bluuebunny/crossref_metadata_2025 huggingface dataset:
Ways for determining the intermediate dimensions when designing the machining technology
Authors: Slătineanu L , Coteaţă M , Dodun O , Nagîţ G , Hriţuc A , Beşliu-Băncescu I
Published: January 2021

Among other problems to be solved, the design of a technological process of machining by cutting a part involves establishing the dimensions that can be achieved in the pre-final machining of the same surface of the part. There are distinct ways to calculate the so-called intermediate dimensions and, in particular, to define the dimensions for adjusting the position of the cutting tool tip before starting the actual machining process. The paper analyzes some such ways of establishing the intermediate dimensions, highlighting the conditions under which they can be applied, their advantages and limitations of use. Subsequently, the double-entry matrix method was applied to identify one or more methods with wider possibilities of use. It was concluded that the method of tolerance chart and respectively a method that takes into account a statistical processing of the results accumulated over time are methods likely to lead to an efficient solving the problem of determining the intermediate dimensions.
Brief review of methods and techniques used in Learning Factories in the context of Industry 4.0
Authors: Neacsu G C , Pascu I G , Nitu E L , Gavriluta A C
Published: January 2021

The rapid evolution of science and technology has forced the processes and systems of production, training and learning to adapt to innovation and the digital era of industrial technology. In the case of production processes and systems, innovation and digitalization refer to the transformation of production units into smart factories. In the case of training and learning processes and systems, innovation and digitalization lead to the creation of learning factories. Thus, this process involves the use of modern methods and techniques to develop innovative training, learning and production processes and systems. This paper is an analysis of recent studies and seeks to briefly present the evolution of industrial production processes and systems and Industry 4.0 but also the concept of learning factory. The paper also presents a review of the main methods and techniques used in innovative industrial training, learning and production processes and systems. Finally, some conclusions related to the use of these methods and techniques are summarized.
Improvement of the grain cargo handling technology on the basis of resource-saving
Authors: Kovalov Anton , Prodashchuk Svitlana , Kravets Anna , Mkrtychian Dmytro , Prodashchuk Mikola
Published: January 2021

The article considers the state of grain cargo transportation and related technical and technological problems. As a solution, the possibility of using multiple grain shipping containers and the introduction of a new modern grain cargo handling technology at the station based on inventory management and proper selection of vehicles was considered. The considered measures will contribute to simplifying, improving and reducing the number of cargo operations performed during grain handling, making their implementation more practical and energy-efficient.
Main criteria of complex evaluation of subway train power facility technological productive potential
Authors: Kulbovskyi I I , Aharkov O V , Kharuta V S , Halushko M M
Published: January 2021

Maintaining the train safety and passenger transportation safety is regulated by the technical condition of rolling stock, which meets the requirements of regulatory documentation. Modern conditions of operation of traction rolling stock units (UTRS) are characterized by insufficient use of production and technological potential.

One of the main reasons for this situation is the lack of necessary scientific and methodological developments that describe and improve system methods, models and criteria for the effectiveness of the production processes of UTRS.
Investigation of the Influence of Dynamic Loads of Industrial Equipment on the Occurrence of Prolonged Yielding of their Foundation Soils
Authors: Aleksandrovych V A , Havryliuk O V
Published: January 2021

The parameters of oscillations of the foundations and structures of the dynamic equipment of the new production workshop located in the Kharkiv region were experimentally investigated. For this purpose, appropriate measurements of the amplitude of oscillations in the vertical and orthogonal horizontal directions were performed. To compare the parameters of the amplitudes of forced oscillations and determine the damping properties of the applied rubber spacers placed between the frame and the slides, as well as the quenching effect of the foundation massif, several measurements of oscillation parameters were performed at the locations mentioned above. The amplitude of oscillations of the vertical component of the vibration load on different sides of the rubber dampers was reduced by 2-3 times, the horizontal component was completely attenuated. It was also established that there was no transmission of vibrations to the foundations of the production workshop. The safety of the measured parameters of oscillations from the point of view of long significant unstabilized subsidence of the foundations, both equipment and building, was determined. Recommendations for monitoring are given from the point of view of the possible deterioration of the properties of the used rubber dampers over time.
Environmental assessment of small scale solar thermal electricity generation
Authors: Koltun Paul , Klymenko Vasyl , Soldatenko Valentyn , Kononchuk Serhii , Teliuta Ruslan
Published: January 2021

Solar thermal electricity probably has the greatest potential of any single renewable energy process and it can be economically competitive with other technologies, if environmental costs are accounted for. In spite of the many investigations conducted so far there is no one dominant technology and no single life cycle assessment study conducted to compare different STE technologies. This life cycle study has been undertaken to identify potential materials flow, energy consumption and emissions for small scale STE options. The processes are described by the typical process inputs and outputs including energy, materials, solid wastes and other emissions. The results show sufficient efficiency for Australian conditions of small scale.
Research of Integrity of Fire Insulation Cladding with Mineral Wool of Steel Beam under Fire Impact
Authors: Pozdieiev Serhii , Nuianzin Oleksandr , Borsuk Olena , Nedilko Inna
Published: January 2021

