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A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences,Bulk RNA-seq,and Single-cell RNA-seq

Genomics, Proteomics & Bioinformatics 2023年第1期21卷 67-83页

作者： Wenbin ye Qiwei Lian Congting ye xiaohui Wu Pasteurien College Suzhou Medical College of Soochow UniversitySoochow UniversitySuzhou 215000China Department of Automation Xiamen UniversityXiamen 361005China Key Laboratory of the Coastal and Wetland Ecosystems Ministry of EducationCollege of the Environment and EcologyXiamen UniversityXiamen 361005China

Alternative polyadenylation(APA)plays important roles in modulating mRNA stability,translation,and subcellular localization,and contributes extensively to shaping eukaryotic transcriptome complexity and proteome diversity.Identification of poly(A)sites(pAs)on a genomewide scale is a critical step toward understanding the underlying mechanism of APA-mediated gene regulation.A number of established computational tools have been proposed to predict pAs from diverse genomic data.Here we provided an exhaustive overview of computational approaches for predicting pAs from DNA sequences,bulk RNA sequencing(RNA-seq)data,and single-cell RNA sequencing(scRNA-seq)data.Particularly,we examined several representative tools using bulk RNA-seq and scRNA-seq data from peripheral blood mononuclear cells and put forward operable suggestions on how to assess the reliability of pAs predicted by different tools.We also proposed practical guidelines on choosing appropriate methods applicable to diverse scenarios.Moreover,we discussed in depth the challenges in improving the performance of pA prediction and benchmarking different methods.Additionally,we highlighted outstanding challenges and opportunities using new machine learning and integrative multi-omics techniques,and provided our perspective on how computational methodologies might evolve in the future for non-30 untranslated region,tissuespecific,cross-species,and single-cell pA prediction.

关键词： Polyadenylation Predictive modeling RNA-seq scRNA-seq Machine learning

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Population-based incremental learning for the prediction of Homo sapiens’ protein secondary structure

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International Journal of Biomathematics 2019年第3期12卷 1-21页

作者： ye Chen Xiaoping Yuan xiaohui Cang School of Information and Control Engineering China University of Mining and Technology Xuzhou Jiangsu 221008 P. R. China Institute of Genetics Zhejiang University School of Medicine Hangzhou Zhejiang 310058 P. R. China

prediction of the protein secondary structure of Homo sapiens is one of the more important domains. Many methods have been used to feed forward neural networks or SVMs combined with a sliding window. This method’s mechanisms are too complex to be able to extract clear and straightforward physical meanings from it. This paper explores population-based incremental learning (PBIL), which is a method that combines the mechanisms of a generational genetic algorithm with simple competitive learning. The result shows that its accuracies are particularly associated with the Homo species. This new perspective reveals a number of different possibilities for the purposes of performance improvements.

关键词： Population-based incremental learning Homo sapiens prediction of protein secondary structure

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Laser-ablated violet phosphorus/graphene heterojunction as ultrasensitive ppb-level room-temperature NO sensor

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中国化学快报:英文版 2023年第9期34卷 248-253页

作者： xiaohui Ye Ming Qi Hao Qiang Mengzhen Chen Xi Zheng Mengyue Gu Xuewen Zhao Yanling Yang Chaozheng He Jinying Zhang School of Material Science and Engineering Shaanxi University of Science and TechnologyXi’an 710021China Center of Nanomaterials for Renewable Energy(CNRE) School of Electrical EngineeringXi’an Jiaotong UniversityXi’an 710049China Institute of Environmental and Energy Catalysis School of Materials Science and Chemical EngineeringXi’an Technological UniversityXi’an 710021China

Two dimensional(2D)materials are promising gas sensing materials,but the most of them need to be heated to show promising sensing performance.Sensing structures with high sensing performance at room-temperature are urgent.Here,another 2D material,violet phosphorus(VP)nanoflake is investigated as gas sensing material.The VP nanoflakes have been effectively ablated to have layers of 1–5 layers by laser ablation in glycol.The VP nanoflakes are combined with graphene to form VP/G heterostructuresbased NO sensor.An ultra-high gauge factor of 3×10^(7)for ppb-level sensing and high resistance response of 59.21%with ultra-short recovery time of 6s for ppm-level sensing have been obtained.The sensing mechanism is also analysed by density functional theory(DFT)calculations.The adsorption energy of VP/G is calculated to be-0.788 e V,resulting in electrons migration from P to N to form a P-N bond in the gap between VP and graphene sheet.This work provides a facile approach to ablate VP for mass production.The as-produced structures have also provided potential gas sensors with ultrasensitive performance as ppb-level room-temperature sensors.

