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Transcriptome sequencing reveals novel biomarkers and immune cell infiltration in esophageal tumorigenesis

World Journal of Gastrointestinal Oncology 2024年第4期16卷 1500-1513页

作者： Jian-Rong Sun Dong-Mei Chen Rong Huang rui-tao wang Li-Qun Jia School of Clinical Medicine Beijing University of Chinese MedicineBeijing 100029China Integrated Chinese and Western Medicine Oncology China-Japan Friendship HospitalBeijing 100029China

BACKGROUND Esophageal squamous cell carcinoma(ESCC)is one of the most common malignancies worldwide,and its development comprises a multistep process from intraepithelial neoplasia(IN)to carcinoma(CA).However,the critical regulators and underlying molecular mechanisms remain largely *** To explore the genes and infiltrating immune cells in the microenvironment that are associated with the multistage progression of ESCC to facilitate diagnosis and early *** A mouse model mimicking the multistage development of ESCC was established by providing warter containing 4-nitroquinoline 1-oxide(4NQO)to C57BL/6 ***,we established a control group without 4NQO treatment of ***,transcriptome sequencing was performed for esophageal tissues from patients with different pathological statuses,including low-grade IN(LGIN),high-grade IN(HGIN),and CA,and controlled normal tissue(NOR)*** expressed genes(DEGs)were identified in the LGIN,HGIN,and CA groups,and the biological functions of the DEGs were analyzed via Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment *** CIBERSORT algorithm was used to detect the pattern of immune cell ***(IHC)was also conducted to validate our ***,the Luminex multiplex cytokine analysis was utilized to measure the serum cytokine levels in the *** Compared with those in the NOR group,a total of 681541,and 840 DEGs were obtained in the LGIN,HGIN,and CA groups,*** the intersection of the three sets of DEGs,we identified 86 genes as key genes involved in the development of *** analysis revealed that these genes were enriched mainly in the keratinization,epidermal cell differentiation,and interleukin(IL)-17 signaling *** analysis revealed that,compared with those in the NOR group,M0 and M1 macrophages in the 4NQO group showed stronger infiltration,which was validated by *** cytok

关键词： Esophageal squamous cell carcinoma Intraepithelial neoplasia Tumorigenesis Transcriptome sequencing Biomarkers Immune cell infiltration 4-nitroquinoline 1-oxid

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A Two-Layer Encoding Learning Swarm Optimizer Based on Frequent Itemsets for Sparse Large-Scale Multi-Objective Optimization

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IEEE/CAA Journal of Automatica Sinica 2024年第6期11卷 1342-1357页

作者： Sheng Qi rui wang tao Zhang Xu Yang ruiqing Sun Ling wang College of Systems Engineering National University of Defense TechnologyChangsha 410073China Xiangjiang Laboratory Changsha 410205China College of Computer National University of Defense TechnologyChangsha 410073China Department of Automation Tsinghua UniversityBeijing 100084China IEEE

Traditional large-scale multi-objective optimization algorithms(LSMOEAs)encounter difficulties when dealing with sparse large-scale multi-objective optimization problems(SLM-OPs)where most decision variables are *** a result,many algorithms use a two-layer encoding approach to optimize binary variable Mask and real variable Dec ***,existing optimizers often focus on locating non-zero variable posi-tions to optimize the binary variables ***,approxi-mating the sparse distribution of real Pareto optimal solutions does not necessarily mean that the objective function is *** data mining,it is common to mine frequent itemsets appear-ing together in a dataset to reveal the correlation between *** by this,we propose a novel two-layer encoding learning swarm optimizer based on frequent itemsets(TELSO)to address these *** mined the frequent terms of multiple particles with better target values to find mask combinations that can obtain better objective values for fast ***-mental results on five real-world problems and eight benchmark sets demonstrate that TELSO outperforms existing state-of-the-art sparse large-scale multi-objective evolutionary algorithms(SLMOEAs)in terms of performance and convergence speed.

