bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermal Decomposition of GAP Studied by Dynamic Pressure-measuring Thermal Analysis
Authors: Keqi Huang , Lianghong Xia , Maohao Long , Zhimin Li , Tonglai Zhang
Published: November 2022

The thermal decomposition process of GAP in a vacuum confined space was measured by Dynamic Pressure-measuring Thermal Analysis(DPTA). In order to avoid the test error, the test process was improved: the method of liquid nitrogen condensation was used to prevent GAP volatilization in the process of vacuum pumping in the reaction test tube, and the vapor pressure at different temperatures was measured by thermogravimetric analysis. The results show that at 80°C to 120°C, the mechanism function of GAP non-isothermal decomposition reaction is Jander equation, the apparent activation energy is 159.8kJ·mol-1, and the pre-exponential factor lnA is 25.8. At the GAP isothermal reaction stage, the mechanism function changes with the temperature. When the temperature increases, the thermal decomposition reaction changes from diffusion reaction to activation reaction. The decomposition rate constant K increases exponentially with increasing temperature. When T=80°C, K=1.27×10-6; when T=120°C, K=36.93×10-6. According to the data of the decomposition time of 0.1% in the temperature range of 80~120 °C, the Semenov equation is lntT = 19039.90/T- 43.012. The storage life is 35.96 years at 25°C.
Kevlar 49 yarn pull-out test and numerical analysis
Authors: Hong Xiang , Lei Zhenkun , Ma Yu , Bai Ruixiang , Li Weikang
Published: November 2022

The yarn pull-out tests are of great importance to study the frictional energy dissipation mechanism between yarns and the overall deformation behavior of fabrics. In this study, the stress transfer mechanism of the yarn pull-out process of Kevlar 49 woven fabric is investigated by the digital image correlation (DIC) marker method, considering both the warp waves and transverse preload variables, and have analyzed the shear deformation behavior of textile by the change history of fabric shear angle. The results show that the peak load of the yarn pull-out process increases nonlinearly with the increase of the transverse preload force and the number of warp waves, the maximum pull-out displacement of the yarn is sensitive to the preload force only and is largely independent of warp waves. Finally, the finite element (FE) calculation of the single yarn pull-out process was carried out by using the mixed element method with the restart analysis technique, and the numerical simulation results achieved a good match with the peak load of the experimental data.
Fatigue Damage Characteristics and Morphology of Fiber Braided Laminated Flexible Composites
Authors: Yang Yuqi , Liu Longbin , Ding Shaozhe
Published: November 2022

In this paper, the fatigue damage evolution law and damage failure mode of flexible braided thin film composites are studied by stress fatigue damage test and scanning electron microscopy morphology test of uniaxial 45° off-axis sample. The results show that the failure mode of the specimens with 45°off-axis angle is characterized by fatigue damage of both the matrix and the functional film and the fracture of the fiber bundle has little influence. In addition, the pattern fatigue stress and fatigue life data of the fatigue test of viscose matrix and functional film under different fatigue loads have the rule of linear equation, which has predictive significance on the safety of aircraft.
Evaluation interfacial properties of resin with bond exchange reaction / T700 carbon fiber by micro-drop test and FEM
Authors: Bai Heshan , Zhao Tianyu , Bai Ruixiang , Lei Zhenkun , Liu Chen
Published: November 2022

Vitrimer epoxy resin is a newly developed resin with bond exchange reaction, which has potential applications in the field of recyclable fiber composites. The force-displacement curve of T700 carbon fiber monofilament pulled out from Vitrimer epoxy microdroplet was obtained by the microdrop test, and the interfacial shear strength of the composite system was obtained. Based on the cohesive contact theory, the finite element model (FEM) of the micro-drop test was set up. The calculated force-displacement curve is consistent with experimental data. The fracture strength and parameter characterization of the interface between Vitrimer epoxy and carbon fiber composites are further discussed.
Residual Stress Simulation of Heterogeneous Cladding Layer Between SiC/Ti6Al4V
Authors: Liu Junjun , Jiang Hao , Yu Shen , Lei Zhenkun
Published: November 2022

SiC cladding on the alloy surface can significantly improve the high temperature resistance and oxidation resistance of the material. However, heterogeneous cladding usually produces large residual stress and affects the service life of the material. In the process of laser cladding simulated by finite element method, the mechanism of residual stress during SiC deposition on alloy surface is studied by using moving double ellipsoid heat source model. The simulation results show that the residual stress is unevenly distributed near the cladding layer, and the residual stress presents a compression-tension-compression distribution in the thickness direction due to the mixing law of material properties, which provides a reliable numerical prediction method for the residual stress of SiC cladding layer cladding on the alloy base.
Processing and Evaluation of Ceramic Filler Reinforced Polymer Matrix Composites
Authors: Hassan Azzam D. , Naeem Usama J. , Bachi Imad O.
Published: November 2022

Tensile strength, Young modulus, impact strength, creep resistance, recovery measures, and thermal conductivity are used to evaluate the polymer matrix composite containing ceramic particles as degradation of spongy iron by oxidation to a ferric oxide which is used in steelmaking and low-density polyethylene. The results reveal that the mechanical and thermal properties are affected by the ratio of filler particles (360 μm). Six specimens were prepared and tested in time-dependent conditions at a constant temperature. As a result, increasing the filler ratio added to low-density polyethylene does not accelerate creep with nonlinear viscoelastic behavior. The composite with 0.7 percent ferric oxide particles was found to have the best thermal and mechanical qualities.
Design of Power Supply System for High Power SAR Satellite
Authors: Liu Yongwei , Cheng Yu , Bao Kehai , Li Houchun , Wan Zhihao
Published: November 2022

