demonstrates a fast depletion of the reserves with favorable geological factors of mining which meet the requirements of traditional mining technologies. In the coming years meeting the demand on certain technological coal ranks (K, KZh, KC, KCN, KO, OC, TC, CC) cannot be provided without exploiting coal deposit sites that contain hard to recover reserves and without developing and implementing new mining technologies oriented on complex mining and geological conditions. It requires a special program for fulfilling scientific researches on the development of methodological approaches, technical and technological solutions and testing new technologies for hard to recover coal reserves which can provide rational subsurface resources utilization and protection.
Electrical resistivity tomography at the “roll along” profile in comparison with geochemical testing of the tailing dump (Salair, Kemerovo region)
Authors: Nataliya Yurkevich , Sofia Grakhova , Tatyana Fedorova , Dmitriy Kucher
Published: August 2021

Mining tailings are the source of a wide range of chemical elements in the environment. One of the main mechanisms of substance migration is the filtration of solutions into groundwater and the river network. In this paper, we consider the results of geophysical studies along the side of the tailings mine production (Salair, Kemerovo region) by the method of Electrical resistivity tomography (ERT). The aim of the research was to identify the leakage of industrial water from a hydraulic structure, as well as to compare the geoelectric parameters of the environment with the geochemical testing of solutions near the tailings. It was found that the direction of the underground fluid flow from the tailings can be traced using geophysical methods, as well as to show the exact anomalous drainage zone on the profile of ERT.
The resource regions resilience in the conditions of Industry 4.0. and the COVID-19 pandemic: theoretical and applied aspects
Authors: Goosen E V , Matveeva E V , Kagan E S , Nikitenko S M , Kavkaeva O N
Published: August 2021

Currently, global changes are taking place, accompanied by a change in the socio-economic structure, in these conditions, states and societies lose their resistance to stress and become especially “fragile”, unable to maintain the integrity of their economic and socio-political structures. Within the framework of this article, the authors developed an interdisciplinary concept of the concept of stress resistance, which is most fully manifested during periods of global crises such as the economic transition to Industry 4.0 and the COVID-19 pandemic, and also made an attempt to form indicators for assessing the stress resistance of regions in the new economic and socio-political realities. The problem of stress resistance is becoming especially relevant for the resource regions of Russia. The concept of stress resistance is studied from the standpoint of economic and socio-political approaches. Within the framework of this article, under the concept of resistance to stress, the authors consider the state of stability of all levels of government in relation to stressful situations in the economic, social and political spheres of society, as well as the ability to develop adaptive mechanisms based on forms of strategic partnership between the state and society, in particular civil society institutions. The aim of the study was to develop the main risk factors and factors-stabilizers of stress resistance at the regional level in the context of the global crisis, influencing the system of interaction between government institutions and society. The factors-stabilizers of stress resistance at the regional level are distinguished. Taking into account Industry 4.0 and COVID-19 in the Russian Federation, such “points of growth” may be changes in the modernization of medicine, support from the state for business and non-governmental organizations. Measures to provide stabilization measures to support various categories of the population were taken as a “point”, but quite justified measure to support the economic level of development of regional economies and stabilize the situation in the social sphere.
Development of the digital model of the loading and transport enterprise infrastructure in a coal mining region
Authors: Pristupa Yu D , Pavlova L D , Fryanov V N
Published: August 2021

An argument for developing an infrastructure digital model of the loading and transport enterprise in a coal mining region is presented on the example of Kuzbass in accordance with the natural resources of the coal basin, the existing transport and logistics infrastructure and the needs of the domestic and world coal market. Optimization of traffic flows from producer to consumer is the main direction for development of facilities of transport and logistics infrastructure at a loading and transport enterprise. The scheme of the transport and logistics infrastructure of the loading and transport enterprise was digitized. A computer program for cognitive modeling was developed based on the construction of a fuzzy cognitive map and the choice of an optimal graph scheme from a set of options according to a given criterion. The strength of the system impact on the concept, the strength of the concept impact on the system, the consonances of the concepts impact on the system and the system on concepts are taken as indicators for assessing the options for developing the transport and logistics infrastructure of the loading and transport enterprise. Based on the simulation results, the main significant factors-concepts were identified, which are ranked as follows: the coal market, internal control actions, seasonal phenomena, communication and signaling.
A study on the effect of the deformations in flexiblocks on the behavior of the vehicle axle suspension mechanisms
Authors: Alexandru C
Published: August 2021