关键词： Laser ablation Violet phosphorus nanoflakes Heterostructures ppb level NO sensor

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Hard-rock tunnel lithology identification using multiscale dilated convolutional attention network based on tunnel face images

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Frontiers of Structural and Civil Engineering 2023年第12期17卷 1796-1812页

作者： Wenjun ZHANG Wuqi ZHANG Gaole ZHANG Jun HUANG Minggeng LI xiaohui WANG Fei ye Xiaoming GUAN School of Civil Engineering Tianjin UniversityTianjin 300350China School of Civil Engineering and Architecture Guangxi UniversityNanning 530004China Jiangxi Communications Design and Research Institute Co. Ltd.Nanchang 330000China China Railway 18th Bureau Group Co. Ltd.Tianjin 300222China School of Highway Chang'an UniversityXi'an 710064China School of Civil Engineering Qingdao University of TechnologyQingdao 266033China

For real-time classification of rock-masses in hard-rock tunnels,quick determination of the rock lithology on the tunnel face during construction is essential.Motivated by current breakthroughs in artificial intelligence technology in machine vision,a new automatic detection approach for classifying tunnel lithology based on tunnel face images was developed.The method benefits from residual learning for training a deep convolutional neural network(DCNN),and a multi-scale dilated convolutional attention block is proposed.The block with different dilation rates can provide various receptive fields,and thus it can extract multi-scale features.Moreover,the attention mechanism is utilized to select the salient features adaptively and further improve the performance of the model.In this study,an initial image data set made up of photographs of tunnel faces consisting of basalt,granite,siltstone,and tuff was first collected.After classifying and enhancing the training,validation,and testing data sets,a new image data set was generated.A comparison of the experimental findings demonstrated that the suggested approach outperforms previous classifiers in terms of various indicators,including accuracy,precision,recall,F1-score,and computing time.Finally,a visualization analysis was performed to explain the process of the network in the classification of tunnel lithology through feature extraction.Overall,this study demonstrates the potential of using artificial intelligence methods for in situ rock lithology classification utilizing geological images of the tunnel face.

关键词： hard-rock tunnel face intelligent lithology identification multi-scale dilated convolutional attention network image classification deep learning

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Hydrolysis hydrogen production mechanism of Mg10Ni10Ce alloy surface modified by SnO_(2) nanotubes in different aqueous systems

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Green Energy & Environment 2021年第1期6卷 124-137页

作者： Xiaojiang Hou Lu Yang Kaiming Hou Hongchang Shi Lei Feng Guoquan Suo xiaohui Ye Li Zhang Yanling Yang School of Material Science and Engineering Shaanxi Key Laboratory of Green Preparation and Functionalization for Inorganic MaterialsShaanxi University of Science and TechnologyXi'an710021China State Key Laboratory of Solidification Processing Northwestern Polytechnical UniversityXi'an710072China

(Mg-10wt%Ni)-10wt%Ce(Mg10Ni10Ce)was ball-milled with SnO_(2)nanotubes and Mg10Ni10Ce-xSnO_(2)(x¼0,5,10 and 15 wt%)composites have been prepared.The phase compositions,microstructures,morphologies and hydrolysis H2 generation performance in different aqueous systems(distilled water,tap water and simulated seawater)have been investigated and the corresponding hydrolysis mechanism of Mg10Ni10Ce and Mg10Ni10CeeSnO_(2)has been proposed.Adding a small amount of SnO_(2)nanotubes can significantly enhance the hydrolysis reaction of Mg10Ni10Ce,especially the initial hydrolysis kinetics and the final H_(2) generation yield.Unfortunately,the Mg10Ni10Ce-xSnO_(2)hardly reacts with distilled water at room temperature.The hydrolysis reaction rate of Mg10Ni10Cee5SnO_(2)composite in tap water is still very slow with only 17.3%generation yield after 1 h at 303 K.Fortunately,in simulated seawater(3.5 wt%NaCl solution),the hydrolytic H2 generation behavior of the Mg10Ni10Cee5SnO_(2)composite has been greatly improved,which can release as high as 468.6 mL g^(-1 )H_(2) with about 60.9%generation yield within 30 s at 303 K.The Cl destroys the passivation layer on MgeNieCe alloy surface and the added SnO_(2)nanotubes accelerate the hydrolysis reaction rate and enhance the H2 generation yield.The Mg10Ni10Cee5SnO_(2)composite can rapidly generate a large amount of H2 in simulated seawater in a short time,which is expected to be applied on portable H2 generators in the future.