In the article, the processes of integrity loss of fire-retardant cladding from mineral wool of a steel I-beam are considered. The relation between fire-retardant cladding integrity and its thermal insulating ability was studied. Computer model of a steel beam with fire-retardant cladding of mineral wool, which takes into account its own weight, current mechanical load and temperature mode of heating under the heat-insulating effect of the cladding, using the computer system LS-DINA, is developed in this article. It is shown that the fire-retardant cladding loses its integrity under the thermal influence of fire long before the onset of the limit state of loss of fire resistance in terms of bearing capacity. The conditions under which fire-retardant cladding loses its integrity and fire-retardant ability are investigated. Having considered the time of fire-retardant cladding integrity loss the fire resistance limit can be significantly clarified and allows to avoid early collapse of building structures cause by fire.
Simulation of the oil film thickness on a friction surface in the presence of fullerene compositions in the lubricant
Authors: Kravtcov A , Gradiskiy Y , Tsymbal B , Borak K
Published: January 2021

The paper contains theoretical studies of the oil film formation on a friction surface in the presence of fullerene solutions in a lubricant. The mathematical model is developed on the basis of the interaction between electrically active heterogeneous finely dispersed systems at the interface between the friction surface and the lubricating medium and is described by the Poisson differential equation. The role of the friction surface on the formation of clusters and micelles in an adsorbed film of the lubricant near the friction surface is established. It is shown that in the stress-strain state of triboelement material surface layers, the friction surface acts as an “electrostatic field generator”. Expressions are obtained for the simulation of the oil film thickness in the presence of fullerenes in the base lubricant. Based on the simulation results, the most significant factors in the formation of the oil film thickness have been established: these are the electric field strengths of the friction surface and the base lubricating medium; the load on the tribosystem; the temperature, and dynamic viscosity of the lubricating medium.
A targeted rheological bioink development guideline and its systematic correlation with printing behavior
Authors: Pössl Axel , Hartzke David , Schmidts Thomas M , Runkel Frank E , Schlupp Peggy
Published: January 2021

Bioprinting for tissue or disease models is a promising but complex process involving biofabrication, cell culture and a carrier material known as bioink. The native extracellular matrix (ECM), which forms the scaffold for cells in vivo, consists of several components including collagen as a gelling agent to confer mechanical stiffness and provide a substrate for cell attachment. Bioprinting therefore needs an artificial ECM that fulfills the same functions as its natural counterpart during and after the printing process. The combination of bioink materials determines the immune response of the host, cell compatibility and adhesion. Here we evaluate multi-material blending with four pre-selected components using a design of experiments approach. Our exemplary designed hydrogel is highly reproducible for the development of artificial ECM and can be expanded to incorporate additional requirements. The bioink displays shear-thinning behavior and a high zero-shear viscosity, which is essential for the printing process. We assessed the printing behavior of our bioink over a wide range of the key process parameters for extrusion-based bioprinting (temperature, pressure, feed rate, and nozzle geometry). Several processing temperatures were linked by rheological measurements directly to the 3D printing process. The printing results were evaluated using a self-developed categoric strand screening process, varying the feed rate and pressure with a fixed nozzle. Accordingly, nozzles differing in size and shape were evaluated and the interactions between printing pressure and feed rate were characterized separately by applying a modified O-R-O test. We tested the short-term cultivation stability of our bioink to mimic the hypothermic and hyperthermic conditions of the human body. As result we present an expandable concept for bioink development and a highly reproducible and well-characterized procedure for printing with the newly developed hydrogel. We provide detailed insights into the relationship between printing parameters, rheological parameters and short-term cultivation stability.
The effect of micro and nano hydroxyapatite powder on biocompatibility and surface integrity of Ti6Al4V (ELI) in powder mixed electrical discharge machining
Authors: Yaşar Hamidullah , Ekmekci Bülent
Published: January 2021

The problem of achieving functional surface is receiving substantial attention with the demand for efficient medical devices in biomedical industry. To satisfy both mechanical and biomedical concerns, researchers try to develop appropriate commercial machining techniques. This study analyzes the micro and nano Hydroxyapatite (HAp) powder size effect on surface topography and biocompatibility of Ti-6Al-4V (ELI) biomaterial in Electrical Discharge Machining (EDM). We compare thoroughly the titanium surfaces that EDM’ed with three different HAp powder concentrations in Deionized Water (DW) (0 g l−1, 20 g l−1 Micro HAp, 20 g l−1 Nano HAp) and three pulse current levels (7 A, 12 A, 22 A). The roughness of surfaces varies between 0.38 μm and 6.61 μm. Using micro HAp powder in dielectric liquid lowered the surface roughness and enhanced the wettability whereas the nano HAp effect could be negligible. The Energy Dispersive x-ray Spectrometer results show the Ca and P ion migration from the HAp mixed dielectric to the workpiece surface during EDM. The x-ray Diffraction results affirmed the existence of HAp compounds and oxide phases in the surface structure. Biocompatibility tests employing MG63 osteoblast-like cells revealed that for 24 h culture period all EDM samples showed higher viability than the control in vitro. According to the statistical analyses ANOVA (Tukey), the MTT viability results showed a significant difference especially for those machined in micro HAp mixed DW dielectrics. On the other hand, for 72 h culture period, samples machined in DW with 7 and 12 A currents are more biocompatible and have a proliferative effect on MG63 cells. In conclusion, however the dependency on pulse current, powder additive, and topography of the surface exist; EDM can be employed as an effectual treatment to enhance the biocompatibility.
Structural and magnetodielectric properties of BiFeO3-GdMnO3 multiferroics
Authors: Masso R , Tripathy S N , Aponte F A , Pradhan D K , Martinez R , Palai R
Published: January 2021