This work deals with a study on the effect of the deformations in flexiblocks (bushings) on the behavior of the vehicle axle suspension mechanisms. The mechanism in study is a representatiove one for the structural group/class of mono-mobile axle suspension systems, namely the guiding mechanism by five points - on five spheres (so called 5SS). In a previous work, it was established that the rigid joint model for this class of mechanisms does not provide results close to the real flexible bushing model, reason for which the research in this paper is directed towards the identification of a theoretical model of joint which, at a lower complexity than that of the real model, would still provide viable results, in terms of axle guidance accuracy in the spatial movement relative to car body. In this regard, static and kinematic models were developed and analyzed by using the MBS (Multi-Body Systems) software solution ADAMS.
The effect of chitosan derived silver nanoparticles on mechanical properties, color stability of glass ionomer luting cements
Authors: Qasim Syed Saad Bin , Ali Dena , Soliman Mahmoud Shahat , Zafiropoulos Gregor-Georg
Published: August 2021

Glass ionomer cements (GIC) also known as polyalkenoate cements have been used as dental luting material for decades. However, there are certain limitations with respect to its biomechanical properties. Therefore, the aim of current investigation was to synthesize and characterize silver nanoparticles (SNP) using a green approach and incorporating the synthesized SNP in commercially available GIC formulation. Methodology. SNP were synthesized using a green approach of chemical reduction and analysed by spectroscopy and Transmission Electron microscopy. SNP reinforced GIC in 10, 30 and 50% formulations were assessed for microhardness, compressive strength, color stability and Nano-computerized tomography was used for pore analysis. Results. Results from UV–vis spectroscopy, Dynamic Light Scattering, Zeta potential, Transmission Electron Microscopy and Fourier Transform Infrared Spectroscopy revealed that the particles were spherical and polydisperse in nature with an average diameter of 122 nm. The synthesized particles had a positive surface charge of 74 mV. Their incorporation into the Glass ionomer cement (GIC) revealed non-significant results on microhardness and compressive strength. Significant color change was observed and Nano-CT revealed pores within the set cements. Conclusion. Nevertheless, the biosynthesized silver nanoparticles have much broader clinical application and can be used to reinforce properties of existing dental biomaterials. They can be conveniently synthesized by the biogenic route adapted in the current investigation. However, their addition to the luting cement still warrants further in-depth investigation.
Effect of Al and Cr alloying by arc cladding on the high-temperature oxidation resistance of MoSi2 materials
Authors: Wang Bin , Sun ShunPing , Wang HongJin , Li XiaoPing , Lei WeiNing
Published: August 2021

Different proportions of Al and Cr alloying MoSi2 were prepared by arc cladding with different mass fractions of MoSi2, Al, and Cr as raw materials. The work studied the effects about of Al and Cr on the phase, high-temperature oxidation morphology, products, and high-temperature oxidation property of MoSi2. The results confirmed that the volume expansion coefficient of Al2O3 generated by material oxidation was low which could reduce the degree of mismatch and the cracks in the oxide film. Cr element had a poor effect on enhancing the continuity and compactness of the oxide film, however, it could improve the stability of t-MoSi2 formation after arc cladding. MoO3 was not formed in the MoSi2 material added with Al and Cr show the surface oxidation. A dense and continuous Al2O3–SiO2 oxide film was formed, and no cracks holes were found in the oxide film. After oxidation at 800 °C–1200 °C for 120 h, the sample still maintained good oxidation protection. According to the calculation of oxidation kinetics, the MoSi2 material added with Al and Cr had good oxidation resistance. 3% Al + 9% Cr + 88% MoSi2 had the optimal high-temperature oxidation resistance about four times than pure MoSi2.
Analysis of inverse synthetic aperture radar imaging in the presence of time-varying plasma sheath
Authors: XIE Yaocong , LI Xiaoping , SHEN Fangfang , BAI Bowen , LIU Yanming , CHEN Xuyang , SHI Lei
Published: August 2021

The plasma sheath can induce radar signal modulation, causing not only ineffective target detection, but also defocusing in inverse synthetic aperture radar (ISAR) imaging. In this paper, through establishing radar echo models of the reentry object enveloped with time-varying plasma sheath, we simulated the defocusing of ISAR images in typical environment. Simulation results suggested that the ISAR defocusing is caused by false scatterings, upon which the false scatterings’ formation mechanism and distribution property are analyzed and studied. The range of false scattering correlates with the electron density fluctuation frequency. The combined value of the electron density fluctuation and the pulse repetition frequency jointly determines the Doppler of false scattering. Two measurement metrics including peak signal-to-noise ratio and structural similarity are used to evaluate the influence of ISAR imaging.
Geographic variation in dispersal of western burrowing owl (Athene cunicularia hypugaea) populations across North America
Authors: Macías-Duarte Alberto , Conway Courtney J
Published: August 2021