关键词： Evolutionary algorithms learning swarm optimiza-tion sparse large-scale optimization sparse large-scale multi-objec-tive problems two-layer encoding.

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Enhancing Evolutionary Algorithms With Pattern Mining for Sparse Large-Scale Multi-Objective Optimization Problems

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IEEE/CAA Journal of Automatica Sinica 2024年第8期11卷 1786-1801页

作者： Sheng Qi rui wang tao Zhang Weixiong Huang Fan Yu Ling wang the College of Systems Engineering National University of Defense Technology IEEE the Xiangjiang Laboratory the College of Transportation and Engineering Central South University the Department of Automation Tsinghua University

Sparse large-scale multi-objective optimization problems(SLMOPs) are common in science and engineering. However, the large-scale problem represents the high dimensionality of the decision space, requiring algorithms to traverse vast expanse with limited computational resources. Furthermore, in the context of sparse, most variables in Pareto optimal solutions are zero, making it difficult for algorithms to identify non-zero variables efficiently. This paper is dedicated to addressing the challenges posed by SLMOPs. To start, we introduce innovative objective functions customized to mine maximum and minimum candidate sets. This substantial enhancement dramatically improves the efficacy of frequent pattern mining. In this way,selecting candidate sets is no longer based on the quantity of nonzero variables they contain but on a higher proportion of nonzero variables within specific dimensions. Additionally, we unveil a novel approach to association rule mining, which delves into the intricate relationships between non-zero variables. This novel methodology aids in identifying sparse distributions that can potentially expedite reductions in the objective function value. We extensively tested our algorithm across eight benchmark problems and four real-world SLMOPs. The results demonstrate that our approach achieves competitive solutions across various challenges.

关键词： Evolutionary computation Benchmark testing Pareto optimization Linear programming Association rule learning Object recognition Indexes

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Evolutionary Multi-Tasking Optimization for High-Efficiency Time Series Data Clustering

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Tsinghua Science and Technology 2024年第2期29卷 343-355页

作者： rui wang Wenhua Li Kaili Shen tao Zhang Xiangke Liao Xiangjiang Laboratory Changsha 410205China College of Systems Engineering National University of Defense TechnologyChangsha 410073China Ant Group Co. Ltd.Hangzhou 310000China College of Computer Science and Technology NUDTChangsha 410073China

Time series clustering is a challenging problem due to the large-volume,high-dimensional,and warping characteristics of time series *** clustering methods often use a single criterion or distance measure,which may not capture all the features of the *** paper proposes a novel method for time series clustering based on evolutionary multi-tasking optimization,termed i-MFEA,which uses an improved multifactorial evolutionary algorithm to optimize multiple clustering tasks simultaneously,each with a different validity index or distance ***,i-MFEA can produce diverse and robust clustering solutions that satisfy various preferences of *** on two artificial datasets show that i-MFEA outperforms single-objective evolutionary algorithms and traditional clustering methods in terms of convergence speed and clustering *** paper also discusses how i-MFEA can address two long-standing issues in time series clustering:the choice of appropriate similarity measure and the number of clusters.

关键词： time series clustering evolutionary multi-tasking multifactorial optimization clustering validity index distance measure

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Learning to Branch in Combinatorial Optimization With Graph Pointer Networks

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IEEE/CAA Journal of Automatica Sinica 2024年第1期11卷 157-169页

作者： rui wang Zhiming Zhou Kaiwen Li tao Zhang Ling wang Xin Xu Xiangke Liao IEEE the Xiangjiang Laboratory and the College of Systems Engineering National University of Defense TechnologyChangsha 410073China the Institute of Automation Chinese Academy of SciencesBeijing 100190China the College of Systems Engineering National University of Defense TechnologyChangsha 410073 the Hunan Key Laboratory of Multi-Energy System Intelligent Interconnection Technology Changsha 410073China the Department of Automation Tsinghua UniversityBeijing 100084China the College of Intelligence Science and Technology National University of Defense TechnologyChangsha 410073China the College of Computer Science and Technology National University of Defense TechnologyChangsha 410073China

