bluuebunny/crossref_metadata_2025 huggingface dataset:
Editorial Preface
Authors: Jan Pahl Peter , Galishnikova Vera , Vatin Nikolai , Kharun Makhmud , Koroteev Dmitry
Published: November 2020

The present proceedings include a selection of papers submitted to the International Conference on Engineering Systems 2020 (ICES 2020), which was held during 14-16 October 2020 in the RUDN University, Moscow, Russia.

ICES 2020 was dedicated to the 60th anniversary of RUDN University. International Conference on Engineering Systems (ICES), held annually at the Peoples’ Friendship University of Russia (RUDN University), has created a platform for summarizing research in various areas of engineering. The aim of the conference is to foster and conduct collaborative interdisciplinary research amongst the researchers, professionals and industrialists to share their research experiences and indulge in interactive discussions and special sessions at the event.

In light of travel restrictions around the world to control COVID-19 pademic, ICES 2020 adopted the format of virtual conference through Google Meet network to provide a forum for experts and scholars to share real-time information and discuss the latest findings on various engineering fields. The conference included keynote speech and online discussion, and each presenter has 20–25 minutes (including Q&A).

With the full support from the International Scientific Committee, all submissions have been through rigorous review and process to meet the requirements of international publication standard. Accepted papers were presented in five sessions of the conference: 1) Fundamental Engineering, 2) Civil and Structural Engineering, 3) Mechanical Engineering, 4) Composite Materials, 5) Hydraulic and Geological Engineering. We hope that this collection will be useful for many specialists and researchers from various engineering fields.

List of Conference Chair, Conference secretary, International Scientific Committee and Guest Editors are available in this pdf.
Systems thinking ontology of emergent properties for complex engineering systems
Authors: Nikolaev M Y , Fortin C
Published: November 2020

This paper presents a developed ontology of emergent properties characterizing the emergent behavior of complex engineering systems, which is the emergence of greater functionality of the overall system compared to the sum of the functionalities of system components. The ontology is based on the systems thinking approach used in systems architecture, one of the key points to consider in the conceptual design of engineering systems and used to manage the complexity of systems. Firstly, in the paper, research attributes and the adaptation of the term “ontology” for systems thinking are given. Secondly, the coverage of analyzed literature sources in the description of the literature search is demonstrated. Thirdly, the developed ontology consisting of semantics and relationships of systems emergent properties is presented. The proposed ontology is followed by highlighting its possible systems engineering applications. Finally, in conclusion, the benefits of the developed ontology are mentioned. Overall, the current paper combines aspects of systems engineering with key elements of the design of complex systems.
Features of the stress-strain state in the corner zones of structures
Authors: Frishter L
Published: November 2020

Corner regions of structures are characterized by a complex stress-strain state (SSS), caused by both the shape of the boundary or the “geometric factor”, and the finite rupture of the specified forced deformations, mechanical properties that go to the contact surface of the elements of composite structures. The relevance of the work consists in the analysis of local SSS in the corner zone of the region boundary with various study approaches: theoretical, experimental. For the theoretical analysis of the SSS of the region, we consider the resolving system of equations of the problem of the theory of elasticity in the zone of the cutout of the boundary and elements of the similarity theory; the photoelasticity method is used for experimental studies. An experimental solution was obtained on polymer composite models with an angle cut of the boundary under the action of forced deformations in one of the regions. The analysis of possibilities of theoretical, experimental approaches of SSS studies in zones with irregular point of border allows to reveal zones of applicability of solutions of linear elasticity problem.
Planning of an experimental research of the organization of townhouses’ construction
Authors: Svintsov A P , Abd Noor A A
Published: November 2020

One of the most important ways in improving the research’s efficiency is an experiment’s planning. The aim of the study is to identify and study various factors that can affect the productivity of brick layers during bricklaying of townhouses in Iraq. Visual observation, timing and photographs of the working day were carried out during eight working weeks. In the process of daily monitoring, causal relationships of the formation of downtime and overtime work of bricklayers were identified. The most significant factors are untimely delivery of materials and alteration of performed work. The data obtained are the basis for the development of a mathematical model of labor productivity indicators. An analysis of the data on the functioning of the construction technological system for erecting brick walls of buildings shows that its states can be modeled by regular Markov processes. The data obtained are the basis for the development of a mathematical model of labor productivity indicators.
Properties of metallic materials near the edges of fatigue crack
Authors: Kornilova A V , Zaya Kyaw , Paing Thet , Dobrolyubova M F
Published: November 2020

This paper discusses the condition in the magnetic and mechanical properties of metal materials near the edges of a fatigue crack (samples example – steel20). On the special samples with straight fatigue cracks, the coercive force and hardness were measured near the crack edges. The coercive force drop on the crack was 25%. Therefore, if the magnetic properties of ferromagnetic material fall during the survey, this means that there is a crack in the structure being examined, which is not always detected visually or by non-destructive testing methods with a different physical basis. The obtained results of hardness measurements allowed us to formalize the dependence of the straight crack depth on the drop in hardness near its edges relative to the same parameter in the defect-free section. By calculating and experimentally, the relationship angle between normal and the tangent to the surface of crack inclinationswas identified and formalized. The results of the work can be used in the technical diagnostics of engineering objects.
Synthesis of core-shell Al/Al2O3 composite through aluminum powder oxidation in hot water and its characterization
Authors: Ambaryan G N , Vlaskin M S , Shkolnikov E I , Zhuk A Z
Published: November 2020