Synthetic Aperture Radar (SAR) satellite power system has the characteristics of high power, pulse power supply and fast response speed. Based on the combination of domestic and foreign SAR satellite power supply structures, a SAR satellite power supply system scheme with a composite bus architecture is proposed in this paper. By adding battery discharge regulators (BDR) between the platform bus and the SAR load bus as a grid-connected controller, the SAR load bus can supply power to the platform load, and the solar array and battery pack can be used efficiently while achieving dual bus output. Aiming at the composite bus, this paper also proposes an efficient high-power filter technology. Finally, the ground test results verify the correctness of the scheme, which can meet the different power supply requirements of the SAR satellite stable and pulse load equipment.
MSCNN-BLSTM based Prediction of the Remaining Useful Life of Aeroengine
Authors: Wang Lei , Chang Dongrun , Li Zongshuai
Published: November 2022

Accurate prediction of the aeroengine remaining useful life (RUL) is essential to improve engine availability and reliability. Aiming at the reliable prediction of residual life of aeroengine system, an engine residual life prediction model based on the fusion of multiscale fusion two-dimensional convolutional neural network and bidirectional long and short term memory (MSCNN-BLSTM) is proposed. Based on the fusion of two-dimensional convolutional neural network and bidirectional long and short time memory (BLSTM) network, the engine medium and advanced features extracted by the convolutional neural network are integrated to make residual life prediction. Finally, C-MAPSS dataset provided by NASA was used for validation. It is shown that the proposed multiscale hybrid model, compared with other model predictions, reduces the performance index score and root mean square error by 32.2% and 14.7% respectively. It can be seen that the data-driven model can effectively extract the information from the degradation data, which improves the prediction performance of aeroengine remaining life.
Numerical Analysis of the Effect of Ducted Propeller Configuration Parameters on Aerodynamic Performance
Authors: Li Zeyu , Wu Jianghao , Lin Haiying
Published: November 2022

In this paper, a numerical calculation method is applied to investigate the influences of ducted propeller aerodynamic configuration parameters. The thrust, torque and power of the propeller in the duct and the decoupled propeller are compared under identical conditions. The performance with equal input power is analysed considering the additional thrust of the duct. The relationships of system thrust, power and efficiency with the axial position of the propeller disk in the duct, the propeller disk diameter and the propeller-duct clearance are investigated.
Hollow Pin Optimization of Compression Ignition Aviation Engine Crankshaft
Authors: Galata S , Ünlü E , Işın Ö , Tuzlu E
Published: November 2022

In this article, a crankshaft design has been made for a compression ignition internal combustion engine that is planned to be used in an aerial vehicle. Alternative models were designed as hollow pins with different diameters. Finite element analysis was performed on 1 reference model and 3 alternative models using AISI 1045 and AISI 4140 materials. As the hollow diameter increases for both materials; maximum of equivalent stress has increased and minimum of safety factor has decreased. As a result of the study, it has been evaluated that the alternative 3 with AISI 4140 material is suitable for use on the crankshaft.
Optimal Design of Shock Absorption for Hexapod Robot based on Magnetorheological Fluid
Authors: Huang Sihao , Chen Boyang , Yin Maoxin , Ren Yiming , Xie Zikang
Published: November 2022

To achieve the best shock absorption effect of the hexapod robot, the influence of three leg structures on the stability of the hexapod robot under different path environments was studied, and a set of highly implementable solutions was designed. Use SolidWorks to build a hexapod robot model, import it into ADAMS to build a dynamic model and build different path environments, and conduct forward and inverse kinematics analysis at the same time. Using the Simulink plug-in in MATLAB and ADAMS joint kinematics simulation, the spring damping and magnetorheological fluid components are established in Simulink, which are connected in parallel with the model in ADMAS, and the stability of the hexapod robot under three-leg structures in different environments is obtained. According to the results, the optimal shock-absorbing leg structure is obtained.
Experimental Study Based on Fuel Nozzles Capable of Achieving Wide Fuel Supply
Authors: Wang Jiaxin
Published: November 2022

In order to overcome the limitation of fuel supply to the nozzle of an aero-engine, a nozzle with two main and secondary fuel paths and accompanied by air-assisted atomization can be used to solve this kind of problem. The two fuel paths make the fuel centrifugal and direct injection respectively, which can achieve the purpose of combining the advantages of centrifugal and direct injection nozzles, thus realizing a wide working range of fuel flow. The results show that when the fuel pressure reach a certain range, the main and secondary fuel lines start to work simultaneously, the atomization cone angle and fuel flow rate increase with the increase of pressure, and when the pressure reaches a certain value, continuing to increase the fuel pressure has little effect on the atomization angle. For the case of air supply and simultaneous operation of the main and secondary fuel lines, with the increase of fuel pressure, the atomization particle size changes gradually and evenly and has a tendency to increase, which is in line with the expected goal.
Sensitivity analysis regarding the structural parameters of the inner cylinder embedded fluidlastic base
Authors: Dai Zhixiong , Yuan Xi , Qian Feng , Feng Zhizhuang , Li Zhenkun
Published: November 2022