We report on structural, microstructural, spectroscopic, dielectric, electrical, ferroelectric, ferromagnetic, and magnetodielectric coupling studies of BiFeO3–GdMnO3[(BFO)1–x
–(GMO)
x
], where x is the concentration of GdMnO3 (x = 0.0, 0.025, 0.05, 0.075, 0.1, 0.15, and 0.2), nanocrystalline ceramic solid solutions by auto-combustion method. The analysis of structural property by Rietveld refinement shows the existence of morphotropic phase boundary (MPB) at x = 0.10, which is in agreement with the Raman spectroscopy and high resolution transmission electron microscopy (HRTEM) studies. The average crystallite size obtained from the transmission electron microscopy (TEM) and x-ray line profile analysis was found to be 20–30 nm. The scanning electron micrographs show the uniform distribution of grains throughout the surface of the sample. The dielectric dispersion behavior fits very well with the Maxwell-Wagner model. The frequency dependent phase angle (θ) study shows the resistive nature of solid solutions at low frequency, whereas it shows capacitive behavior at higher frequencies. The temperature variation of dielectric permittivity shows dielectric anomaly at the magnetic phase transition temperature and shifting of the phase transition towards the lower temperature with increasing GMO concentration. The Nyquist plot showed the conduction mechanism is mostly dominated by grains and grain boundary resistances. The ac conductivity of all the samples follows the modified Jonscher model. The impedance and modulus spectroscopy show a non-Debye type relaxation mechanism which can be modeled using a constant phase element (CPE) in the equivalent circuit. The solid-solutions of BFO-GMO show enhanced ferromagnetic-like behavior at room temperature. The ferroelectric polarization measurement shows lossy ferroelectric behavior. The frequency dependent magnetocapacitance and magnetoimpedance clearly show the existence of intrinsic magnetodielectric coupling. The (BFO)1–x
–(GMO)
x
solid solutions with x = 0.025–0.075 show significantly higher magnetocapacitance and magnetoimpedance compared to the pure BFO.
Research on the dielectric constant of graphene solution at the microwave frequency of 9.212GHz
Authors: Jiao Tian-Yi , Shi Na-Yue , Wu Chuang , Chen Xiu-Yan
Published: January 2021

In order to measure the graphene’s dielectric constant, the microwave cavity perturbation method was employed. At the frequency of 9.212 GHz, graphene with three concentrations of 5 g ml−1, 2.5 g ml−1 and 1.25 g ml−1 was studied respectively. For these three solutions, as inserted depth in the microwave resonator, concentration and capillary’s diameter changed, the dielectric constant’s real part and imaginary part were all measured, calculated and discussed. The results showed that the real part of the graphene’s dielectric constant increased with the increase of the depth of the capillary into the resonator, decreased with the increase of the capillary diameter. The conductivity of graphene solution was measured which decreased with the increase of liquid concentration.
Kinetic-theory-based investigation of electronegative plasma–wall transition with two populations of electrons
Authors: BASNET Suresh , DEUJA Atit , KHANAL Raju
Published: January 2021

Kinetic theory has been employed to investigate the magnetized plasma-sheath structure and its characteristics in the presence of more than one species of negatively charged particles: hot electrons, cold electrons, and negative ions. The cold electrons and negative ions are considered to obey a Maxwellian distribution, whereas the hot electrons follow a truncated Maxwellian distribution. The Bohm sheath condition has been extended for the case of more than one species of negatively charged particles, in which the concentration of hot electrons has a crucial role in achieving the Bohm velocity. The thermal motion of hot electrons is much higher compared to cold electrons and negative ions, such that the variation of hot electron concentrations and the temperature ratio of hot to cold electrons play a key role in the determination of the plasma-sheath parameters: particle densities, electrostatic potential, the flow of positive ions towards the wall, and sheath thickness. We have estimated the deviation of the resultant drift velocity of positive ions on the plane perpendicular to the wall from the parallel component at the presheath–sheath interface. It is found that the deviation between the two velocity components increases with an increase in the obliqueness of the magnetic field. Furthermore, the results obtained from the kinetic trajectory simulation model are compared with the results obtained using a fluid model; the results are qualitatively similar, although the potential varies by less than 4% in terms of the magnitude at the wall.
Kink solutions in a generalized scalar φ
4
G field model
Authors: Lozano-Mayo Jonathan , Torres-Labansat Manuel
Published: January 2021