Dispersal is one of the key elements of species’ metapopulation dynamics and, hence, influences global conservation status. Furthermore, determining the geographic variation in magnitude and direction of dispersal throughout a species’ distribution may expand our understanding of the causes of population declines in species of conservation concern. For instance, western burrowing owl (Athene cunicularia hypugaea) populations have declined at the northern and eastern edge of their breeding distribution during the 20th century. In the same period, large areas of thornscrub that did not support breeding owls were converted to irrigated agriculture in the southern edge of the subspecies’ breeding distribution in northwestern Mexico. These farmlands now support some of the highest breeding densities of owls. We tested the hypothesis that owls that colonized this recently created habitat originated from declining migratory populations from the northern portion of the subspecies’ range. We used stable isotopes 2H, 13C, and 15N in owl feathers to infer breeding dispersal patterns throughout the subspecies’ breeding range. Populations near the northern edge of the subspecies’ breeding range had immigrants that dispersed over larger distances than immigrants at low and mid latitude populations. However, agricultural populations in northwestern Mexico disrupted this latitudinal pattern, attracting owls from more distant locations. We also found immigrants originated from further distances in declining populations than increasing populations. Stable isotopes provided no evidence of contemporaneous breeding dispersal from Canadian populations to northwestern Mexico but suggest that agricultural areas in the southern edge of the subspecies’ distribution have altered the continental dispersal pattern.
Resolving complex structures at oncovirus integration loci with conjugate graph
Authors: Jia Wenlong , Xu Chang , Li Shuai Cheng
Published: August 2021

Oncovirus integrations cause copy number variations and complex structural variations (SVs) on host genomes. However, the understanding of how inserted viral DNA impacts the local genome remains limited. The linear structure of the oncovirus integrated local genomic map (LGM) will lay the foundations to understand how oncovirus integrations emerge and compromise the host genome’s functioning. We propose a conjugate graph model to reconstruct the rearranged LGM at integrated loci. Simulation tests prove the reliability and credibility of the algorithm. Applications of the algorithm to whole-genome sequencing data of human papillomavirus (HPV) and hepatitis B virus (HBV)-infected cancer samples gained biological insights on oncovirus integrations. We observed four affection patterns of oncovirus integrations from the HPV and HBV-integrated cancer samples, including the coding-frame truncation, hyper-amplification of tumor gene, the viral cis-regulation inserted at the single intron and at the intergenic region. We found that the focal duplicates and host SVs are frequent in the HPV-integrated LGMs, while the focal deletions are prevalent in HBV-integrated LGMs. Furthermore, with the results yields from our method, we found the enhanced microhomology-mediated end joining might lead to both HPV and HBV integrations and conjectured that the HPV integrations might mainly occur during the DNA replication process. The conjugate graph algorithm code and LGM construction pipeline, available at https://github.com/deepomicslab/FuseSV.
Deep learning-based classification of breast cancer cells using transmembrane receptor dynamics
Authors: Kim Mirae , Hong Soonwoo , Yankeelov Thomas E , Yeh Hsin-Chih , Liu Yen-Liang
Published: August 2021

Motivation

Motions of transmembrane receptors on cancer cell surfaces can reveal biophysical features of the cancer cells, thus providing a method for characterizing cancer cell phenotypes. While conventional analysis of receptor motions in the cell membrane mostly relies on the mean-squared displacement plots, much information is lost when producing these plots from the trajectories. Here we employ deep learning to classify breast cancer cell types based on the trajectories of epidermal growth factor receptor (EGFR). Our model is an artificial neural network trained on the EGFR motions acquired from six breast cancer cell lines of varying invasiveness and receptor status: MCF7 (hormone receptor positive), BT474 (HER2-positive), SKBR3 (HER2-positive), MDA-MB-468 (triple negative, TN), MDA-MB-231 (TN) and BT549 (TN).