The inner cylinder embedded fluidlastic base is a device installed on the main reduction transmission channel of the helicopter to isolate the vibration load of the fuselage from the rotor system, whose vibration isolation efficiency is quite high. Compared with the traditional combined fluidlatic isolator, the fluidlastic base has higher reliability and safety in engineering application prospects. In this paper, taking a UAV as the research object, the structure of the fluidlastic base is preliminarily designed in light of structure space of its main reduction system, and its dynamic equation is established according to the working principle of the fluidlastic base to deduce the force transmission rate expression. Finally, taking the minimum force transmission rate as the research target, sensitivity analysis of the structural parameters is carried out for the fluidlastic base, which provides an optimization method for the optimal design of the vibration isolator.
Eggshell-Graphene Oxide Layer as Membrane Filtration for Removal Methylene Blue in Waste Water
Authors: Maulida G , Fauziah Y , Syakir N , Fitrilawati
Published: November 2022

Eggshell (ES) membrane is a semipermeable membrane that is insoluble in water and has a high surface area. We modified ES membranes with graphene oxide (GO) using self-assembled technique and used it to remove dye pollutants such as methylene blue (MB) in water. The ES membranes were obtained from fresh eggs that have been removed from albumen and yolk, then immersed in 15% acetic acid for 30 minutes. The ES membranes were immersed in 0.5 mg/mL dispersed GO and ultrasonicated for 3 hours. The modified ES-GO membrane was then used to filter 5 mg/L MB solutions. Filtration of MB solution was performed by pouring the solution over the ES-GO membrane with a help of constant pressure of 45 psi. We found that the modified ES-GO membrane could filter MB up to 33.53% and reduce MB concentration from 4.91 mg/L to 3.53 mg/L. The result of membrane permeability is 2.488 x10−3 darcy and the flow rate of the filtration is relatively constant about 4 mL/s.
Photoactivity Enhancement of TiO2 Nanoparticle-decorated ZnO as a Photocatalyst in Methylene Blue Degradation
Authors: Ramadhika L N , Suryaningsih S , Aprilia A
Published: November 2022

Zinc Oxide (ZnO) and Titanium Dioxide (TiO2) are metal oxides that are commonly used as photocatalysts material due to photoactivity characteristics. ZnO has a better reduction potential, and high electron mobility, but has a lower contact surface area than TiO2. On the other side, TiO2 has a better photoactivity to degrade pollutants referring to high surface area but has lower electron mobility compared to that ZnO. The combination of these two metal oxides is estimated can produce a better photocatalytic activity due to the advantages of each characteristic. Therefore, in this research, the ZnO-TiO2 (1:1) was prepared and investigated. ZnO nanoparticle was synthesized by the sol-gel method using zinc acetate dihydrate as a precursor, before calcining process, anatase TiO2 powder was added to form the composite. Structural, morphological, and optical characteristics of composite powders were analyzed by using XRD, TEM, UV-Vis Spectroscopy, and PL Spectroscopy. The concentration degradation of methylene blue in a solution containing composite material was observed to determine the photocatalytic activity under UV light irradiation for 30 minutes. The XRD spectrum shows the anatase phase of TiO2 and hexagonal wurtzite of ZnO crystal structure. Based on TEM imaging ZnO nanoparticles were attaching to TiO2 surfaces estimated due to van der walls bond. The ZnO/TiO2 shows a better photoactivity up to 20 minutes reaction with a higher degradation constant rate that indicates faster methylene blue degradation.
Effect of Gas Sources on the Oxygen Transfer Efficiency Produced by Fine Bubbles Generator
Authors: Hanam E S , Sofia D R , Azhary S Y , Panatarani C , Joni I M
Published: November 2022

Fine bubbles (micro to nanometer-sized) have rapidly gained popularity in academia and industry due to their unique properties, such as their high surface area, stability, and longevity. In this study, the performance of oxygen transfer rate efficiency in fine bubbles with high purity oxygen and atmospheric air was analyzed. In this study, the developed fine bubbles generator with power requirement 300 watt was used to evaluate the production of fine bubbles and oxygen transfer efficiency at two type gas sources i.e., ambient air and high-purity oxygen in the small bench aqueous media (5 L water tank). The fine bubbles generator was set up at the pressure in 50 psi and gas flow rate at 0.3 L/min to produce fine bubbles in water medium. The effect of water recirculation process in the bubbles production was measured using particles size analyzer (PSA), zeta potential and dissolved oxygen (DO) meter to measure temperature and dissolved oxygen on the water. Dissolved Oxygen (DO) measurement shows the saturation value of oxygen concentration in water, for high purity oxygen is 30 mg/L higher than air which has a value of 8.64 mg/L. This causes the efficiency of gas transfer in high-purity oxygen to reach 72.09% higher than ambient air at 35.39%. The particle size distribution shows that the mean size of bubbles after 10 minutes recirculation was 465.5 nm and 599.9 nm correspondingly for ambient air and oxygen gas source. High purity oxygen also affect to the zeta potential value tends to be more negative than in ambient air. The type of high-purity oxygen gas can increase the efficiency of the oxygen transfer rate so that the gas containing high-purity oxygen increases the volumetric oxygen transfer rate coefficient which is 2 times higher than using ambient air.
Effect of Protonation Doping of Polyaniline Electrodes using Hydrochloric Acid on Its Pseudocapacitor Capacitance
Authors: Fitriantika L A , Fitrilawati  , Syakir N
Published: November 2022