We study a scalar field model in a two dimensional space-time with a generalized

ϕ

G

4

potential which has four minima, obtaining novel kink solutions with well defined properties although the potential is non-analytical at the origin. The model contains a control parameter δ that breaks the degeneracy of the potential minima, giving rise to two different phases for the system. The δ < 0 phases do not possess solitary wave solutions. At the transition point δ = 0 all the potential minima are degenerate and three different kink solutions result. As the transition to the δ > 0 phase takes place, the minima of the potential are no longer degenerate and a unique kink ϕ

δ
solution is produced. Remarkably, this kink is a coherent structure that results from the merge of three kinks that can be identified with those observed at the transition point. To support the interpretation of ϕ

δ
as a bound state of three kinks, we calculate the force between the kink-kink pair components of ϕ

δ
, obtaining an expression that has both exponentially repulsive and constant attractive contributions that yields an equilibrium configuration, explaining the formation of the ϕ

δ
multi-kink state. We further investigate kink properties including their stability guaranteed by the positive defined spectrum of small fluctuations around the kink configurations. The findings of our work together with a semiclassical WKB quantization, including the one loop mass renormalization, enable computing quantum corrections to the kink masses. The general results could be relevant to the development of effective theories for non-equilibrium steady states and for the understanding of the formation of coherent structures.
Do LED lightbulbs save natural gas? Interpreting simultaneous cross-energy program impacts using electricity and natural gas billing data
Authors: Adekanye Oluwatobi G , Davis Alex , Azevedo Inês L
Published: January 2021

Local and state governments have made significant advances in creating, implementing, and evaluating energy efficiency programs in the buildings sector. Evaluations commonly use ex-post statistical models to complement ex-ante engineering estimates when determining program impacts. A critical assumption of data-driven evaluations is that reductions would not occur in the absence of the program. This assumption is difficult to test, particularly if other unobserved changes to the building’s energy profile coincide with the program’s adoption. We provide a method to detect a class of unobserved simultaneous cross-energy changes in a building’s energy profile by examining the treatment effects of electricity-only programs on natural gas use and vice versa. We apply the method to a panel of residential energy efficiency implementations with monthly electricity and gas data from 2010 to 2016 in the City of Palo Alto, California. Using difference-in-differences and event history analyses, we find evidence of significant gas reductions estimated for some electricity-only programs, suggesting that households implemented unobserved changes at the same time as those programs. Our results highlight how data-driven analyses may not adequately estimate program impacts, and the value of simultaneous electricity and natural gas measurements for detecting and interpreting unobserved changes to energy use at the household level. Lastly, we present evidence that energy savings from non-monetary interventions can exceed those which offer financial rewards for energy efficiency.
Temporal optical besselon waves for high-repetition rate picosecond sources
Authors: Sheveleva Anastasiia , Andral Ugo , Kibler Bertrand , Boscolo Sonia , Finot Christophe
Published: January 2021

We analyse the temporal properties of the optical pulse wave that is obtained by applying a discrete set of spectral π/2 phase shifts to continuous-wave light that is phase-modulated by a temporal sinusoidal wave. We develop an analytical model to describe this new optical waveform that we name ‘besselon’. We also discuss the reduction of sidelobes in the pulse intensity profiles by means of an additional spectral π phase shift, and show that the resulting pulses can be efficiently time-interleaved. The various predicted properties of the besselon are confirmed by experiments demonstrating the generation of low duty cycle, high-quality pulses at repetition rates up to 28 GHz.
Repetitive heating performance of MgO-activated ground granulated blast furnace slag composites containing MWCNTs
Authors: Bang Jinho , Park Hyeong Min , Yang Beomjoo
Published: January 2021

Recently, various studies have been conducted in an effort to apply the outstanding properties of nanomaterials to construction fields. The present study aims to investigate the repetitive heating characteristics of magnesium oxide (MgO)-activated slag composites containing multi-walled carbon nanotubes (MWCNTs). MgO-activated slag composites with various mix proportions were fabricated through facile mechanical mixing method and cured at various temperatures. The electrical resistivity and compressive strength of the specimens were measured, and the cyclical heating performance was also analyzed under a constant ampere condition. Microstructural and thermal analyses of the MgO-activated slag composites were carried out by means of a scanning electron microscope and a thermogravimetry analysis, respectively. The content of MWCNTs and the curing conditions affected the overall electrical resistivity, compressive strength, and heat-generation properties of the composites. Here, related mechanisms are addressed in connection with the hydration process of the binder material.
A comprehensive review of aluminium matrix composite reinforcement and fabrication methodologies
Authors: Singh Hartaj , Singh Kapil , Vardhan Sachit , Mohan Sanjay , Singh Vishal
Published: January 2021

