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Machine learning and bioinformatics to identify biomarkers in response to Burkholderia pseudomallei infection in mice

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BIOCELL 2024年第4期48卷 613-621页

作者： YAO fang FEI XIA FEIFEI TIAN L EI QU fang YANG juan fang ZHENHONG HU HAICHAO LIU Department of Respiratory and Critical Care Medicine General Hospital of Center Theater of PLAWuhan430070China School of Medicine Wuhan University of Science and TechnologyWuhan430065China School of Life Science and Engineering Southwest Jiaotong UniversityChengdu611756China

Objective:In the realm of Class I pathogens,Burkholderia pseudomallei(BP)stands out for its propensity to induce severe pathogenicity.Investigating the intricate interactions between BP and host cells is imperative for comprehending the dynamics of BP infection and discerning biomarkers indicative of the host cell response process.Methods:mRNA extraction from BP-infected mouse macrophages constituted the initial step of our study.Employing gene expression arrays,the extracted RNA underwent conversion into digital signals.The percentile shift method facilitated data processing,with the identiﬁcation of genes manifesting signiﬁcant differences accomplished through the application of the t-test.Subsequently,a comprehensive analysis involving Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway was conducted on the differentially expressed genes(DEGs).Leveraging the ESTIMATE algorithm,gene signatures were utilized to compute risk scores for gene expression data.Support vector machine analysis and gene enrichment scores were instrumental in establishing correlations between biomarkers and macrophages,followed by an evaluation of the predictive power of the identiﬁed biomarkers.Results:The functional and pathway associations of the DEGs predominantly centered around G protein-coupled receptors.A noteworthy positive correlation emerged between the blue module,consisting of 416 genes,and the StromaScore.FZD4,identiﬁed through support vector machine analysis among intersecting genes,indicated a robust interaction with macrophages,suggesting its potential as a robust biomarker.FZD4 exhibited commendable predictive efﬁcacy,with BP infection inducing its expression in both macrophages and mouse lung tissue.Western blotting in macrophages conﬁrmed a signiﬁcant upregulation of FZD4 expression from 0.5 to 24 h post-infection.In mouse lung tissue,FZD4 manifested higher expression in the cytoplasm of pulmonary epithelial cells in BP-infected lungs than in the control group.Conclusion:Theseﬁndings underscor

关键词： Burkholderia pseudomallei Microarray assay Machine learning Bioinformatics FZD4

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Decade Milestone Advancement of Defect-Engineered g-C_(3)N_(4) for Solar Catalytic Applications

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Nano-Micro Letters 2024年第4期16卷 153-218页

作者： Shaoqi Hou Xiaochun Gao Xingyue Lv Yilin Zhao Xitao Yin Ying Liu juan fang Xingxing Yu Xiaoguang Ma Tianyi Ma Dawei Su School of Mathematical and Physical Sciences Faculty of ScienceUniversity of Technology Sydney(UTS)SydneyNSW 2007Australia Laboratory of Plasma and Energy Conversion School of Physics and Optoelectronic EngineeringLudong University186 Middle Hongqi RoadYantai 264025People’s Republic of China School of Energy and Environmental Engineering University of Science and Technology BeijingBeijing 100083People’s Republic of China Department of Chemistry The University of Tokyo7‑3‑1 HogoBunkyoTokyoJapan School of Science STEM CollegeRMIT UniversityMelbourneVIC 3000Australia

Over the past decade, graphitic carbon nitride(g-C_(3)N_(4)) has emerged as a universal photocatalyst toward various sustainable carbo-neutral technologies. Despite solar applications discrepancy, g-C_(3)N_(4) is still confronted with a general fatal issue of insufficient supply of thermodynamically active photocarriers due to its inferior solar harvesting ability and sluggish charge transfer dynamics. Fortunately, this could be significantly alleviated by the “all-in-one” defect engineering strategy, which enables a simultaneous amelioration of both textural uniqueness and intrinsic electronic band structures. To this end, we have summarized an unprecedently comprehensive discussion on defect controls including the vacancy/non-metallic dopant creation with optimized electronic band structure and electronic density, metallic doping with ultraactive coordinated environment(M–N_(x), M–C_(2)N_(2), M–O bonding), functional group grafting with optimized band structure, and promoted crystallinity with extended conjugation π system with weakened interlayered van der Waals interaction. Among them, the defect states induced by various defect types such as N vacancy, P/S/halogen dopants, and cyano group in boosting solar harvesting and accelerating photocarrier transfer have also been emphasized. More importantly, the shallow defect traps identified by femtosecond transient absorption spectra(fs-TAS) have also been highlighted. It is believed that this review would pave the way for future readers with a unique insight into a more precise defective g-C_(3)N_(4) “customization”, motivating more profound thinking and flourishing research outputs on g-C_(3)N_(4)-based photocatalysis.

关键词： Defect engineering g-C_(3)N_(4) Electronic band structures Photocarrier transfer kinetics Defect states

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Monomorphic epitheliotropic intestinal T-cell lymphoma with bone marrow involved: A case report

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World Journal of Clinical Cases 2024年第4期12卷 814-819页

作者： Fen-juan Zhang Wen-juan fang Cang-Jian Zhang Department of Hematology Lishui Municipal Central HospitalLishui 323000Zhejiang ProvinceChina

BACKGROUND Monomorphic epithelial intestinal T-cell lymphoma(MEITL)is a rare type of peripheral T-cell lymphoma.The clinical manifestations are diarrhea,abdominal pain,perforation and an abdominal mass.CASE SUMMARY We present a 52-year-old female patient who was diagnosed with MEITL.Further disease progression was observed after multiline chemotherapy.Eventually,the patient died of a severe infection.CONCLUSION MEITL is a rare intestinal primary T-cell lymphoma with aggressive behavior,a high risk of severe life-threatening complications,and a poor prognosis.