Results

The model successfully classified the trajectories within individual cell lines with 83% accuracy and predicted receptor status with 85% accuracy. To further validate the method, epithelial–mesenchymal transition (EMT) was induced in benign MCF10A cells, noninvasive MCF7 cancer cells and highly invasive MDA-MB-231 cancer cells, and EGFR trajectories from these cells were tested. As expected, after EMT induction, both MCF10A and MCF7 cells showed higher rates of classification as TN cells, but not the MDA-MB-231 cells. Whereas deep learning-based cancer cell classifications are primarily based on the optical transmission images of cell morphology and the fluorescence images of cell organelles or cytoskeletal structures, here we demonstrated an alternative way to classify cancer cells using a dynamic, biophysical feature that is readily accessible.

Availability and implementation

A python implementation of deep learning-based classification can be found at https://github.com/soonwoohong/Deep-learning-for-EGFR-trajectory-classification.

Supplementary information

Supplementary data are available at Bioinformatics online.
Unipept Visualizations: an interactive visualization library for biological data
Authors: Verschaffelt Pieter , Collier James , Botzki Alexander , Martens Lennart , Dawyndt Peter , Mesuere Bart
Published: August 2021

The Unipept Visualizations library is a JavaScript package to generate interactive visualizations of both hierarchical and non-hierarchical quantitative data. It provides four different visualizations: a sunburst, a treemap, a treeview and a heatmap. Every visualization is fully configurable, supports TypeScript and uses the excellent D3.js library.

Availability and implementation

The Unipept Visualizations library is available for download on NPM: https://npmjs.com/unipept-visualizations. All source code is freely available from GitHub under the MIT license: https://github.com/unipept/unipept-visualizations
Excess Invasive Meningococcal Disease Associated With Seasonal Influenza, South Africa, 2003–2018
Authors: Meiring Susan , Tempia Stefano , Dominic Emanuel M , de Gouveia Linda , McAnerney Jo , von Gottberg Anne , Cohen Cheryl
Published: August 2021

Background

Invasive meningococcal disease (IMD) is a devastating illness with high mortality rates. Like influenza, endemic IMD is seasonal, peaking in winter. Studies suggest that circulation of influenza virus may influence the timing and magnitude of IMD winter peaks.

Methods

This ecological study used weekly data from 2 nationwide surveillance programs: Viral Watch (proportion of outpatient influenza-positive cases from throat or nasal swab samples) and GERMS-SA (laboratory-confirmed cases of IMD), occurring across South Africa from 2003 through 2018 in all age bands. A bivariate time series analysis using wavelet transform was conducted to determine cocirculation of the diseases and the time lag between the peak seasons. We modeled excess meningococcal disease cases attributable to influenza cocirculation, using univariate regression spline models. Stata and R statistical software packages were used for the analysis.

Results

A total of 5256 laboratory-confirmed IMD cases were reported, with an average annual incidence of 0.23 episodes per 100 000 population and a mean seasonal peak during week 32 (±3 weeks). Forty-two percent of swab samples (10 421 of 24 741) were positive for influenza during the study period. The mean peak for all influenza occurred at week 26 (±4 weeks). There was an average lag time of 5 weeks between annual influenza and IMD seasons. Overall, 5% (1%–9%) of IMD cases can be attributable to influenza cocirculation, with, on average, 17 excess IMD cases per year attributable to influenza.

Conclusions

A quantifiable proportion of IMD in South Africa is associated with influenza cocirculation; therefore, seasonal influenza vaccination may have an effect on preventing a small portion of IMD in addition to preventing influenza.
Simulated heatwave and fishing stressors alter corticosteroid and energy balance in neonate blacktip reef sharks, Carcharhinus melanopterus.
Authors: Schoen Alexandra N , Bouyoucos Ian A , Anderson W Gary , Wheaton Catharine J , Planes Serge , Mylniczenko Natalie D , Rummer Jodie L
Published: August 2021