Aluminium-based composites are extensively employed for high-performance applications in the automotive and aircraft industries on the basis of their superior mechanical characteristics comprising light weight, high specific strength and excellent malleability. Different metals and alloys are fabricated as composites using various combinations of materials with various fabrication methods. The current article explores a detailed overview of the methodologies, including solid, semi-solid, liquid and vapour routes, adopted by many researchers for the synthesis of reinforced aluminium-based materials. The influence of reinforcement in terms of natural resources and industrial waste considered recently is briefly discussed. Based on the literature review, research work has also focused on exploring the most economical and frequently employed synthesis methods for the fabrication of aluminium matrix composites.
Study of designable coefficient of thermal expansion in cellular structures
Authors: Ning Wang , Deng Qingtian , Zhichun Yang , Xinbo Li
Published: January 2021

In this work, a model of cellular structures in thermal fields has been established based on methods of material mechanics, structural mechanics and thermodynamics. Cellular structures have different deformation behaviors in thermal environment with different coefficients of thermal expansion (CTE), the desirable equivalent coefficient of thermal expansion (ECTE) of cellular structures can be achieved by introduce members with different CTEs. Three different configurations are proposed to study the relationship between ECTE and geometrical configuration. The results show that: desirable ECTE can be obtained by designing configuration shape of cellular structures, inclined angle of members and positions of different CTE materials.
Recent progress and applications of gold nanotechnology in medical biophysics using artificial intelligence and mathematical modeling
Authors: Moore Julia A , Chow James C L
Published: January 2021

In this topical review, we will explore and challenge how artificial intelligence (AI) and mathematical modeling apply towards the future in medical applications, focusing on their interactions with gold nanotechnology. There have been rapid advancements towards the applications of AI and mathematical modeling in medical biophysics. These specific techniques help to improve studies related to nanoscale technology. Many works have been published in relation to this topic; it is now time to collectively analyze and review them to assess the contributions these applications made within nanotechnology. Through this review, both theoretical and clinical data is examined for a fresh and present-day understanding. Observations of set parameters and defined equations through AI and mathematical modeling are made to help give explanation towards variable interaction. This review focuses on gold nanoparticle synthesis and preparation via the Turkevich and Brust and Schiffrins one-pot method. From this, findings show that gold nanoparticle size, shape, and overall functionality affect its synthetic properties. Depending on the characteristics within the gold nanoparticle, its ability to maximize light absorbency, wavelengths, and optical densities within the particle is limited. Finding an ideal wavelength (dependent on nanoparticle sizing) allows for higher absorbency of light within the nanoparticle itself. Examining the cellular uptake and cytotoxicity within the nanoparticle is done so via transmission electron microscope (TEM) and Fourier transform infrared radiation (FT-IR) spectroscopy. By manipulating AI and stochastic and diagnostic models, nanoparticle efficiency within precision cancer therapy is set to ensure maximal treatment. Set conditions allow ideal tumor treatment planning, where manipulated nano-probes are used in gold nanoparticle-based therapy. Versatility in nanoparticle sensors allow for multimodal imaging and assistance towards further diagnostic and therapeutic imaging practices. Drawn conclusions will help expand further knowledge and growth for future gold nanoparticle technology research in medical biophysics application using AI and mathematical modeling.
Optimal control for the infinity obstacle problem
Authors: Mawi Henok , Ndiaye Cheikh
Published: January 2021

In this note, we show that a natural optimal control problem for the

∞
\infty

-obstacle problem admits an optimal control which is also an optimal state. Moreover, we show the convergence of the minimal value of an optimal control problem for the

p
p

-obstacle problem to the minimal value of our optimal control problem for the

∞
\infty

-obstacle problem, as

p
→
∞

p\to \infty

.
Your Hair or Your Service: An Issue of Faith for Sikh Healthcare Professionals During the COVID-19 Pandemic
Authors: Singh Rajinder , Grewal Bhajneek
Published: January 2021

Sikh healthcare professionals make up a small but significant proportion of the workforce in the United Kingdom. The COVID-19 pandemic has presented healthcare staff across the country with challenges relating to safe clinical practice whilst wearing personal protective equipment (PPE). Practising Sikhs are mandated to keep their hair unshorn and have been negatively impacted by some standard PPE requirements. This article aims to raise awareness of this issue and provide suggestions on how this conflict can be resolved.
Synthesis of (+)-solenopsin via Pd-catalyzed N-alkylation and cyclization
Authors: Suzuki Kana , Hattori Yasunao , Kawamura Atsushi , Makabe Hidefumi
Published: January 2021

Synthesis of (+)-solenopsin, a 2,6-disubstituted piperidine alkaloid, isolated from fire ants (Solenopsis), was achieved. Stereoselective construction of trans-2,6-piperidine ring moiety was performed using palladium-catalyzed cyclization. Chain elongation using Grubbs 2nd catalyst followed by the reduction of double bond and the deprotection of the Cbz group afforded (+)-solenopsin.
Liver choline metabolism and gene expression in choline-deficient mice offspring differ with gender
Authors: Miyachi Yukino , Akiyama Kei , Tsukuda Yoshiko , Kumrungsee Thanutchaporn , Yanaka Noriyuki
Published: January 2021