Pseudocapacitor is a supercapacitor that can store charge faradically through a reversible redox reaction. Polyaniline (PANi) is one of the promising active materials for pseudocapacitor electrodes since it can produce theoretical specific capacitance up to 750 F/g. We prepared leucomeraldine base polyaniline (LB-PANi) electrodes by deposition of dissolved LB-PANi powder in N,N-Dimethylformamide (DMF) using spraycoating technique. The LB-PANi electrodes was then doped with 1 M HCl through protonation process to obtain emeraldine salt polyaniline (ES-PANi) electrodes. We used both electrode materials and 1 M KCl to prepare a symmetrical sandwich supercapacitor model of  and , as well as measured their performance. The results show a significant increase of the specific capacitance of PANi supercapacitor from 15.02 F/kg to 1876.87 F/kg when the electrodes of the LB-PANi were changed with the ES-PANi electrodes.
Effect of Fe Magnetic Impurity to the Crystal Structure and Magnetic Properties of Eu
1.83+y
Ce
0.17−y
Cu
1−y
Fe
y
O
4+α−δ
Authors: Anggia H D , Rochman L P , Pratama R , Maryati Y , Syakuur M A , Widyaiswari U , Sari D P , Saragi T , Risdiana
Published: November 2022

In the overdoped regime of superconductors, both electron- and hole-doped superconductors exhibit intriguing phenomena like the Quantum Critical Point. Other phenomena, such as cooper-pair breaking and stripe pinning, can be observed by eliminating superconductivity by the addition of impurities. In this study, we investigate the crystal structure and magnetic properties of electron-doped superconducting cuprates of Eu2-x+y
Ce
x-y
Cui1-y
Fe
y
O4+α-δ
in the overdoped regime of x = 0.17 for Ce doping with y = 0.005, 0.01 and 0.03 for Fe impurity. The material has a tetragonal T’ structure that matches the ECCO crystal structure, according to the XRD analysis of the crystal structure. The addition of magnetic impurity has no effect on the structure but does decrease the lattice parameter. SQUID was used to measure the magnetic susceptibility at low temperatures between 2 K and 30 K. The spin-glass was observed at y = 0.03, due to the Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction as shown in a hole-doped system. Due to the significant contribution from the magnetic moment of the Fe ion, the addition of Fe concentrations increases the effective magnetic moment. The conduction layer’s spin correlation of Cu is dramatically disrupted by the addition of Fe, resulting in the breakage of the copper-pair and the elimination of superconductivity.
Pressure-dependent electronic properties in the rocksalt structure of lithium fluoride: A DFT Study
Authors: Gunawan A F , Astuti F
Published: November 2022

Density functional theory (DFT) calculation are carried out for the cubic structure of lithium fluoride (LiF). Variation of applied pressure is considered, ranging from 0 to 120 GPa with an increment of 30 GPa based on PBE and SCAN functional scheme. In zero pressure and energy-cut off 100 Ry, best result on lattice parameter is obtained by using PBE functional with the value of 4.06 Å, while SCAN functional overestimates the lattice parameter at 4.15 Å. The insulating gap of both results is significantly underestimated with 8.82 eV and 9.26 eV for PBE and SCAN functionals respectively. With the applied hydrostatic pressure, the lattice parameter are reduced exponentially, while still retaining the insulating behaviour with an increased value of gap energy.
First-principle calculation of silicon carbide (SiC) for the superhard material applications
Authors: Alfanny D , Piliang M Z , Ramadhan M R
Published: November 2022

Silicon carbide is considered to be one of the superhard material with the microhardness value more than 20 GPa. Here we report the theoretical study based on density functional theory methods on the SiC system. Three different semilocal functionals of LDA-PZ, GGA-PBE, and SCAN are utilized. The cubic crystal structure of SiC are used in all of our calculations that is fully-relaxed to obtain realistic description of both structural and electronical parameters. For the lattice parameter and insulating gap estimation, SCAN functional gives the best comparison with the experimental value with 4.34 Å and 1.67 eV respectively. The calculated Vickers hardness formula based on the SCAN functional gives the value of 36 GPa
Development of a mass spectrometer for high-precision mass measurements of superheavy elements at JINR
Authors: Yavor M.I. , Gall N.R. , Muradymov M.Z. , Pomozov T.V. , Kurnin I.V. , Monakov A.G. , Arsenev A.N. , Oganessian Yu. Ts. , Karpov A.V. , Rodin A.M. , Krupa L. , Dickel T. , Plaß W.R. , Scheidenberger C.
Published: November 2022

A multiple-reflection time-of-flight (MR TOF) mass spectrometer for mass measurements of superheavy elements is currently being developed for an experimental cave of the Superheavy Element Factory at the Joint Institute for Nuclear Research in Dubna. Its conceptual and ion-optical designs are described in the present paper. The spectrometer is designed to achieve a mass measurement accuracy of 10^-7 at low measurement statistics (~5 events) for nuclides with half-lives down to 50 ms. To reach this goal, a new generation MR TOF analyzer with an ultra-high mass resolving power and highly-stable power supplies has been designed. An advanced set of ion-optical solutions for preparation and mass separation of the sample and calibrant ion beams is proposed for the spectrometer: a radiofrequency multiplexer trap separator of charge states, high vacuum quadrupole filters with two-stage differential pumping, operated in the “beat node coincidence” mode, a focused beam transport through the gate valve gaps, as well as a fullerene soot electron ionization calibrant ion source.
Set1 regulates telomere function via H3K4 methylation–dependent and -independent pathways and calibrates the abundance of telomere maintenance factors
Authors: Jezek Meagan , Sun Winny , Negesse Maraki Y. , Smith Zachary M. , Orosz Alexander , Green Erin M.
Published: November 2022