Simple and potentially energy efficient way for synthesis of Al/Al2O3 composites is described. Synthesis method is based on aluminum powder oxidation in water at 100-200 °C and following drying and calcination at 600 °C. Aluminum powder with average size of about 40 urn that is currently applied in additive manufacturing was used. Present work was devoted to the study of oxidation degree of aluminum and so the propagation depth and structure of Al2O3 shell in composite’s matrix. AI/Al2O3 composites were produced in different regimes with different maximum temperature and duration of the process of aluminium oxidation in water. Aluminum oxidation degree and aluminium content in obtained Al/Al2O3 were changed in the range from 5.5 % and 90.1 % to 21.3 % and 66.2 % respectively. The size of single crystals of Al2O3 in shell was changed from about 6 nm to 200 nm and the thickness of Al2O3 shell was changed from about 400 nm to 1000 nm by changing the regime for Al/Al2O3 composite production. Experimental results showed that Al2O3 shell was well clutched with aluminum core. Shell structure had cracks aroused by calcination process. Size distribution for obtained composites was very close for that of initial aluminum powder. All of these characteristics recommend the obtained Al/Al2O3 composites for additive manufacturing.
Effect of high pressure processing in the formation of castings of aluminum alloys
Authors: Batyshev K A , Yu Malkova M , Zadiranov A N , Zaya Kyaw
Published: November 2020

The effect of high pressure on the formation conditions of aluminum castings has been investigated. It was established experimentally that the crystallization of castings under high mechanical pressure proceeds at a higher temperature difference across the cross section than at atmospheric pressure. The cooling rate of a cylindrical casting in various zones on the section, which is characteristic for cooling alloy in the crystallization range, is determined. The formula for calculating the solidification time of a casting and the time of its holding pressure during piston compression is recommended. The influence of the scale factor on the solidification time of cylindrical castings is considered. It is shown that with increasing height at a constant diameter of the casting, the relationship between the solidification time and diameter of the casting is linear. It has been experimentally established that the solidification coefficient of an alloy depends on its thermophysical properties of the alloy and the applied pressure. Its value increases with decreasing silicon content in the alloy and increasing pressure. The pressure significantly reduces the difference in the values of the solidification coefficient of castings from alloys of different compositions.
Monolayer MoS2 on sapphire: an azimuthal reflection high-energy electron diffraction perspective
Authors: Xiang Yu , Sun Xin , Valdman Lukas , Zhang Fu , Choudhury Tanushree H , Chubarov Mikhail , Robinson Joshua A , Redwing Joan M , Terrones Mauricio , Ma Yuan , Gao Lei , Washington Morris A , Lu Toh-Ming , Wang Gwo-Ching
Published: November 2020

Molybdenum disulfide (MoS2) on the c-plane sapphire has been a very popular system to study in the two-dimensional (2D) materials community. Bottom-up synthesis of monolayer (ML) MoS2 with excellent electrical properties has been achieved on sapphire by various methods, making it a very promising candidate to be used in the next generation nano-electronic devices. However, large-area ML MoS2 with comparable quality as the relatively small size exfoliated ML remains quite a challenge. To overcome this bottle neck, a comprehensive understanding of the structure of the as-grown ML material is an essential first step. Here, we report a detailed structural characterization of wafer-scale continuous epitaxial ML MoS2 grown by metalorganic chemical vapor deposition on sapphire using an azimuthal reflection high-energy electron diffraction (ARHEED) technique. With ARHEED we can map not only 2D but also 3D reciprocal space structure of the ML statistically. From the oscillation in the ARHEED intensity profile along the vertical direction of the ML, we derived a real space distance of ~3 Å at the interface of ML and sapphire. Quantitative diffraction spot broadening analyses of the 3D reciprocal space map reveals low density defects and a small angular misalignment of orientation domains in ML MoS2. Based on atomic force microscopy height distribution analysis, cross-section scanning transmission electron microscopy, and density functional theory calculations, we suggest that there exists a passivation layer between MoS2 ML and sapphire substrate. This ARHEED methodology also has been applied to ML WS2 and is expected to be applicable to other ML transition metal dichalcogenides on arbitrary crystalline or non-crystalline substrates.
Study on precipitates in AgGaSe2 single crystal grown by vertical gradient freezing method
Authors: Yang Deng-Hui , Cao Xin-Ling , Yang Ling , Zhou Yong-Ling
Published: November 2020

In this study, AgGaSe2 single crystal was successful grown by vertical gradient freezing method. Meanwhile, the precipitates on AgGaSe2 single crystal were investigated by x-ray photoelectron spectroscopy (XPS). This technique was recommended as a practicable method to study the precipitates while they are difficult to be detected by other measurements owing to their components and fairly low content. In addition, Energy Disperse Spectroscopy (EDS) and x-ray diffraction (XRD) were employed to characterize the quality of the as-grown AgGaSe2 single crystal. The EDS results indicate a slight deviation from stoichiometric ratio along growth defects. The XRD results manifest that AgGaSe2 crystal has single phase and high purity. The XPS results indicate that precipitates exist on as-grown AgGaSe2 single crystal mainly in the form of Ga2Se3. Ga2O3 and Ag2O were detected by XPS on the polished surface of the as-grown crystal wafer which was regarded as an oxide layer. The study on precipitates may provide important reference for growth process improvement and post-treatment to obtain high quality AgGaSe2 single crystal.
Adsorptive defluoridation from aqueous solution using a novel blend of eggshell powder and chitosan nanofibers
Authors: Abbasi Aamir , Memon Sheeraz Ahmed , Qureshi Raja Fahad , Mehdi Mujahid , Khatri Muzamil , Ahmed Farooq , Khatri Zeeshan , Kim Ick Soo
Published: November 2020