Choline is an important nutrient during pregnancy and lactation. Maternal choline deficiency in CD-1 mice lowers liver betaine levels in male offspring. By contrast, it increases elovl3 and vanin-1 mRNA levels in female offspring. Taken together, these observations suggest gender-specific responses to a choline-deficient diet.
Advances in bulk and single-cell multi-omics approaches for systems biology and precision medicine
Authors: Li Yunjin , Ma Lu , Wu Duojiao , Chen Geng
Published: January 2021

Multi-omics allows the systematic understanding of the information flow across different omics layers, while single omics can mainly reflect one aspect of the biological system. The advancement of bulk and single-cell sequencing technologies and related computational methods for multi-omics largely facilitated the development of system biology and precision medicine. Single-cell approaches have the advantage of dissecting cellular dynamics and heterogeneity, whereas traditional bulk technologies are limited to individual/population-level investigation. In this review, we first summarize the technologies for producing bulk and single-cell multi-omics data. Then, we survey the computational approaches for integrative analysis of bulk and single-cell multimodal data, respectively. Moreover, the databases and data storage for multi-omics, as well as the tools for visualizing multimodal data are summarized. We also outline the integration between bulk and single-cell data, and discuss the applications of multi-omics in precision medicine. Finally, we present the challenges and perspectives for multi-omics development.
Current status and future perspectives of computational studies on human–virus protein–protein interactions
Authors: Lian Xianyi , Yang Xiaodi , Yang Shiping , Zhang Ziding
Published: January 2021

The protein–protein interactions (PPIs) between human and viruses mediate viral infection and host immunity processes. Therefore, the study of human–virus PPIs can help us understand the principles of human–virus relationships and can thus guide the development of highly effective drugs to break the transmission of viral infectious diseases. Recent years have witnessed the rapid accumulation of experimentally identified human–virus PPI data, which provides an unprecedented opportunity for bioinformatics studies revolving around human–virus PPIs. In this article, we provide a comprehensive overview of computational studies on human–virus PPIs, especially focusing on the method development for human–virus PPI predictions. We briefly introduce the experimental detection methods and existing database resources of human–virus PPIs, and then discuss the research progress in the development of computational prediction methods. In particular, we elaborate the machine learning-based prediction methods and highlight the need to embrace state-of-the-art deep-learning algorithms and new feature engineering techniques (e.g. the protein embedding technique derived from natural language processing). To further advance the understanding in this research topic, we also outline the practical applications of the human–virus interactome in fundamental biological discovery and new antiviral therapy development.
Robust gene coexpression networks using signed distance correlation
Authors: Pardo-Diaz Javier , Bozhilova Lyuba V , Beguerisse-Díaz Mariano , Poole Philip S , Deane Charlotte M , Reinert Gesine
Published: January 2021

Motivation

Even within well-studied organisms, many genes lack useful functional annotations. One way to generate such functional information is to infer biological relationships between genes/proteins, using a network of gene coexpression data that includes functional annotations. However, the lack of trustworthy functional annotations can impede the validation of such networks. Hence, there is a need for a principled method to construct gene coexpression networks that capture biological information and are structurally stable even in the absence of functional information.

Results

We introduce the concept of signed distance correlation as a measure of dependency between two variables, and apply it to generate gene coexpression networks. Distance correlation offers a more intuitive approach to network construction than commonly used methods, such as Pearson correlation and mutual information. We propose a framework to generate self-consistent networks using signed distance correlation purely from gene expression data, with no additional information. We analyse data from three different organisms to illustrate how networks generated with our method are more stable and capture more biological information compared to networks obtained from Pearson correlation or mutual information.

Availability and implementation

Code is available online (https://github.com/javier-pardodiaz/sdcorGCN).

Supplementary information

Supplementary data are available at Bioinformatics online.
A gene-level methylome-wide association analysis identifies novel Alzheimer’s disease genes
Authors: Wu Chong , Bradley Jonathan , Li Yanming , Wu Lang , Deng Hong-Wen
Published: January 2021

Motivation

Transcriptome-wide association studies (TWAS) have successfully facilitated the discovery of novel genetic risk loci for many complex traits, including late-onset Alzheimer’s disease (AD). However, most existing TWAS methods rely only on gene expression and ignore epigenetic modification (i.e. DNA methylation) and functional regulatory information (i.e. enhancer-promoter interactions), both of which contribute significantly to the genetic basis of AD.

Results

We develop a novel gene-level association testing method that integrates genetically regulated DNA methylation and enhancer–target gene pairs with genome-wide association study (GWAS) summary results. Through simulations, we show that our approach, referred to as the CMO (cross methylome omnibus) test, yielded well controlled type I error rates and achieved much higher statistical power than competing methods under a wide range of scenarios. Furthermore, compared with TWAS, CMO identified an average of 124% more associations when analyzing several brain imaging-related GWAS results. By analyzing to date the largest AD GWAS of 71 880 cases and 383 378 controls, CMO identified six novel loci for AD, which have been ignored by competing methods.