Traditional expert-designed branching rules in branch-and-bound(B&B) are static, often failing to adapt to diverse and evolving problem instances. Crafting these rules is labor-intensive, and may not scale well with complex *** the frequent need to solve varied combinatorial optimization problems, leveraging statistical learning to auto-tune B&B algorithms for specific problem classes becomes attractive. This paper proposes a graph pointer network model to learn the branch rules. Graph features, global features and historical features are designated to represent the solver state. The graph neural network processes graph features, while the pointer mechanism assimilates the global and historical features to finally determine the variable on which to branch. The model is trained to imitate the expert strong branching rule by a tailored top-k Kullback-Leibler divergence loss function. Experiments on a series of benchmark problems demonstrate that the proposed approach significantly outperforms the widely used expert-designed branching rules. It also outperforms state-of-the-art machine-learning-based branch-and-bound methods in terms of solving speed and search tree size on all the test instances. In addition, the model can generalize to unseen instances and scale to larger instances.

关键词： Branch-and-bound(B&B) combinatorial optimization deep learning graph neural network imitation learning

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A combined experimental and DEM investigation of grain interlocking in sheared granular assemblies

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Particuology 2024年第7期90卷 436-451页

作者： rui Lu Qiang Luo Tengfei wang David P.Connolly tao Xie School of Civil Engineering Southwest Jiaotong UniversityChengdu 610031China Key Laboratory of High-Speed Railway Engineering(Southwest Jiaotong University) Ministry of EducationChengdu 610031China School of Civil Engineering University of LeedsLeeds LS29JTUK Department of Civil Engineering McMaster UniversityHamiltonONCanada

Compacted granular material,integral to geotechnical engineering,undergoes translation,rotation,and interlocking when subject to shear displacements or external *** present study focuses on the interlocking of heterogeneous granular materials,a complex behavior influenced by gradation,compaction,and varying particle geometry,and has consequently received limited attention in existing *** address this research gap,we conducted an analysis on the effect of grain interlocking on the shear resistance of granular assemblies,using a combination of laboratory testing and the discrete element method(DEM).Initially,large-scale direct shear tests were conducted on gravel−sand mixes with varying degrees of compaction and normal *** of the mixes also underwent subsequent shear reversal to explore the differences in grain interlocking between the two shearing processes on the shear *** analyzing the laboratory results,a mesoscopic scale investigation was performed by replicating the test using discrete element *** facilitate this,granular particle geometries were measured using 3D laser scanning based on the physical lab ***,based on these scans,discrete element R-block and ball models were utilized to construct both the coarse and fine particles within the *** vibro-compaction was employed to regulate the degree of *** results indicate that an increase in vertical pressure,coupled with a zero dilatancy angle,results in a rising stress ratio,indicative of grain *** interlocking exhibits a positive correlation with both the coarse content and the degree of compaction,and varies depending on the shear *** interlocking progresses,the shear band,induced by particle movement,expands and is associated with reduced particle rotation near the shear *** study further reveals a consistent positive correlation between interlocking and the principal orientation angle of strong normal c

关键词： Granular material Interlocking Shear resistance Direct shear Discrete element method Vibro-compaction

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Vortex identification based on the Liutex method and its effect on fish passage upstream

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Journal of Hydrodynamics 2024年第1期36卷 130-141页

作者： Chun-ying Shen rui-guo Yang Xiao-tao Shi Ming-ming wang Shi-hua He Faculty of Electrical Power Engineering Kunming University of Science and TechnologyKunming650500China Hubei International Science and Technology Cooperation Base of Fish Passage China Three Gorges UniversityYichang443002China Shanghai Investigation Design and Research Institute Co.LtShanghai200434China