Groundwater mostly contains many impurities thus can not be consumed as drinking water directly. The acceptable limit of fluoride in drinking water is 0.5–1.5 mg l−1 recommended by World Health Organization (WHO). In this research, a novel nanofiber hybrid; based on Chitosan (CTS) and Eggshell (EGG) was prepared via electrospinning technique and investigated for deflouridation from aqueous solution. SEM images reveal bead-free, smooth morphology and the FTIR confirmed the presence of chitosan and egg within the novel nanofiber blend. The defluoridation efficiency was assessed by varying the different parameters like pH, mass of nanofibers, contact time and initial concentration for adsorption. Studies revealed that CTS/EGG nanofibers hybrid shows incredible adsorption efficiency of 86%. Furthermore, isotherm studies show that the Langmuir isotherm model was well fitted for both CTS and CTS/EGG nanofibers.
Effect of Sn addition on the microstructure and mechanical properties of AZ31 alloys
Authors: Ma Jiaxuan , Wei Qi , Le Taihe , Wang Jinhui , Jin Peipeng
Published: November 2020

An Mg-3Al-1Zn-xSn (x = 0, 3, 6, 9) alloy was prepared by die-casting and analyzed by XRD, SEM, and EBSD. The microstructure, second phase, and grain orientation of the AZT31x alloy were characterized. As the Sn content increased from 3 wt.% to 9 wt.%, the tensile and yield strength of the alloy were effectively improved. With the addition of Sn, the grain size of alloys decreases gradually blocking the dislocation by the grain boundary and the dispersion of the Mg2Sn second phase in the AZT31x(x = 3, 6, 9) alloys contributes to the strength via grain boundary pinning. According to theoretical analysis and calculation, the high strength of AZT319 alloy is partly attributed to the grain fine strengthening

σ

H

P

=
13.76

Mpa

) and second phase strengthening

Δ
σ
=
9.27
∼
12.67

MPa

.

The total increased strengthening value is lower than experimental value (

Δ
σ
=
31.82

MPa

). The ratio about

τ

p
r
i
s
m

/

τ

b
a
s
a
l

and

τ

c
+
a

/

τ

b
a
s
a
l

in die-cast alloys tensioned to 0.08 deformation gradually decrease, which can reflect that high-Sn content contributes to the strain hardening behavior. The ductility of AZT313 alloy was lightly improved due to the {10-12} tensile twins. When excessive Sn was added, the Mg2Sn second phase coarsened and acted as the nucleus of micro-cracks during the stretching process, thereby reducing the ductility of the alloy.
Study of gadolinium aluminate nanoparticles with perovskite structure prepared by citric acid chelation method
Authors: Dai Shiyu , Wang Gang , Qi Pengyuan , Xu Xiaochen , Jiang Lili , Zhong Jingyu , Yuan Shuo , Wang Lei
Published: November 2020

Gadolinium aluminate (GdAlO3, GAP) is a rare earth compound with perovskite structure. Its optical isotropic structure prevents the defects of refractive index difference in any direction. GAP has unique and excellent properties in electricity, magnetism, luminescence and catalysis, especially as a high-quality luminescent matrix material. Sol-gel method has the advantages of accurate control of chemical composition, particle size and purity of products. The main preparation parameters include chelating agent concentration, alcohol water ratio, calcination temperature and so on. In this paper, the citric acid chelating agent was used to prepare gadolinium aluminate nanoparticles by sol-gel method, thermogravimetry-differential thermal analysis (TG-DTA), x-ray diffraction (XRD) and scanning electron microscope (SEM) were employed to analyze the effects of chelating agent, dispersant, solvent and calcination temperature on the phase and morphology changing in precursor and final product. The results show that GAP nanoparticles with high degree of crystallinity, nearly spherical morphology and 60–100 nm particle size can be obtained at the molar ratio of citric acid to cationic of 1:1, the ammonium citrate to citric acid of 1.5:1 and the calcination temperature of 900 °C for 4 h. When the calcination temperature is higher than 1100 °C, a new phase of Gd3Al5O12 (GdAG) will be formed with calcination neck shape.
Percolative magnetic correlation and competing-antiferromagnetism in highly oriented pyrolytic graphite with hexagonal Moiré superlattices at the magic-angle
Authors: Boi Filippo S , Gao Shuai , He Yi , Wang Shanling
Published: November 2020