Availabilityand implementation

The data used in this work were obtained from the following publicly available datasets: IGAP1, GWAX, UK Biobank, a 2019 meta-analyzed AD GWAS results and a imaging-derived phenotype GWAS results. The data resources are summarized in Supplementary Table S7. We used the publicly available software and tools for competing methods. All codes used to generate results that are reported in this manuscript and software for our newly proposed method CMO are available at https://github.com/ChongWuLab/CMO.

Supplementary information

Supplementary data are available at Bioinformatics online.
Intrapartum Antibiotic Exposure and Body Mass Index in Children
Authors: Koebnick Corinna , Sidell Margo A , Getahun Darios , Tartof Sara Y , Rozema Emily , Taylor Brianna , Xiang Anny H , Spiller Michael W , Sharma Andrea J , Mukhopadhyay Sagori , Puopolo Karen M , Schrag Stephanie J
Published: January 2021

Background

Intrapartum antibiotic prophylaxis (IAP) reduces a newborn’s risk of group B streptococcal infection (GBS) but may lead to an increased childhood body mass index (BMI).

Methods

This was a retrospective cohort study of infants (n = 223 431) born 2007–2015 in an integrated healthcare system. For vaginal delivery, we compared children exposed to GBS-IAP and to any other type or duration of intrapartum antibiotics to no antibiotic exposure. For cesarean delivery, we compared children exposed to GBS-IAP to those exposed to all other intrapartum antibiotics, including surgical prophylaxis. BMI over 5 years was compared using nonlinear multivariate models with B-spline functions, stratified by delivery mode and adjusted for demographics, maternal factors, breastfeeding, and childhood antibiotic exposure.

Results

In vaginal deliveries, GBS-IAP was associated with higher BMI from 0.5 to 5.0 years of age compared to no antibiotics (P < .0001 for all time points, ΔBMI at age 5 years 0.12 kg/m2, 95% confidence interval [CI]: .07–.16 kg/m2). Other antibiotics were associated with higher BMI from 0.3 to 5.0 years of age. In cesarean deliveries, GBS-IAP was associated with increased BMI from 0.7 years to 5.0 years of age (P < .05 for 0.7–0.8 years, P < .0001 for all other time points) compared to other antibiotics (ΔBMI at age 5 years 0.24 kg/m2, 95% CI: .14–.34 kg/m2). Breastfeeding did not modify these associations.

Conclusions

GBS-IAP was associated with a small but sustained increase in BMI starting at very early age. This association highlights the need to better understand the effects of perinatal antibiotic exposure on childhood health.
Assessment of US Healthcare Personnel Attitudes Towards Coronavirus Disease 2019 (COVID-19) Vaccination in a Large University Healthcare System
Authors: Shaw Jana , Stewart Telisa , Anderson Kathryn B , Hanley Samantha , Thomas Stephen J , Salmon Daniel A , Morley Christopher
Published: January 2021

Background

As a priority group, healthcare personnel (HCP) will be key to the success of coronavirus disease 2019 (COVID-19) vaccination programs. This study assessed HCP willingness to get vaccinated and identified specific concerns that would undermine vaccination efforts.

Methods

We conducted a cross-sectional survey of HCP, including clinical and nonclinical staff, researchers, and trainees, between 23 November and 5 December 2020. The survey evaluated attitudes, beliefs, and willingness to get vaccinated.

Results

There were 5287 respondents with a mean (SD) age of 42.5 (13.56) years; 72.8% were female (n = 3842). Overall, 57.5 % of individuals expressed intent to receive COVID-19 vaccine; 80.4% were physicians and scientists representing the largest group. 33.6% of registered nurses, 31.6% of allied health professionals, and 32% of master’s level clinicians were unsure they would take the vaccine (P < .001). Respondents who were older, male, White, or Asian were more likely to get vaccinated than other groups. Vaccine safety, potential adverse events, efficacy, and speed of vaccine development dominated concerns listed by participants. Fewer (54.0%) providers of direct care versus non–care providers (62.4%) and 52.0% of those who had provided care for COVID-19 patients (vs 60.6% of those who had not) indicated they would take the vaccine if offered (P < .001).