The increasing frequency and duration of marine heatwaves attributed to climate change threatens coastal elasmobranchs and may exacerbate existing anthropogenic stressors. While the elasmobranch stress response has been well studied, the role of the unique corticosteroid—1α-hydroxycorticosterone (1α-OHB)—in energy balance is not understood. Therefore, 1α-OHB’s utility as a stress biomarker in elasmobranch conservation physiology is equivocal. Here, we analyse the roles of corticosteroids, 1α-OHB and corticosterone, and metabolites, glucose and 3-hydroxybutyrate (3-HB), in response to stress in a protected tropical shark species, the blacktip reef shark (Carcharhinus melanopterus). Wild-caught neonates were exposed to ambient (27°C) or heatwave conditions (29°C) and subsequently a simulated fishing stressor (1 min air exposure). Blood samples were taken prior to temperature exposure, prior to air exposure, and 30 min, 1 h, 24 h, and 48 h post-air exposure at treatment temperatures. Plasma 1α-OHB was elevated for 48 h in 27°C-exposed sharks but declined over time in 29°C-exposed sharks. Plasma 1α-OHB was not correlated with either metabolite. Plasma glucose was higher and plasma 3-HB was lower in 29°C-exposed sharks. In a separate experiment, blood samples were collected from both neonate and adult sharks immediately following capture and again 5 min later, and analysed for corticosteroids and metabolites. Plasma 1α-OHB increased in neonates within 5 min, but neonates displayed lower plasma 1α-OHB and higher glucose concentrations than adults. We conclude that 1α-OHB does not serve as a classic glucocorticoid role in C. melanopterus under these stressors. Furthermore, we show for the first time, ontogenetic differences in plasma 1α-OHB. Ultimately, our findings provide insights into hormonal control of energy mobilization during stress in C. melanopterus, particularly during simulated heatwave conditions, which seem to alter both endocrine and energy mobilization. Further work is needed to determine the utility of 1α-OHB as a biomarker for the mobilization of energy during a stress event in elasmobranchs.
Telomerase therapy reverses vascular senescence and extends lifespan in progeria mice
Authors: Mojiri Anahita , Walther Brandon K , Jiang Chongming , Matrone Gianfranco , Holgate Rhonda , Xu Qiu , Morales Elisa , Wang Guangyu , Gu Jianhua , Wang Rongfu , Cooke John P
Published: August 2021

Aims

Hutchinson-Gilford progeria syndrome (HGPS) is an accelerated ageing syndrome associated with premature vascular disease and death due to heart attack and stroke. In HGPS a mutation in lamin A (progerin) alters nuclear morphology and gene expression. Current therapy increases the lifespan of these children only modestly. Thus, greater understanding of the underlying mechanisms of HGPS is required to improve therapy. Endothelial cells (ECs) differentiated from induced pluripotent stem cells (iPSCs) derived from these patients exhibit hallmarks of senescence including replication arrest, increased expression of inflammatory markers, DNA damage, and telomere erosion. We hypothesized that correction of shortened telomeres may reverse these measures of vascular ageing.

Methods and results

We generated ECs from iPSCs belonging to children with HGPS and their unaffected parents. Telomerase mRNA (hTERT) was used to treat HGPS ECs. Endothelial morphology and functions were assessed, as well as proteomic and transcriptional profiles with attention to inflammatory markers, DNA damage, and EC identity genes. In a mouse model of HGPS, we assessed the effects of lentiviral transfection of mTERT on measures of senescence, focusing on the EC phenotype in various organs. hTERT treatment of human HGPS ECs improved replicative capacity; restored endothelial functions such as nitric oxide generation, acetylated low-density lipoprotein uptake and angiogenesis; and reduced the elaboration of inflammatory cytokines. In addition, hTERT treatment improved cellular and nuclear morphology, in association with a normalization of the transcriptional profile, effects that may be mediated in part by a reduction in progerin expression and an increase in sirtuin 1 (SIRT1). Progeria mice treated with mTERT lentivirus manifested similar improvements, with a reduction in inflammatory and DNA damage markers and increased SIRT1 in their vasculature and other organs. Furthermore, mTERT therapy increased the lifespan of HGPS mice.

Conclusion

Vascular rejuvenation using telomerase mRNA is a promising approach for progeria and other age-related diseases.
A Metabolomic Aging Clock Using Human Cerebrospinal Fluid
Authors: Hwangbo Nathan , Zhang Xinyu , Raftery Daniel , Gu Haiwei , Hu Shu-Ching , Montine Thomas J , Quinn Joseph F , Chung Kathryn A , Hiller Amie L , Wang Dongfang , Fei Qiang , Bettcher Lisa , Zabetian Cyrus P , Peskind Elaine , Li Gail , Promislow Daniel E L , Franks Alexander
Published: August 2021