Occurrence of magnetic-correlation-phenomena in multi-layered carbon-materials has recently attracted an important attention for applications in magnetic devices and spintronics. In this study, exfoliated highly-oriented-pyrolytic-graphite (HOPG) lamellae exhibiting hexagonal-Moiré-superlattices, with periodicity of ∼13 nm (1st category, θ
rot ∼ 1.09° ) and ∼36 nm (2nd category, θ
rot ∼ 0.39°) were investigated. Raman-spectroscopy evidenced weak D, D’ and intense G bands. In 1st category, magnetization versus field, ZFC- FC magnetic-curves from 2 K to 300 K and T-ESR revealed presence of uncorrelated and correlated ferromagnetic clusters at T* ∼ 150 K together with a critical transition at Tc ∼ 50 K, compatible with percolative-ferromagnetic-correlation. Comparative measurements on the 2nd category, revealed an analogue trend, with at T* ∼ 50–60 K together with an irreversibility at Tc ∼ 40 K, indicative of competing ferromagnetic/antiferromagnetic-correlations.
Boron doping in gallium oxide from first principles
Authors: Lehtomäki Jouko , Li Jingrui , Rinke Patrick
Published: November 2020

We study the feasibility of boron doping in gallium oxide (Ga2O3) for neutron detection. Ga2O3 is a wide band gap, radiation-hard material with potential for neutron detection, if it can be doped with a neutron active element. We investigate the boron-10 isotope as possible neutron active dopant. Intrinsic and boron induced defects in Ga2O3 are studied with semi-local and hybrid density-functional-theory calculations. We find that it is possible to introduce boron into gallium sites at moderate concentrations. High concentrations of boron, however, compete with the boron-oxide formation.
High-fidelity imaging through multimode fibers via deep learning
Authors: Zhao Jun , Ji Xuanxuan , Zhang Minghai , Wang Xiaoyan , Chen Ziyang , Zhang Yanzhu , Pu Jixiong
Published: November 2020

Imaging through multimode fibers (MMFs) is a challenging task. Some approaches, e.g. transmission matrix or digital phase conjugation, have been developed to realize imaging through MMF. However, all these approaches seem sensitive to the external environment and the condition of MMF, such as the bent condition and the movement of the MMF. In this paper, we experimentally demonstrate the high-fidelity imaging through a bent MMF by the conventional neural network (CNN). Two methods (accuracy and Pearson correlation coefficient) are employed to evaluate the reconstructed image fidelity. We focus on studying the influence of MMF conditions on the reconstructed image fidelity, in which MMF for imaging is curled to different diameters. It is found that as an object passes through a small bent diameter of the MMF, the information of the object may loss, resulting in little decrease of the reconstructed image fidelity. We show that even if MMF is curled to a very small diameter (e.g. 5 cm), the reconstructed image fidelity is still good. This novel imaging systems may find applications in endoscopy, etc.
Effect of camera position on egocentric localisation with Simulated Prosthetic Vision
Authors: Prabhu Deepa , Wise Lisa , MacMahon Clare , De Man Marten , Petoe Matthew , McCarthy Chris
Published: November 2020

Objective: The positioning of the external camera in current designs of retinal prostheses may affect the egocentric spatial frame of reference and lead to pointing and localisation errors. The present simulated prosthetic vision (SPV) study investigated the immediate effects of four camera positions: (i) centre-mounted (CM), (ii) head-mounted (HM), (iii) left-mounted (LM), (iv) right-mounted (RM) on egocentric localisation. Approach: Fifteen sighted participants performed a pointing task while viewing the stimulus through a simulation of Bionic Vision Technologies’ 44-channel retinal prosthesis. Pointing responses were recorded immediately after exposure to different camera positions and prior to adaptation. The direction and magnitude of pointing errors and associated head movement behaviour were analysed using linear mixed effects analysis. Main results: Our results showed lower errors for medial camera positions (CM and HM) and overall improved accuracy and precision for CM position. Head orientation was found to largely influence the direction of pointing. There was a high positive correlation between direction of head orientation and direction of pointing with CM and HM camera positions, suggesting medial camera positions facilitated intuitive head orientation cues that are important for reliable egocentric direction estimation. Significance: The empirical evidence derived from the present SPV study offers practical guidance to reduce the effect on spatial dissociation of camera position in localisation tasks and inform design of future prosthetic vision devices and improve rehabilitation approaches.
An XFEM-based computational homogenization framework for thermal conductivity evaluation of composites with imperfectly bonded inclusions
Authors: Erkmen E , Malek S , Ayranci C
Published: November 2020

In many engineering applications, such as thermal coating and structural insulation, 2D modelling is deemed sufficient to identify design parameters. For the effective thermal conductivity evaluation of heterogeneous composites, a 2D computational homogenization procedure is developed in this study. The inclusions are distributed randomly within the plane. The boundary conditions tested for homogenization procedure introduced include the periodic temperature, uniform temperature, and uniform flux boundary conditions. The bond between the inclusions and the surrounding matrix is assumed imperfect allowing partial heat transfer at the interface. Randomly distributed inclusions can be introduced without altering the underlying regular mesh of the matrix by using the XFEM, providing an efficient way of introducing the inclusions. Implementation details of the proposed computational homogenization scheme based on the XFEM are provided. The results are validated by comparisons with available analytical solutions. Effect of assumed boundary conditions on the results are shown. Parametric studies illustrate the influence of the interface properties, volume ratio of inclusions as well as the distributions of the inclusions on the effective thermal conductivity of composites.
Emerging antibody-based therapeutics against SARS-CoV-2 during the global pandemic
Authors: Sun Yaping , Ho Mitchell
Published: November 2020