Set1 regulates subtelomeric gene repression and telomere length via H3K4 methylation–dependent and -independent pathways, respectively. Set1 and H3K4 methylation also control the abundance of components of the telomerase holoenzyme and the CST complex.
Agroecosystem engineering extended from plant-microbe interactions revealed by multi-omics data
Authors: Fujiwara Fuki , Miyazawa Kae , Nihei Naoto , Ichihashi Yasunori
Published: November 2022

In an agroecosystem, plants and microbes coexist and interact with environmental factors such as climate, soil, and pests. However, agricultural practices that depend on chemical fertilizers, pesticides, and frequent tillage often disrupt the beneficial interactions in the agroecosystem. To reconcile the improvement of crop performance and reduction in environmental impacts in agriculture, we need to understand the functions of the complex interactions and develop an agricultural system that can maximize the potential benefits of the agroecosystem. Therefore, we are developing a system called the agroecosystem engineering system, which aims to optimize the interactions between crops, microbes, and environmental factors, using multi-omics analysis. This review first summarizes the progress and examples of omics approaches, including multi-omics analysis, to reveal complex interactions in the agroecosystem. The latter half of this review discusses the prospects of data analysis approaches in the agroecosystem engineering system, including causal network analysis and predictive modeling.
PlDBPred: a novel computational model for discovery of DNA binding proteins in plants
Authors: Pradhan Upendra Kumar , Meher Prabina Kumar , Naha Sanchita , Pal Soumen , Gupta Ajit , Parsad Rajender
Published: November 2022

DNA-binding proteins (DBPs) play crucial roles in numerous cellular processes including nucleotide recognition, transcriptional control and the regulation of gene expression. Majority of the existing computational techniques for identifying DBPs are mainly applicable to human and mouse datasets. Even though some models have been tested on Arabidopsis, they produce poor accuracy when applied to other plant species. Therefore, it is imperative to develop an effective computational model for predicting plant DBPs. In this study, we developed a comprehensive computational model for plant specific DBPs identification. Five shallow learning and six deep learning models were initially used for prediction, where shallow learning methods outperformed deep learning algorithms. In particular, support vector machine achieved highest repeated 5-fold cross-validation accuracy of 94.0% area under receiver operating characteristic curve (AUC-ROC) and 93.5% area under precision recall curve (AUC-PR). With an independent dataset, the developed approach secured 93.8% AUC-ROC and 94.6% AUC-PR. While compared with the state-of-art existing tools by using an independent dataset, the proposed model achieved much higher accuracy. Overall results suggest that the developed computational model is more efficient and reliable as compared to the existing models for the prediction of DBPs in plants. For the convenience of the majority of experimental scientists, the developed prediction server PlDBPred is publicly accessible at https://iasri-sg.icar.gov.in/pldbpred/.The source code is also provided at https://iasri-sg.icar.gov.in/pldbpred/source_code.php for prediction using a large-size dataset.
From single- to multi-omics: future research trends in medicinal plants
Authors: Yang Lifang , Yang Ye , Huang Luqi , Cui Xiuming , Liu Yuan
Published: November 2022

Medicinal plants are the main source of natural metabolites with specialised pharmacological activities and have been widely examined by plant researchers. Numerous omics studies of medicinal plants have been performed to identify molecular markers of species and functional genes controlling key biological traits, as well as to understand biosynthetic pathways of bioactive metabolites and the regulatory mechanisms of environmental responses. Omics technologies have been widely applied to medicinal plants, including as taxonomics, transcriptomics, metabolomics, proteomics, genomics, pangenomics, epigenomics and mutagenomics. However, because of the complex biological regulation network, single omics usually fail to explain the specific biological phenomena. In recent years, reports of integrated multi-omics studies of medicinal plants have increased. Until now, there have few assessments of recent developments and upcoming trends in omics studies of medicinal plants. We highlight recent developments in omics research of medicinal plants, summarise the typical bioinformatics resources available for analysing omics datasets, and discuss related future directions and challenges. This information facilitates further studies of medicinal plants, refinement of current approaches and leads to new ideas.
PhaTYP: predicting the lifestyle for bacteriophages using BERT
Authors: Shang Jiayu , Tang Xubo , Sun Yanni
Published: November 2022