关键词： Mg10Ni10Ce Hydrogen production Surface modification Hydrolysis behavior Aqueous systems

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Midsummer nights in Wuhan

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Changjiang Weekly 2022年第32期 10-11页

作者： Yang xiaoyu xiaohui ye Feiyan 不详

"Fantastic Forest"night tour at Wuhan Botanical Garden The first phase of the"Fantastic Forest"night tour has kicked off at the Wuhan Botanical Garden and will continue through mid-September.The tour is composed of tw... 详细信息

关键词： Forest Wuhan night

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Construction of SnS2/SnO2 heterostructures with enhanced potassium storage performance

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Journal of Materials Science & Technology 2020年第20期52卷 167-172页

作者： Guoquan Suo Dan Li Lei Feng Xiaojiang Hou xiaohui Ye Li Zhang Qiyao Yu Yanling Yang Wei(Alex)Wang School of Materials Science and Engineering Shaanxi University of Science and TechnologyXi’an710021China Institute of Advanced Structure Technology Beijing Institute of TechnologyBeijing 100081China Department of Materials Science and Engineering College of EngineeringPeking UniversityBeijing 100871China

Increasing attention has been focused on potassium ion batteries(KIBs) as promising energy-sto rage system(ESS) owing to the abundance and low-cost of potassium resources.Here,SnS2/SnO2 hete rostructures were successfully fixed onto stainless steel mesh(SnS2/SnO2/SSM) through a facile two-step hydrothermal method and used as anodes for KIBs.Due to the advantages of SnS2/SnO2 heterostructures and good conductivity of SSM substrate,the SnS2/SnO2/SSM anodes display enhanced electrochemical performance.The SnS2/SnO2/SSM anodes deliver specific capacity of 394 mA h g^-1 at 50 mA g^-1 over 100 cycles,better than SnO2/SSM.Even at 500 mA g^-1 after 250 cycles,high capacity of 155 mA h g^-1 can still be obtained.

关键词： SnS2/SnO2 Heterostructures Potassium-ion batteries Anode

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Effect of Curing Temperature on Intermediate Temperature Properties of Calcium Aluminate Cement Bonded Corundum Castables

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China's Refractories 2021年第3期30卷 33-36页

作者： LI ye LIU Kun DING Dafei WANG Qingfeng FU xiaohui ye Guotian Henan Key Laboratory of High Temperature Functional Ceramics Zhengzhou UniversityZhengzhou 450001China Materials Engineering Department Luoyang Institute of Science and TechnologyLuoyang 471023China

In order to study the effect of the curing temperature on the intermediate temperature properties of calcium aluminate cement bonded corundum castables,the prepared castables were cured at 5,10,25,40 and 50℃,respectively,dried at 110℃ for 24 h and heat treated at 800 and 1100 ℃,respectively.Then the apparent porosity,the cold modulus of rupture and the cold crushing strength were measured.The phase composition of castable matrix specimens treated under the same conditions and the influence of the curing temperature on the intermediate temperature strength of the castables were also analyzed.The results show that with the increase of the curing temperature,the hydration degree of calcium aluminate cement increases,which promotes the uniform distribution of hydration products with AI203 after decomposition,thus enhancing the intermediate temperature strength of castables.

关键词： curing temperature calcium aluminate cement corundum castable intermediate temperature strength

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H_2 generation kinetics/thermodynamics and hydrolysis mechanism of high-performance La-doped Mg-Ni alloys in Na Cl solution——A large-scale and quick strategy to get hydrogen

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Journal of Magnesium and Alloys 2021年第3期9卷 1068-1083页

作者： Xiaojiang Hou Hongchang Shi Lu Yang Kaiming Hou Yi Wang Lei Feng Guoquan Suo xiaohui Ye Li Zhang Yanling Yang School of Material Science and Engineering Shaanxi Key Laboratory of Green Preparation and Functionalization for Inorganic MaterialsShaanxi University of Science and TechnologyXi'an 710021China State Key Laboratory of Solidification Processing Northwestern Polytechnical UniversityXi'an 710072China