SARS-CoV-2 antibody therapeutics are being evaluated in clinical and preclinical stages. As of 11 October 2020, 13 human monoclonal antibodies targeting the SARS-CoV-2 spike protein have entered clinical trials with three (REGN-COV2, LY3819253/LY-CoV555, and VIR-7831/VIR-7832) in phase 3. On 9 November 2020, the US Food and Drug Administration issued an emergency use authorization for bamlanivimab (LY3819253/LY-CoV555) for the treatment of mild-to-moderate COVID-19. This review outlines the development of neutralizing antibodies against SARS-CoV-2, with a focus on discussing various antibody discovery strategies (animal immunization, phage display and B cell cloning), describing binding epitopes and comparing neutralizing activities. Broad-neutralizing antibodies targeting the spike proteins of SARS-CoV-2 and SARS-CoV might be helpful for treating COVID-19 and future infections. VIR-7831/7832 based on S309 is the only antibody in late clinical development, which can neutralize both SARS-CoV-2 and SARS-CoV although it does not directly block virus receptor binding. Thus far, the only cross-neutralizing antibody that is also a receptor binding blocker is nanobody VHH-72. The feasibility of developing nanobodies as inhaled drugs for treating COVID-19 and other respiratory diseases is an attractive idea that is worth exploring and testing. A cocktail strategy such as REGN-COV2, or engineered multivalent and multispecific molecules, combining two or more antibodies might improve the efficacy and protect against resistance due to virus escape mutants. Besides the receptor-binding domain, other viral antigens such as the S2 subunit of the spike protein and the viral attachment sites such as heparan sulfate proteoglycans that are on the host cells are worth investigating.
Reduced Remodeling Biomarkers Tissue Expression in Nanotextured Compared With Polyurethane Implants Capsules: A Study in Rats
Authors: Pontes Gisela Hobson , Carneiro Filho Fernando Sérgio Mendes , Vargas Guerrero Luis Alejandro , Lipinski Leandro Cavalcante , de Noronha Lucia , Silva Eduardo Nascimento , Serra-Guimarães Fernando
Published: November 2020

Background

In the biological response to biomaterials, the implant shell plays a key role in immune and inflammatory reactions. We hypothesized that the capsules formed around nanotextured implants exhibit an immunohistochemical behavior different to those formed around polyurethane implants.

Objectives

The aim of this study was to evaluate through immunohistochemistry markers the capsules formed around nanotextured and polyurethane implants.

Methods

Sixty albino female Wistar rats were divided into 2 groups (nanotextured and polyurethane), with 30 animals in each group. A mini silicone implant was inserted on the back of the animals. After a predetermined period, the animals were killed, and the capsules formed around the implants were studied. The capsules in the 30-, 60-, and 90-day subgroups were analyzed via immunohistochemistry to detect markers for fibroblast α smooth muscle actin (α-SMA), transforming growth factor β (TGF-β), cluster of differentiation 34 (CD34), and CD68, via picrosirius staining to determine the density of type I and III collagen fibers and via hematoxylin and eosin staining to assess capsule thickness. A Wilcoxon-Mann-Whitney test was used to compare the groups, and a Kruskal-Wallis test was used to compare the subgroups.

Results

Lower α-SMA, TGF-β, CD34 and CD68 immunoexpression was observed in the nanotextured 30- and 60-day subgroups than in the corresponding polyurethane subgroups. In the 90-day subgroup, more pronounced α-SMA and CD34 immunoexpression was observed in the nanotextured group; however, TGF-β and CD68 immunoexpression remained lower. The nanotextured implants showed reduced capsular thickness and greater formation of type I collagen in all the analyzed subgroups.

Conclusions

Nanotextured implants led to reduced immune and inflammatory reactions compared with polyurethane implants according to all analyzed variables.
SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs
Authors: Alser Mohammed , Shahroodi Taha , Gómez-Luna Juan , Alkan Can , Mutlu Onur
Published: November 2020

Motivation

We introduce SneakySnake, a highly parallel and highly accurate pre-alignment filter that remarkably reduces the need for computationally costly sequence alignment. The key idea of SneakySnake is to reduce the approximate string matching (ASM) problem to the single net routing (SNR) problem in VLSI chip layout. In the SNR problem, we are interested in finding the optimal path that connects two terminals with the least routing cost on a special grid layout that contains obstacles. The SneakySnake algorithm quickly solves the SNR problem and uses the found optimal path to decide whether or not performing sequence alignment is necessary. Reducing the ASM problem into SNR also makes SneakySnake efficient to implement on CPUs, GPUs and FPGAs.

Results

SneakySnake significantly improves the accuracy of pre-alignment filtering by up to four orders of magnitude compared to the state-of-the-art pre-alignment filters, Shouji, GateKeeper and SHD. For short sequences, SneakySnake accelerates Edlib (state-of-the-art implementation of Myers’s bit-vector algorithm) and Parasail (state-of-the-art sequence aligner with a configurable scoring function), by up to 37.7× and 43.9× (>12× on average), respectively, with its CPU implementation, and by up to 413× and 689× (>400× on average), respectively, with FPGA and GPU acceleration. For long sequences, the CPU implementation of SneakySnake accelerates Parasail and KSW2 (sequence aligner of minimap2) by up to 979× (276.9× on average) and 91.7× (31.7× on average), respectively. As SneakySnake does not replace sequence alignment, users can still obtain all capabilities (e.g. configurable scoring functions) of the aligner of their choice, unlike existing acceleration efforts that sacrifice some aligner capabilities.