Bacteriophages (or phages), which infect bacteria, have two distinct lifestyles: virulent and temperate. Predicting the lifestyle of phages helps decipher their interactions with their bacterial hosts, aiding phages’ applications in fields such as phage therapy. Because experimental methods for annotating the lifestyle of phages cannot keep pace with the fast accumulation of sequenced phages, computational method for predicting phages’ lifestyles has become an attractive alternative. Despite some promising results, computational lifestyle prediction remains difficult because of the limited known annotations and the sheer amount of sequenced phage contigs assembled from metagenomic data. In particular, most of the existing tools cannot precisely predict phages’ lifestyles for short contigs. In this work, we develop PhaTYP (Phage TYPe prediction tool) to improve the accuracy of lifestyle prediction on short contigs. We design two different training tasks, self-supervised and fine-tuning tasks, to overcome lifestyle prediction difficulties. We rigorously tested and compared PhaTYP with four state-of-the-art methods: DeePhage, PHACTS, PhagePred and BACPHLIP. The experimental results show that PhaTYP outperforms all these methods and achieves more stable performance on short contigs. In addition, we demonstrated the utility of PhaTYP for analyzing the phage lifestyle on human neonates’ gut data. This application shows that PhaTYP is a useful means for studying phages in metagenomic data and helps extend our understanding of microbial communities.
A Bayesian model for identifying cancer subtypes from paired methylation profiles
Authors: Fan Yetian , S Chan April , Zhu Jun , Yi Leung Suet , Fan Xiaodan
Published: November 2022

Aberrant DNA methylation is the most common molecular lesion that is crucial for the occurrence and development of cancer, but has thus far been underappreciated as a clinical tool for cancer classification, diagnosis or as a guide for therapeutic decisions. Partly, this has been due to a lack of proven algorithms that can use methylation data to stratify patients into clinically relevant risk groups and subtypes that are of prognostic importance. Here, we proposed a novel Bayesian model to capture the methylation signatures of different subtypes from paired normal and tumor methylation array data. Application of our model to synthetic and empirical data showed high clustering accuracy, and was able to identify the possible epigenetic cause of a cancer subtype.
A bilateral lung transplant and giant pulmonary artery aneurysm reconstruction with an aortic graft in a woman with pulmonary hypertension
Authors: Poveda David , Fadel Elie , Lorenzi William , Menager Jean Baptiste
Published: November 2022

An aneurysm of the pulmonary artery is a rare but severe complication in patients suffering from pulmonary arterial hypertension. For these patients, a lung or heart-lung transplant is the only definitive therapy available. Our goal was to show a reconstruction strategy in a patient with a mismatch between the pulmonary artery and the donor aorta.
ArabidopsisN6-methyladenosine methyltransferase FIONA1 regulates floral transition by affecting the splicing ofFLCand the stability of floral activatorsSPL3andSEP3
Authors: Cai Jing , Hu Jianzhong , Amara Umme , Park Su Jung , Li Yuxia , Jeong Daesong , Lee Ilha , Xu Tao , Kang Hunseung
Published: November 2022

N 6-methyladenosine (m6A) RNA methylation has been shown to play a crucial role in plant development and floral transition. Two recent studies have identified FIONA1 as an m6A methyltransferase that regulates the floral transition in Arabidopsis through influencing the stability of CONSTANS (CO), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), and FLOWERING LOCUS C (FLC). In this study, we confirmed that FIONA1 is an m6A methyltransferase that installs m6A marks in a small group of mRNAs. Furthermore, we show that, in addition to its role in influencing the stability of CO, SOC1, and FLC, FIONA1-mediated m6A methylation influences the splicing of FLC, a key floral repressor, and the stability of SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 3 (SPL3) and SEPALLATA3 (SEP3), floral activators, which together play a vital role in floral transition in Arabidopsis. Our study confirms the function of FIONA1 as an m6A methyltransferase and suggests a close molecular link between FIONA1-mediated m6A methylation and the splicing of FLC and the destabilization of SPL3 and SEP3 in flowering time control.
A simple linear model to aid in analyses of the β Pictoris moving group
Authors: Barbosa Valmir C , do Nascimento Josina O
Published: November 2022

We build a 4D linear model of object membership in the $\beta$ Pictoris moving group (BPMG), using two nested applications of Principal Component Analysis (PCA) for ∼1.5 million objects with high-quality data. These data consist of 3D-Galactic space velocities and Gaia G magnitudes. Through PCA, they ultimately result in a 4D straight line, referred to as PC 1′, about which both the bona fide members used to obtain the straight line and the candidate members used to test the model congregate at generally small distances. As a proof of concept, we select bona fide members from a recent, Gaia DR2-based compilation and candidate members mostly from a (pre-Gaia DR2) compilation from 2017. Using a standard procedure to flag groups of outliers in data sets, we find possible outliers flagged on account of their large distances to PC 1′, and find evidence that discrepant radial velocity measurements may indeed bring into question their validity as BPMG members. We propose that PC 1′ be added to the tool set for BPMG analyses and potentially extended to other young stellar moving groups.
SirA inhibits the essential DnaA:DnaD interaction to block helicase recruitment duringBacillus subtilissporulation
Authors: Winterhalter Charles , Stevens Daniel , Fenyk Stepan , Pelliciari Simone , Marchand Elie , Soultanas Panos , Ilangovan Aravindan , Murray Heath
Published: November 2022