Fishway research is important for mitigating the fragmentation of river habitats caused by hydraulic *** vertical slit fishway is a broadly used fishway type because of its high efficiency and adaptability to water ***,the resulting vortex current disrupts the fish passage hence directly affecting fish *** study aims to accurately capture the vortex structure in the fishway and analyze the effect of vortex elements(vortex structure,vortex intensity,etc.)on *** conducted an analysis of the 3-D current flow field in the fishway through the utilization of an experimental model and the large eddy simulation(LES)***,we captured the vortex information in the fishway at different flow rates using the Liutex vortex identification method and investigated the effect of the vortex on fish *** results revealed that the structures inside the fishway pool occupy most of the room,however,the areas with higher vortex strength were primarily located in the vortex near the vertical seam and the mainstream,the vortex strength inside the fishway gradually increases with increasing flow,suppressing fish *** experienced significantly increased resistance when encountering strong *** suggests that the vortex may act as a physical barrier to fish *** findings highlight the potential negative effects of vortex on fish movement and reiterate the importance of understanding vortex dynamics for aquatic environmental *** an effective tool for identifying vortices in fluid flow,the Liutex method demonstrates features of vortex within the fishway,thereby providing important insights into the interaction between fluid dynamics and aquatic organisms.

关键词： Vertical slit fishway vortex identification method Liutex large eddy simulation(LES) fish experiment computational fluid dynamics

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Theoretical analysis of the double-differential cross-sections of neutron,proton,deuteron,^(3)He,andαfor the p+^(6) Li reaction

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Nuclear Science and Techniques 2024年第3期35卷 181-197页

作者： Fang-Lei Zou Xiao-Jun Sun Jing-Shang Zhang Hai-rui Guo Yin-Lu Han rui-rui Xu Xi tao Ji-Min wang Xiao-Dong Sun Yuan Tian tao Ye Yong-Li Xu Chun-Tian Liang College of Physics Guangxi Normal University541004 GuilinChina Guangxi Key Laboratory of Nuclear Physics and Nuclear Technology 541004 GuilinChina China Institute of Atomic Energy P.O.Box 275(41)102413 BeijingChina Institute of Applied Physics and Computational Mathematics 10094 BeijingChina College of Physics and Electronic Shanxi Datong University037009 DatongChina School of Science Tianjin Chengjian University300384 TianjinChina

Based on the unified Hauser–Feshbach and exciton model,which can describe the particle emission processes between discrete energy levels with energy,angular momentum,and parity conservations,a statistical theory of light nucleus reaction(STLN)is developed to calculate the double-differential cross-sections of the outgoing neutron and light charged particles for the proton-induced^(6) Li reaction.A significant difference is observed between the p+^(6) Li and p+^(7) Li reactions owing to the discrepancies in the energy-level structures of the *** reaction channels,including sequential and simultaneous emission processes,are analyzed in *** the double-differential cross-sections of the outgoing proton as an example,the influence of contaminations(such as^(1) H,^(7)Li,^(12)C,and^(16)O)on the target is identified in terms of the kinetic energy of the first emitted *** optical potential parameters of the proton are obtained by fitting the elastic scattering differential *** calculated total double-differential cross-sections of the outgoing proton and deuteron at E_(p)=14 MeV agree well with the experimental data for different outgoing ***,the mixed double differential cross-sections of^(3) He andαare in good agreement with the *** agreement between the measured data and calculated results indicates that the two-body and three-body breakup reactions need to be considered,and the pre-equilibrium reaction mechanism dominates the reaction *** on the STLN model,a PLUNF code for the p+^(6) Li reaction is developed to obtain an ENDF-6-formatted file of the double-differential cross-sections of the nucleon and light composite charged particles.