Availabilityand implementation

https://github.com/CMU-SAFARI/SneakySnake.

Supplementary information

Supplementary data are available at Bioinformatics online.
Liftoff: accurate mapping of gene annotations
Authors: Shumate Alaina , Salzberg Steven L
Published: November 2020

Motivation

Improvements in DNA sequencing technology and computational methods have led to a substantial increase in the creation of high-quality genome assemblies of many species. To understand the biology of these genomes, annotation of gene features and other functional elements is essential; however, for most species, only the reference genome is well-annotated.

Results

One strategy to annotate new or improved genome assemblies is to map or ‘lift over’ the genes from a previously annotated reference genome. Here, we describe Liftoff, a new genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely related species. Liftoff aligns genes from a reference genome to a target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript and gene. We show that Liftoff can accurately map 99.9% of genes between two versions of the human reference genome with an average sequence identity >99.9%. We also show that Liftoff can map genes across species by successfully lifting over 98.3% of human protein-coding genes to a chimpanzee genome assembly with 98.2% sequence identity.

Availability and implementation

Liftoff can be installed via bioconda and PyPI. In addition, the source code for Liftoff is available at https://github.com/agshumate/Liftoff.

Supplementary information

Supplementary data are available at Bioinformatics online.
MorphOT: transport-based interpolation between EM maps with UCSF ChimeraX
Authors: Ecoffet Arthur , Poitevin Frédéric , Dao Duc Khanh
Published: November 2020

Motivation

Cryogenic electron microscopy (cryo-EM) offers the unique potential to capture conformational heterogeneity, by solving multiple three-dimensional classes that co-exist within a single cryo-EM image dataset. To investigate the extent and implications of such heterogeneity, we propose to use an optimal-transport-based metric to interpolate barycenters between EM maps and produce morphing trajectories.

Results

While standard linear interpolation mostly fails to produce realistic transitions, our method yields continuous trajectories that displace densities to morph one map into the other, instead of blending them.

Availability and implementation

Our method is implemented as a plug-in for ChimeraX called MorphOT, which allows the use of both CPU or GPU resources. The code is publicly available on GitHub (https://github.com/kdd-ubc/MorphOT.git), with documentation containing tutorial and datasets.

Supplementary information

Supplementary data are available at Bioinformatics online.
New computational model for miRNA-mediated repression reveals novel regulatory roles of miRNA bindings inside the coding region
Authors: Bergman Shaked , Diament Alon , Tuller Tamir
Published: November 2020

Motivation

MicroRNAs (miRNAs) are short (∼24nt), non-coding RNAs, which downregulate gene expression in many species and physiological processes. Many details regarding the mechanism which governs miRNA-mediated repression continue to elude researchers.

Results

We elucidate the interplay between the coding sequence and the 3′UTR, by using elastic net regularization and incorporating translation-related features to predict miRNA-mediated repression. We find that miRNA binding sites at the end of the coding sequence contribute to repression, and that weak binding sites are linked to effective de-repression, possibly as a result of competing with stronger binding sites. Furthermore, we propose a recycling model for miRNAs dissociated from the open reading frame (ORF) by traversing ribosomes, explaining the observed link between increased ribosome density/traversal speed and increased repression. We uncover a novel layer of interaction between the coding sequence and the 3′UTR (untranslated region) and suggest the ORF has a larger role than previously thought in the mechanism of miRNA-mediated repression.

Availability and implementation

The code is freely available at https://github.com/aescrdni/miRNA_model.

Supplementary information

Supplementary data are available at Bioinformatics online.
Practical cardiovascular imaging approach to diagnose immune checkpoint inhibitor myocarditis
Authors: Kondapalli Lavanya , Medina Theresa , Groves Daniel W
Published: November 2020

Immuno-oncology employs various therapeutic strategies that harness a patient’s own immune system to fight disease and has been a promising new strategy for cancer therapy over the last decade. Immune checkpoint inhibitors (ICI), are monoclonal antibodies, that increase antitumor immunity by blocking intrinsic down-regulators of immunity, such as cytotoxic T-lymphocyte antigen 4 (CTLA-4) and programmed cell death 1 (PD-1) or its ligand, programmed cell death ligand 1 (PD-L1). Seven ICIs are currently approved by the Food and Drug Administration and have increased the overall survival for patients with various cancer subtypes. These are used either as single agents or in combination with other checkpoint inhibitors, small molecular kinase inhibitors or cytotoxic chemotherapies. There are also many other immune modifying agents including other checkpoint inhibitor antibodies that are under investigation in clinical trials.
Right ventricular function and outcome in patients undergoing transcatheter aortic valve replacement
Authors: Koschutnik Matthias , Dannenberg Varius , Nitsche Christian , Donà Carolina , Siller-Matula Jolanta M , Winter Max-Paul , Andreas Martin , Zafar Amna , Bartko Philipp E , Beitzke Dietrich , Loewe Christian , Aschauer Stefan , Anvari-Pirsch Anahit , Goliasch Georg , Hengstenberg Christian , Kammerlander Andreas A , Mascherbauer Julia
Published: November 2020

Aims

Right ventricular dysfunction (RVD) on echocardiography has been shown to predict outcomes in patients undergoing transcatheter aortic valve replacement (TAVR). However, a comparison with the gold standard, RV ejection fraction (EF) on cardiovascular magnetic resonance (CMR), has never been performed.