Bidirectional DNA replication from a chromosome origin requires the asymmetric loading of two helicases, one for each replisome. Our understanding of the molecular mechanisms underpinning helicase loading at bacterial chromosome origins is incomplete. Here we report both positive and negative mechanisms for directing helicase recruitment in the model organism Bacillus subtilis. Systematic characterization of the essential initiation protein DnaD revealed distinct protein interfaces required for homo-oligomerization, interaction with the master initiator protein DnaA, and interaction with the helicase co-loader protein DnaB. Informed by these properties of DnaD, we went on to find that the developmentally expressed repressor of DNA replication initiation, SirA, blocks the interaction between DnaD and DnaA, thereby restricting helicase recruitment from the origin during sporulation to inhibit further initiation events. These results advance our understanding of the mechanisms underpinning DNA replication initiation in B. subtilis, as well as guiding the search for essential cellular activities to target for antimicrobial drug design.
MobiDB: 10 years of intrinsically disordered proteins
Authors: Piovesan Damiano , Del Conte Alessio , Clementel Damiano , Monzon Alexander Miguel , Bevilacqua Martina , Aspromonte Maria Cristina , Iserte Javier A , Orti Fernando E , Marino-Buslje Cristina , Tosatto Silvio C E
Published: November 2022

The MobiDB database (URL: https://mobidb.org/) is a knowledge base of intrinsically disordered proteins. MobiDB aggregates disorder annotations derived from the literature and from experimental evidence along with predictions for all known protein sequences. MobiDB generates new knowledge and captures the functional significance of disordered regions by processing and combining complementary sources of information. Since its first release 10 years ago, the MobiDB database has evolved in order to improve the quality and coverage of protein disorder annotations and its accessibility. MobiDB has now reached its maturity in terms of data standardization and visualization. Here, we present a new release which focuses on the optimization of user experience and database content. The major advances compared to the previous version are the integration of AlphaFoldDB predictions and the re-implementation of the homology transfer pipeline, which expands manually curated annotations by two orders of magnitude. Finally, the entry page has been restyled in order to provide an overview of the available annotations along with two separate views that highlight structural disorder evidence and functions associated with different binding modes.
High-affinity binding at quadruplex–duplex junctions: rather the rule than the exception
Authors: Vianney Yoanes Maria , Weisz Klaus
Published: November 2022

Quadruplex-duplex (Q–D) junctions constitute unique structural motifs in genomic sequences. Through comprehensive calorimetric as well as high-resolution NMR structural studies, Q–D junctions with a hairpin-type snapback loop coaxially stacked onto an outer G-tetrad were identified to be most effective binding sites for various polycyclic quadruplex ligands. The Q–D interface is readily recognized by intercalation of the ligand aromatic core structure between G-tetrad and the neighboring base pair. Based on the thermodynamic and structural data, guidelines for the design of ligands with enhanced selectivity towards a Q–D interface emerge. Whereas intercalation at Q–D junctions mostly outcompete stacking at the quadruplex free outer tetrad or intercalation between duplex base pairs to varying degrees, ligand side chains considerably contribute to the selectivity for a Q–D target over other binding sites. In contrast to common perceptions, an appended side chain that additionally interacts within the duplex minor groove may confer only poor selectivity. Rather, the Q–D selectivity is suggested to benefit from an extension of the side chain towards the exposed part of the G-tetrad at the junction. The presented results will support the design of selective high-affinity binding ligands for targeting Q–D interfaces in medicinal but also technological applications.
Comprehensive profiling of epigenetic modifications in fast-growing Moso bamboo shoots
Authors: Li Tao , Wang Huihui , Zhang Yaxin , Wang Huiyuan , Zhang Zeyu , Liu Xuqing , Zhang Zekun , Liu Kai , Yang Deming , Zhang Hangxiao , Gu Lianfeng
Published: November 2022

The fast growth of Moso bamboo (Phyllostachys edulis) shoots is caused by the rapid elongation of each internode. However, the key underlying cellular processes and epigenetic mechanisms remain largely unexplored. We used microscopy and multi-omics approaches to investigate two regions (bottom and middle) of the 18th internode from shoots of two different heights (2 and 4 m). We observed that internode cells become longer, and that lignin biosynthesis and glycosyltransferase family 43 (GT43) genes are substantially upregulated with shoot height. Nanopore direct RNA sequencing (DRS) revealed a higher N6-methyladenine (m6A) modification rate in 2-m shoots than in 4-m shoots. In addition, different specific m6A modification sites were enriched at different growth stages. Global DNA methylation profiling indicated that DNA methylation levels are higher in 4-m shoots than in 2-m shoots. We also detected shorter poly(A) tail lengths (PALs) in 4-m shoots compared with 2-m shoots. Genes showing differential PAL were mainly enriched in the functional terms of protein translation and vesicle fusion. An association analysis between PALs and DNA methylation strongly suggested that gene body CG methylation levels are positively associated with PAL. This study provides valuable information to better understand post-transcriptional regulations responsible for fast-growing shoots in Moso bamboo.
Machine learning identifies a profile of inadequate responder to methotrexate in rheumatoid arthritis
Authors: Duquesne Julien , Bouget Vincent , Cournède Paul Henry , Fautrel Bruno , Guillemin Francis , de Jong Pascal H P , Heutz Judith W , Verstappen Marloes , van der Helm-van Mil Annette H M , Mariette Xavier , Bitoun Samuel
Published: November 2022

Objectives

Around 30% of patients with RA have an inadequate response to MTX. We aimed to use routine clinical and biological data to build machine learning models predicting EULAR inadequate response to MTX and to identify simple predictive biomarkers.

Methods

Models were trained on RA patients fulfilling the 2010 ACR/EULAR criteria from the ESPOIR and Leiden EAC cohorts to predict the EULAR response at 9 months (± 6 months). Several models were compared on the training set using the AUROC. The best model was evaluated on an external validation cohort (tREACH). The model's predictions were explained using Shapley values to extract a biomarker of inadequate response.