Quantifying the physiology of aging is essential for improving our understanding of age-related disease and the heterogeneity of healthy aging. Recent studies have shown that, in regression models using “-omic” platforms to predict chronological age, residual variation in predicted age is correlated with health outcomes, and suggest that these “omic clocks” provide measures of biological age. This paper presents predictive models for age using metabolomic profiles of cerebrospinal fluid (CSF) from healthy human subjects and finds that metabolite and lipid data are generally able to predict chronological age within 10 years. We use these models to predict the age of a cohort of subjects with Alzheimer’s and Parkinson’s disease and find an increase in prediction error, potentially indicating that the relationship between the metabolome and chronological age differs with these diseases. However, evidence is not found to support the hypothesis that our models will consistently overpredict the age of these subjects. In our analysis of control subjects, we find the carnitine shuttle, sucrose, biopterin, vitamin E metabolism, tryptophan, and tyrosine to be the most associated with age. We showcase the potential usefulness of age prediction models in a small data set (n = 85) and discuss techniques for drift correction, missing data imputation, and regularized regression, which can be used to help mitigate the statistical challenges that commonly arise in this setting. To our knowledge, this work presents the first multivariate predictive metabolomic and lipidomic models for age using mass spectrometry analysis of CSF.
Source models of long-period seismic events at Galeras volcano, Colombia
Authors: Torres Roberto , Kumagai Hiroyuki , Taguchi Kimiko
Published: August 2021

Long-period (LP) seismic events have occurred repeatedly at Galeras volcano, Colombia, during the transition from effusive dome formation to explosive Vulcanian eruptions. Since 1989, two types of LP events have been observed there: one characterized by long-lasting, decaying harmonic oscillations (NLP events) and the other by non-harmonic oscillatory features (BLP events). NLP events are attributed to resonances of a dusty gas-filled crack in the magma plugging the eruptive conduit. Sixteen episodes of NLP events occurred at Galeras during 1992–2010, each characterized by systematic temporal variations in the frequencies and quality factors of NLP events. Our and previous estimates of crack model parameters during three of those NLP episodes indicate that the similar temporal variations in crack geometry and fluid properties can be explained by an increase in the ash content within the crack and a decrease in crack volume. We found that NLP events, associated with low SO2 fluxes, are anticorrelated with BLP events, which are accompanied by high SO2 emissions. From our observations and analytical results, we inferred that BLP events are generated by resonances of open cracks in the uppermost magma plug, corresponding to tuffisite veins, that efficiently transfer volcanic gases. After sufficient degassing and densification, the magma plug effectively seals the conduit. The growing overpressure in the deeper magma is then released through a shear fracture along the conduit margin. The intrusion of deeper, vesiculated magma into the shear fracture depressurizes and fragments the magma, producing a dusty gas and triggering the crack resonances that generate NLP events. Our results thus indicate that the evolution of the properties of the magma plug controls the occurrences of BLP and NLP events at Galeras. Although NLP events do not always precede explosive eruptions, they indicate that an important overpressure is building in the shallow conduit.
Left ventricular unloading during extracorporeal life support for myocardial infarction with cardiogenic shock: surgical venting versus Impella device
Authors: Radakovic Darko , Zittermann Armin , Knezevic Alen , Razumov Artyom , Opacic Dragan , Wienrautner Nicole , Flottmann Christian , Rojas Sebastian V , Fox Henrik , Schramm René , Morshuis Michiel , Rudolph Volker , Gummert Jan , Deutsch Marcus-André
Published: August 2021

OBJECTIVES

Patients in cardiogenic shock supported with venoarterial extracorporeal membrane oxygenation (VA-ECMO) may experience severe complications from reduced left ventricular (LV) unloading and increased cardiac afterload. These effects are usually modified by adding a percutaneous direct Impella vent or surgical LV vent on top of VA-ECMO in selected patients. However, direct comparisons between 2 LV unloading strategies in patients with cardiogenic shock due to myocardial infarction are lacking. Therefore, we sought to investigate the impact of these 2 different approaches.

METHODS

We enrolled 112 patients treated with an Impella or surgical LV vent during VA-ECMO support between January 2014 and February 2020. The primary endpoint was 30-day mortality. Secondary endpoints included rates of myocardial recovery or transition to durable mechanical circulatory support. Additionally, we assessed adverse events such as peripheral ischaemic complications requiring intervention, sepsis and ischaemic stroke.

RESULTS

At 30 days, 38 patients in the Impella group (54%) and 26 patients in the surgical LV vent group (63%) had died (relative risk with Impella 0.78, 95% confidence interval 0.47–1.30; P = 0.35). Impella group and the surgical LV vent group differed significantly with respect to the secondary end points including rates of myocardial recovery (24% and 7%, respectively; P = 0.022) and rates of durable mechanical circulatory support (17% and 42%, P = 0.012). Complication rates were not statistically different between the 2 groups.

CONCLUSIONS

The use of Impella device as therapeutic unloading therapy during VA-ECMO did not significantly reduce 30-day mortality compared to surgical LV vent in patients with cardiogenic shock due to acute myocardial infarction.