Methods and results

Consecutive patients scheduled for TAVR underwent echocardiography and CMR. RV fractional area change (FAC), tricuspid annular plane systolic excursion, RV free-lateral-wall tissue Doppler (S’), and strain were assessed on echocardiography, and RVEF on CMR. Patients were prospectively followed. Adjusted regression analyses were used to report the strength of association per 1-SD decline for each RV function parameter with (i) N-terminal prohormone of brain natriuretic peptide (NT-proBNP) levels, (ii) prolonged in-hospital stay (>14 days), and (iii) a composite of heart failure hospitalization and death. Two hundred and four patients (80.9 ± 6.6 y/o; 51% female; EuroSCORE-II: 6.3 ± 5.1%) were included. At a cross-sectional level, all RV function parameters were associated with NT-proBNP levels, but only FAC and RVEF were significantly associated with a prolonged in-hospital stay [adjusted odds ratio 1.86, 95% confidence interval (CI) 1.07–3.21; P = 0.027 and 2.29, 95% CI 1.43–3.67; P = 0.001, respectively]. A total of 56 events occurred during follow-up (mean 13.7 ± 9.5 months). After adjustment for the EuroSCORE-II, only RVEF was significantly associated with the composite endpoint (adjusted hazard ratio 1.70, 95% CI 1.32–2.20; P < 0.001).

Conclusion

RVD as defined by echocardiography is associated with an advanced disease state but fails to predict outcomes after adjustment for pre-existing clinical risk factors in TAVR patients. In contrast, RVEF on CMR is independently associated with heart failure hospitalization and death.
How to initiate eHealth in congenital heart disease patients?
Authors: Schuuring Mark J , Kauw Dirkjan
Published: November 2020

Patients with congenital heart disease (CHD) are a vulnerable subgroup of cardiac patients. These patients have a high morbidity and high mortality rate. As the number of patients with CHD keeps growing, while also getting older, new tools for the care and follow-up of these vulnerable patients are warranted. eHealth has an enormous potential to revolutionize health care, and particularly for CHD patients, by expanding care beyond hospital walls and even moving some of the provided care to the comfort of home. As new eHealth tools continue to grow in number, such as invasive eHealth tools, health care delivered through eHealth continues to evolve. This teaching series summarizes current insights and discusses challenges yet to be overcome. Importantly, none of them are insurmountable. This all lays ground for a promising future for eHealth in the care of patients with CHD.
Prices of Peers: Identifying Endogenous Price Effects in the Housing Market
Authors: Szumilo Nikodem
Published: November 2020

The paper identifies neighbourhood price spillovers in the housing market. Although this concept has attracted some theoretical research and is strongly supported by practitioners, it has proven very difficult to show in empirical data. By using the linear-in-means model, which is routinely applied to identify endogenous effects in groups of peers, the study summarises all threats to identification and demonstrates how they can be addressed by exploiting information asymmetry between buyers of different houses and delays in revealing transaction prices. The results show that a 1% increase in the price of a house increases the house price of its neighbour by up to 0.3%.
Three-dimensional changes of the upper airway in patients with Class II malocclusion treated with functional appliances: a systematic review and meta-analysis
Authors: Li Jie , Ge Xiaolei , Guan Huibo , Zhang Shilong , Qiao Xing , Chang Weiwei , Ma Wensheng
Published: November 2020

Background/objective

To evaluate the three-dimensional (3D) changes of the upper airway in patients with Class II malocclusion treated with functional appliances (FAs).

Search methods and eligibility criteria

A comprehensive search of seven electronic databases was conducted from the date of inception to 12 July 2020. Manual search was also performed in relevant Chinese and English periodicals. Prospective and retrospective studies evaluating the 3D airway changes after FAs applied on growing patients with skeletal Class II malocclusion were included.

Data collection and analysis

Risk of bias assessment of each included study was performed referring to ROBINS-I. The effects of FAs on upper airway were evaluated by meta-analysis using STATA software. The outcome variables were the changes of oropharyngeal airway volumes (OAVs), nasopharyngeal airway volumes (NAVs), minimum cross-sectional area (MCA) and antero-posterior position of hyoid bone (HB). The overall quality of evidence for each outcome was rated based on Grading of Recommendations Assessment, Development and Evaluation recommendations.

Results

Nine studies were ultimately included in the systematic review and five were included and analyzed in meta-analysis. The results indicated that the pooled mean differences among these studies were 2162.80 [95 per cent confidence interval (CI): 1264.97, 3060.62), 382.20 (95 per cent CI: 140.95, 623.44), 59.91 (95 per cent CI: 41.45, 78.38), and 0.63 (95 per cent CI: −1.97, 3.23) for changes of OAVs, NAVs, MCA, and antero-posterior position of HB, respectively.

Conclusion

Weak evidence suggests that FAs can increase OAVs, NAVs, and MCA in growing patients with Class II malocclusion. Weak evidence also suggests that antero-posterior position of HB cannot be affected by FAs. Further studies are necessary to assess the stability of its effect on the upper airway in the long term.