关键词： Statistical theory of light nucleus reaction p+^(6)Li reaction Light composite charged particle Double-differential cross-sections Two-body breakup Three-body breakup

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Mechanism of high-energy pulsed current-assisted rolling of 08AL carbon steel ultra-thin strip

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Journal of Iron and Steel Research(International) 2024年第2期31卷 416-427页

作者： Zhong-kai Ren Ya-nan Xu Jia-zhao Chen He Li rui-lin Yuan Zhen-hua wang tao wang Xiao Liu College of Mechanical and Vehicle Engineering Taiyuan University of TechnologyTaiyuan030024ShanxiChina Engineering Research Center of Advanced Metal Composites Forming Technology and Equipment(Ministry of Education) Taiyuan University of TechnologyTaiyuan030024ShanxiChina National Key Laboratory of Metal Forming Technology and Heavy Equipment China National Heavy Machinery Research Institute Co.Ltd.Xi’an710016ShaanxiChina

To improve the plastic deformation performance of a 08AL carbon steel ultra-thin strip,a pulsed electric field was integrated into the plastic processing of the ultra-thin strip,and the effects of high-energy current on its deformation ability were ***-assisted tensile tests were employed,and the results clarified that the pulsed current could reduce the activation energy of faults and promoted dislocation slip within grains and at grain boundaries,leading to a decrease in the deformation resistance of the metal and an increase in its plastic *** the current density of 2.0 A/mm2,the yield strength,tensile strength,and elongation of the rolled sample reached 425 MPa,467 MPa,and 12.5%,*** the rolling process,it was found that the pulsed current promoted the dynamic recrystallization of the ultra-thin strip,reduced its dislocation density and deformation resistance,and promoted the coordinated deformation of the metal.

关键词： 08AL ultra-thin strip High-energy pulsed current Mechanical property Dislocation density Dynamic recrystallization

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Origin and tectonic setting of low-Si alkaline magma

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Science China Earth Sciences 2024年第5期67卷 1417-1435页

作者： Qiushi ZHOU rui wang State Key Laboratory of Geological Processes and Mineral Resources and Institute of Earth SciencesChina University of GeosciencesBeijing 100083China Frontiers Science Center for Deep-time Digital Earth China University of Geosciences(Beijing)Beijing 100083China

Despite of the relatively rare occurrence of alkaline igneous rocks on Earth, they are the most diverse group of igneous rocks due to variations in their mineral assemblages and geochemical compositions. Alkaline igneous rocks are generally characterized by Si undersaturation, and K-Na(and in some cases C) enrichment. Although there is no unified alkaline igneous rock classification scheme, diagrams such as total alkalis-SiO_(2) or K_(2)O-SiO_(2) can be used to classify alkaline igneous rocks. The origins of silica-saturated alkaline rocks(SiO_(2)>52 wt.%) are relatively complex because multiple episodes of magmatism are often involved, therefore most studies have focused on the origins of silica-undersaturated alkaline *** experimental petrological studies have been conducted in the past few decades. Initially, it was considered that enrichment of trace elements was only achieved by low-degree partial melting of mantle peridotite, but the experimental melts could not reproduce the geochemical composition of natural alkaline igneous rocks. Subsequent studies have focused on carbonate-bearing eclogites that represent the average component of subducted oceanic crust. Although experimental studies indicate that silica-undersaturated and alkali-oversaturated melts can be generated from eclogites, some studies have considered that natural silica-undersaturated alkaline igneous rocks are the result of multi-stage source enrichment by incompatible elements. Low-degree partial melts of the mantle can be emplaced in the lithospheric mantle, forming veins consisting of phlogopite, amphibole, and pyroxene. Melting experiments including these components show that the produced melts better reproduce the naturally occurring silica-undersaturated alkaline magmas. Silica-deficient alkaline igneous rocks occur in various tectonic settings. Those in intraplate and divergent settings(i.e., mainly continental rifts) normally involve contributions from recycled components su

关键词： Alkaline igneous rock Tectonic setting Petrogenesis Big data

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