In this work,La-doped Mg-Ni multiphase alloys were prepared by resistance melting furnace(RMF)and then modified by high-energy ball milling(HEBM).The hydrolysis H_(2) generation kinetics/thermodynamics of prepared alloys in Na Cl solutions have been investigated with the help of nonlinear and linear fitting by Avrami-Erofeev and Arrhenius equations.Combining the microstructure information before and after hydrolysis and thermodynamics fitting results,the hydrolysis H_(2) generation mechanism based on nucleation&growth has been elaborated.The final H_(2) generation capacities of 0La,5La,10La and 15 La alloys are 677,653,641 and 770 m L·g^(-1)H_(2) in 240 min at291 K,respectively.While,the final H_(2) generation capacities of HEBM 0La,5La,10La and 15 La alloys are 632,824,611 and 653 m L·g^(-1)H_(2) in 20 min at 291 K,respectively.The as-cast 15La alloy and HEMB 5La alloy present the best H_(2) production rates and final H_(2) production capacities,especially the HEBM 5La can rapidly achieve high H_(2) generation capacity(670 and 824 m L·g^(-1)H_(2) )at low temperature(291 K)within short time(5 and 20 min).The difference between the H_(2) generation capacities is mainly originated from the initial nucleation rate of Mg(OH)_(2) and the subsequent processes affected by the microstructures and phase compositions of the hydrolysis alloys.Relative low initial nucleation rate and fully growth of Mg(OH)_(2) nucleus are the premise of high H_(2) generation capacity due to the hydrolysis H_(2) generation process consisted by the nucleation,growth and contacting of Mg(OH)_(2) nucleus.To utilization H_(2) by designing solid state H_(2) generators using optimized Mg-based alloys is expected to be a feasible H_(2) generation strategy at the moment.

关键词： H_(2)generation La-doped Mg-Ni alloys Kinetics Thermodynamics Hydrolysis mechanism

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Clay minerals and elemental composition of sediments on different sedimentary units in the northern East China Sea shelf:provenance tracing and genetic mechanism analysis

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Acta Oceanologica Sinica 2023年第11期42卷 19-34页

作者： Xiaoyan Xu Yong Zhang Yanguang Dou Jingyi Cong Beibei Mi xiaohui Chen Xia Li Chengfen Xu Yongyu ye Qingdao Institute of Marine Geology China Geological SurveyQingdao 266237China Laboratory for Marine Mineral Resource Pilot National Laboratory for Marine Science and Technology(Qingdao)Qingdao 266237China Laboratory for Marine Geology Pilot National Laboratory for Marine Science and Technology(Qingdao)Qingdao 266237China College of Marine Science and Technology China University of Geosciences(Wuhan)Wuhan 430074China Qingdao Marine Geological Engineering Survey Institute Co. Ltd.Qingdao 266071China

The composition,provenance,and genetic mechanism of sediment on different sedimentary units of the East China Sea(ECS)shelf are essential for understanding the depositional dynamics environment in the ECS.The sediments in the northern ECS shelf are distributed in a ring-shaped distribution centered on the southwestern Cheju Island Mud.From the inside to the outside,the grain size goes from fine to coarse.Aside from the“grain size effect”,hydrodynamic sorting and mineral composition are important restrictions on the content of rare earth elements(REEs).Based on the grain size,REEs,and clay mineral composition of 300 surface sediments,as well as the sedimentary genesis,the northern ECS shelf is divided into three geochemical zones:southwestern Cheju Island Mud Area(ZoneⅠ),Changjiang Shoal Sand Ridges(ZoneⅡ-1),Sand Ridges of the East China Sea shelf(ZoneⅡ-2).The northern ECS shelf is mostly impacted by Chinese mainland rivers(the Changjiang River and Huanghe River),and the provenance and transport mechanism of sediments of different grain sizes is diverse.The bulk sediments come primarily from the Changjiang River,with some material from the Huanghe River carried by the yellow Sea Coastal Current and the North Jiangsu Coastal Current,and less from Korean rivers.Among them,surface sediments in the southwestern Cheju Island Mud Area(ZoneⅠ)come mostly from the Changjiang River and partly from the Huanghe River.It was formed by the counterclockwise rotating cold eddies in the northern ECS shelf,which caused the sedimentation and accumulation of the fine-grained sediments of the Changjiang River and the Huanghe River.The Changjiang Shoal Sand Ridges(ZoneⅡ-1)were developed during the early-middle Holocene sea-level highstand.It is the modern tidal sand ridge sediment formed by intense hydrodynamic action under the influence of the yellow Sea Coastal Current,North Jiangsu Coastal Current,and Changjiang Diluted Water.The surface sediments mainly originate from the Changjiang River and Huanghe River,with the Changjiang River

关键词： the northern East China Sea shelf rare earth element clay mineral provenance genetic mechanism

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