Conclusions

We observed that self-reported willingness to receive vaccination against COVID-19 differs by hospital roles, with physicians and research scientists showing the highest acceptance. These findings highlight important heterogeneity in personal attitudes among HCPs around COVID-19 vaccines and highlight a need for tailored communication strategies.
Building pan-genome infrastructures for crop plants and their use in association genetics
Authors: Jayakodi Murukarthick , Schreiber Mona , Stein Nils , Mascher Martin
Published: January 2021

Pan-genomic studies aim at representing the entire sequence diversity within a species to provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Cost reductions in high-throughput sequencing and advances in sequence assembly algorithms have made it possible to create multiple reference genomes along with a catalogue of all forms of genetic variations in plant species with large and complex or polyploid genomes. In this review, we summarize the current approaches to building pan-genomes as an in silico representation of plant sequence diversity and outline relevant methods for their effective utilization in linking structural with phenotypic variation. We propose as future research avenues (i) transcriptomic and epigenomic studies across multiple reference genomes and (ii) the development of user-friendly and feature-rich pan-genome browsers.
Morbidity and mortality of lung resection candidates defined by the American College of Chest Physicians as ‘moderate risk’: an analysis from the European Society of Thoracic Surgeons database
Authors: Gooseman Michael Richard , Falcoz Pierre-Emmanuel , Decaluwe Herbert , Szanto Zalan , Brunelli Alessandro
Published: January 2021

OBJECTIVES

The American College of Chest Physicians functional guidelines classify patients with predicted postoperative forced expiratory volume in 1 s or predicted postoperative carbon monoxide lung diffusion capacity <60% and with maximal oxygen consumption (VO2max) between 10 and 20 ml/kg/min in a heterogeneous category broadly defined as ‘moderate risk’ with variable morbidity and mortality. Data to support this statement are lacking. Using the European Society of Thoracic Surgeons database, our goal was to test this definition by evaluating the morbidity and mortality of those patients falling into this class.

METHODS

All patients who had anatomical lung resection for lung cancer (2007–2019) and were deemed of moderate risk were identified in the European Society of Thoracic Surgeons database. Cardiopulmonary morbidity and 30-day mortality of these patients were assessed by the type of operation.

RESULTS

A total 2016 patients were identified. The incidence of cardiopulmonary complications in this group was 21% after lobectomy (294/1435), 29% after bilobectomy (33/112), 22% after pneumonectomy (72/333) and 16% after segmentectomy (22/136) (analysis of variance P = 0.07). The 30-day mortality was 3.4% after lobectomy (49/1435), 8.9% after bilobectomy (10/112), 7.8% after pneumonectomy (26/333) and 3.7% after segmentectomy (5/136) (analysis of variance P = 0.0005). The 30-day mortality rate was 1.6-fold higher in patients with a VO2max between 10 and 15 ml/kg/min compared to those with a higher VO2max [49/861 (5.7%) vs 41/1155 (3.5%); P = 0.022]. For operations that were less extensive than a pneumonectomy and were performed by minimally invasive surgery, there was no difference in mortality between patients with a VO2max between 10 and 15 ml/kg/min and those with a higher VO2max [7/181 (3.8%) vs 11/272 (4.0%); P = 0.92]. On the other hand, after open surgery, the mortality of patients with a lower VO2max (10–15 ml/kg/min) was higher than that of those with a higher VO2max [26/501 (5.1%) vs 20/721 (2.8%); P = 0.034]. Linear regression adjusting for the extent and access of the operation confirmed that within the moderate-risk group a VO2max <15 ml/kg/min was associated with higher mortality (P = 0.028; odds ratio 1.61; 95% confidence interval 1.1–2.5).

CONCLUSIONS

Morbidity and mortality rates found in this study are not negligible and reinforce the recommendation to ensure careful patient discussion and informed decision-making prior to lung cancer resection surgery.
Age-related tilt test responses in patients with suspected reflex syncope
Authors: Rivasi Giulia , Torabi Parisa , Secco Gianmarco , Ungar Andrea , Sutton Richard , Brignole Michele , Fedorowski Artur
Published: January 2021

Aims

Tilt testing (TT) is recognized to be a valuable contribution to the diagnosis and the pathophysiology of vasovagal syncope (VVS). This study aimed to assess the influence of age on TT responses by examination of a large patient cohort.

Methods and results

Retrospective data from three experienced European Syncope Units were merged to include 5236 patients investigated for suspected VVS by the Italian TT protocol. Tilt testing-positivity rates and haemodynamics were analysed across age-decade subgroups. Of 5236 investigated patients, 3129 (60%) had a positive TT. Cardioinhibitory responses accounted for 16.5% of positive tests and were more common in younger patients, decreasing from the age of 50–59 years. Vasodepressor (VD) responses accounted for 24.4% of positive tests and prevailed in older patients, starting from the age of 50–59. Mixed responses (59.1% of cases) declined slightly with increasing age. Overall, TT positivity showed a similar age-related trend (P = 0.0001) and was significantly related to baseline systolic blood pressure (P < 0.001). Tilt testing was positive during passive phase in 18% and during nitroglycerine (TNG)-potentiated phase in 82% of cases. Positivity rate of passive phase declined with age (P = 0.001), whereas positivity rate during TNG remained quite stable. The prevalence of cardioinhibitory and VD responses was similar during passive and TNG-potentiated TT, when age-adjusted.

Conclusions

Age significantly impacts the haemodynamic pattern of TT responses, starting from the age of 50. Conversely, TT phase—passive or TNG-potentiated—does not significantly influence the type of response, when age-adjusted. Vagal hyperactivity dominates in younger patients, older patients show tendency to vasodepression.