Results

We included 493 therapeutic sequences from ESPOIR, 239 from EAC and 138 from tREACH. The model selected DAS28, Lymphocytes, Creatininemia, Leucocytes, AST, ALT, swollen joint count and corticosteroid co-treatment as predictors. The model reached an AUROC of 0.72 [95% CI (0.63, 0.80)] on the external validation set, where 70% of patients were responders to MTX. Patients predicted as inadequate responders had only 38% [95% CI (20%, 58%)] chance to respond and using the algorithm to decide to initiate MTX would decrease inadequate-response rate from 30% to 23% [95% CI: (17%, 29%)]. A biomarker was identified in patients with moderate or high activity (DAS28 > 3.2): patients with a lymphocyte count superior to 2000 cells/mm3 are significantly less likely to respond.

Conclusion

Our study highlights the usefulness of machine learning in unveiling subgroups of inadequate responders to MTX to guide new therapeutic strategies. Further work is needed to validate this approach.
Sleep efficiency and the metabolic risk score in very active older women and men
Authors: Madden Kenneth M , Feldman Boris , Chase Jocelyn
Published: November 2022

Study Objectives

Sleep disruption is a risk factor for obesity, diabetes, and cardiovascular disease in older adults. How physical activity (PA) interacts with the negative cardiometabolic effects of poor sleep is not known. We objectively measured sleep efficiency (SE) in very active older adults and examined the association between SE and a continuous Metabolic Syndrome Risk Score (cMSy).

Methods

Very active older adults (age ≥65 years) from a Master’s Ski Team (Whistler, Canada) were recruited. Each participants wore an activity monitor (SenseWear Pro) continuously for 7 days to provide measures of both daily energy expenditure (metabolic equivalents, METs) and SE. All components of the metabolic syndrome were measured and a principal component analysis was used to compute a continuous metabolic risk score (cMSy, sum of eigenvalues ≥1.0).

Results

A total of 54 participants (mean age 71.4 years, SD 4.4 years, and 24 men and 30 women) were recruited and had very high PA levels (>2.5 h per day of exercise). Initially, there was no significant association between SE and cMSy (p = 0.222). When stratified by biological sex, only men showed a significant negative association between SE and cMSy (Standardized β = −0.364 ± 0.159, p = 0.032).

Conclusions

Only older men show a significant negative association between poor SE and increased cardiometabolic risk, despite high levels of PA.
Guardian Trust revisited
Authors: de Lacey Joseph , Herrett Niamh
Published: November 2022

When a third party threatens a claim in relation to trust assets, and the time for distribution has arisen, the trustee is placed in a difficult position. To distribute notwithstanding the threatened claim could result in personal liability for the trustee under the Guardian Trust principle. To not distribute, whilst the threatened claim is outstanding, could lead to the paralysis of the trust for months, if not years. This article considers the availability of ‘put up or shut up’ orders against the threatening party in such circumstances. What is the jurisdiction to make such an order, what are its requirements, and might a trustee be justified in utilising ‘put up or shut up’ orders more often and more quickly?
Responding to the cuts in UK AID to neglected tropical diseases control programmes in Africa
Authors: Anderson Roy M , Cano Jorge , Hollingsworth T Déirdre , Deribe-Kassaye Kebede , Zouré Honorat G M , Kello Amir B , Impouma Benido , Kalu Akpaka A , Appleby Laura , Yard Elodie , Salasibew Mihretab , McRae-McKee Kevin , Vegvari Carolin
Published: November 2022

The early termination of the Accelerating the Sustainable Control and Elimination of Neglected Tropical Diseases (Ascend) programme by the UK government in June 2021 was a bitter blow to countries in East and West Africa where no alternative source of funding existed. Here we assess the potential impact the cuts may have had if alternative funding had not been made available by new development partners and outline new strategies developed by affected countries to mitigate current and future disruptions to neglected tropical disease control programmes.
Virulence, Aggressiveness, and Fungicide Sensitivity of Phytophthora spp. Associated with Soybean in Illinois
Authors: Cerritos-Garcia Daniel G. , Huang Shun-Yuan , Kleczewski Nathan M. , Mideros Santiago X.
Published: November 2022

Phytophthora root and stem rot (PRR), caused by Phytophthora sojae, is one of the most devastating oomycete diseases of soybean in Illinois. Single resistant genes (Rps) are used to manage this pathogen but P. sojae has adapted to Rps, causing failure of resistance in many regions. In addition to P. sojae, recent reports indicate that P. sansomeana could also cause root rot in soybean. Soil samples and symptomatic plants were collected across 40 Illinois counties between 2016 and 2018. P. sojae (77%) was more abundant than P. sansomeana (23%) across Illinois fields. Both species were characterized by virulence, aggressiveness, and fungicide sensitivity. Virulence of all P. sojae isolates was evaluated using the hypocotyl inoculation technique in 13 soybean differentials. Aggressiveness was evaluated in the greenhouse by inoculating a susceptible cultivar and measuring root and shoot dry weight. On average, P. sojae isolates were able to cause disease on six soybean differentials. P. sojae was more aggressive than P. sansomeana. All isolates were sensitive to azoxystrobin, ethaboxam, mefenoxam, and metalaxyl. The characterization of the population of species associated with PRR will inform management decisions for this disease in Illinois.