Registration

The review protocol was not registered prior to the study.
Timing of Food Intake Drives the Circadian Rhythm of Blood Pressure
Authors: Zhang Dingguo , Colson Jackson C , Jin Chunhua , Becker Bryan K , Rhoads Megan K , Pati Paramita , Neder Thomas H , King McKenzi A , Valcin Jennifer A , Tao Binli , Kasztan Malgorzata , Paul Jodi R , Bailey Shannon M , Pollock Jennifer S , Gamble Karen L , Pollock David M
Published: November 2020

Timing of food intake has become a critical factor in determining overall cardiometabolic health. We hypothesized that timing of food intake entrains circadian rhythms of blood pressure (BP) and renal excretion in mice. Male C57BL/6J mice were fed ad libitum or reverse feeding (RF) where food was available at all times of day or only available during the 12-h lights-on period, respectively. Mice eating ad libitum had a significantly higher mean arterial pressure (MAP) during lights-off compared to lights-on (113 ± 2 mmHg vs 100 ± 2 mmHg, respectively; P < 0.0001); however, RF for 6 days inverted the diurnal rhythm of MAP (99 ± 3 vs 110 ± 3 mmHg, respectively; P < 0.0001). In contrast to MAP, diurnal rhythms of urine volume and sodium excretion remained intact after RF. Male Bmal1 knockout mice (Bmal1KO) underwent the same feeding protocol. As previously reported, Bmal1KO mice did not exhibit a diurnal MAP rhythm during ad libitum feeding (95 ± 1 mmHg vs 92 ± 3 mmHg, lights-off vs lights-on; P > 0.05); however, RF induced a diurnal rhythm of MAP (79 ± 3 mmHg vs 95 ± 2 mmHg, lights-off vs lights-on phase; P < 0.01). Transgenic PERIOD2::LUCIFERASE knock-in mice were used to assess the rhythm of the clock protein PERIOD2 in ex vivo tissue cultures. The timing of the PER2::LUC rhythm in the renal cortex and suprachiasmatic nucleus was not affected by RF; however, RF induced significant phase shifts in the liver, renal inner medulla, and adrenal gland. In conclusion, the timing of food intake controls BP rhythms in mice independent of Bmal1, urine volume, or sodium excretion.
Prevalence of Self-reported Cognitive Impairment Among Arab American Immigrants in the United States
Authors: Dallo Florence J , Kindratt Tiffany B , Zahodne Laura
Published: November 2020

Background and Objectives

Studies evaluating self-reported cognitive impairment among Arab American immigrants have not been conducted. Our objective was 2-fold: (a) to estimate and compare the age- and sex-adjusted prevalence of self-reported cognitive impairment between Arab American immigrants and U.S.- and immigrant non-Hispanic Whites, non-Hispanic Blacks, Hispanics and non-Hispanic Asians and (b) to examine associations between race, ethnicity, nativity status, and cognitive impairment among Arab American immigrants and non-Hispanic Whites (U.S.- and foreign-born) after controlling for explanatory factors.

Research Design and Methods

We used 18 years (2000–2017) of National Health Interview Survey data (n = 228 985; ages ≥ 45 years). Weighted percentages, prevalence estimates, and multivariable logistic regression models were calculated.

Results

The age- and sex-adjusted prevalence of self-reported cognitive impairment was significantly higher among Arab American immigrants (9.7%) compared to U.S.-born and non-Hispanic White immigrants (~7.4%).

Discussion and Implications

This is the first study to indicate that ethnic disparities in self-reported cognitive impairment may extend to Arab American immigrants. Additional studies need to be conducted to better understand the prevalence of cognitive impairment.
Optimal plant defence under competition for light and nutrients: an evolutionary modelling approach
Authors: de Vries Jorad , Evers Jochem B , Poelman Erik H , Anten Niels P R
Published: November 2020

Plants compete with their neighbours for limiting resources such as light and nitrogen, which can promote competitive ability at the expense of other functions such as chemical defence against insect herbivory. This trade-off is strongly influenced by dynamic interactions with biotic and abiotic factors. Yet, understanding how these interactions influence the balance between growth and defence remains one of the key challenges in the field of plant evolutionary ecology. In this study, we investigated how resource availability, competition pressure and insect herbivore pressure drive selection on the balance between the acquisition and protection of resources. To this end, we developed a novel simulation model that combines a functional-structural plant (FSP) model of plant growth in a 3D light climate with a model of natural selection. This mechanistic modelling approach simulates plant growth, competition for above- and below-ground resources, and natural selection to investigate selection pressures on traits related to growth and defence as imposed by different levels of plant density, nitrogen availability and herbivory. The model presented in this study was able to recreate the functional equilibria predicted by principal ecological theories on the effects of resource availability and resource-driven trade-offs. This illustrates the potential of mechanistic modelling approaches such as the one presented here for future research on plant responses to dynamic and variable environments. Our results further showed a three-way interaction between plant competition for light, competition for nitrogen and herbivory that determined the optimal balance between the acquisition and protection of resources. This shows that the value of investing in the acquisition or the protection of resources is a dynamic problem that is influenced by multiple ecological interactions, trade-offs and tragedies of the commons, and therefore requires an eco-evolutionary context to be fully understood.