关键词： Monomorphic epithelial intestinal T-cell lymphoma Autologous stem cell transplantation Chemotherapeutics Case report

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The Initial Mesoscale Vortexes Leading to the Formation of Tropical Cyclones in the Western North Pacific

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Advances in Atmospheric Sciences 2023年第5期40卷 804-823页

作者： Shenglan WU juan fang Shanghai Central Meteorological Observatory CMAShanghai 200030China Key Laboratory of Mesoscale Severe Weather(MOE) School of the Atmospheric SciencesNanjing University163 Xianlin RoadNanjing 210046China

A statistical analysis of the initial vortexes leading to tropical cyclone(TC)formation in the western North Pacific(WNP)is conducted with the ECMWF ERA5 reanalysis data from 1999 to 2018.It is found that TCs in the WNP basically originate from three kinds of vortexes,i.e.,a mid-level vortex(MV),a low-level vortex(LV),and a relatively deep vortex with notable vorticity in both the lower and middle troposphere(DV).Among them,LV and DV account for 47.9%and 24.2%of tropical cyclogenesis events,respectively,while only 27.9%of TCs develop from the MV,which is much lower than that which occurs in the North Atlantic and eastern Pacific.Such a difference might be ascribed to the active monsoon systems in the WNP all year round.Due to the nearly upright structure of mid-level convergence in the early pre-genesis stage,TC genesis efficiency is the highest in DV.Compared with MV,LV generally takes a shorter time to intensify to a TC because of the higher humidity and the stronger low-level cyclonic circulation,which is related to air-sea interaction and boundary-layer convergence.Further examination of the relationship between tropical cyclogenesis and large-scale flow patterns indicate that the TC genesis events associated with LV are primarily related to the monsoon shear line,monsoon confluence region,and monsoon gyre,while those associated with MV are frequently connected with easterly waves and wave energy dispersion of preexisting TC.Compared with other flow patterns,tropical cyclones usually form and intensify faster in the monsoon confluence region.

关键词： TC formation initial mesoscale vortexes TC genesis efficiency large-scale flow patterns

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Maneuver control at high angle of attack based on real-time optimization of integrated aero-propulsion

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Chinese Journal of Aeronautics 2022年第12期35卷 173-188页

作者： juan fang Qiangang ZHENG Changpeng CAI Haibo ZHANG College of Energy and Power Engineering Nanjing University of Aeronautics and AstronauticsNanjing 210016China

To reduce the propulsion system installation thrust loss under high angle of attack maneuvering,a control method based on real-time optimization of the integrated aeropropulsion is proposed.Firstly,based on data fitting and physical principle,an integrated onboard model of propulsion system is established,which can calculate various performance parameters of the propulsion system in real time,and has high accuracy and real-time performance.Secondly,to improve the compatibility of optimization real-time performance and search accuracy,the online optimization control of aero-propulsion system is realized based on an improved trust region algorithm.Finally,by controlling the auxiliary intake valve,a good match between inlet and engine is realized,which solves the problems of intake flow reducing and total pressure recovery coefficient declining,and improves the installation performance of propulsion system.The simulation results indicate that,compared with the conventional independent engine control,the real-time integrated optimization method reduces the installed thrust loss by 3.61%under the design condition,and 4.58%under the off-design condition.Furthermore,the simulation on HIL(Hardware-In-theLoop)platform verifies the real-time performance of integrated optimization method.

关键词： High angle of attack Inlet/engine integration Real-time optimization Engine performance Auxiliary intake valve

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A perceptual and predictive batch-processing memory scheduling strategy for a CPU-GPU heterogeneous system

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Frontiers of Information Technology & Electronic Engineering 2023年第7期24卷 994-1006页

作者： juan fang Sheng LIN Huijing YANG Yixiang XU Xing SU SU Faculty of Information Technology Beijing University of TechnologyBeijing 100124China

When multiple central processing unit(CPU)cores and integrated graphics processing units(GPUs)share off-chip main memory,CPU and GPU applications compete for the critical memory resource.This causes serious resource competition and has a negative impact on the overall performance of the system.We describe the competition for shared-memory resources in a CPU-GPU heterogeneous multi-core architecture,and a sharedmemory request scheduling strategy based on perceptual and predictive batch-processing is proposed.By sensing the CPU and GPU memory request conditions in the request buffer,the proposed scheduling strategy estimates the GPU latency tolerance and reduces mutual interference between CPU and GPU by processing CPU or GPU memory requests in batches.According to the simulation results,the scheduling strategy improves CPU performance by8.53%and reduces mutual interference by 10.38%with low hardware complexity.

关键词： CPU-GPU heterogeneous Multi-core Unified memory Access scheduling

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Resource Scheduling Strategy for Performance Optimization Based on Heterogeneous CPU-GPU Platform

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Computers, Materials & Continua 2022年第10期73卷 1621-1635页

作者： juan fang Kuan Zhou Mengyuan Zhang Wei Xiang Faculty of Information Technology Beijing University of TechnologyBeijing100124China La Trobe University MelbourneVIC3086Australia James Cook University CainsQLD4878Australia

In recent years,with the development of processor architecture,heterogeneous processors including Center processing unit(CPU)and Graphics processing unit(GPU)have become the mainstream.However,due to the differences of heterogeneous core,the heterogeneous system is now facing many problems that need to be solved.In order to solve these problems,this paper try to focus on the utilization and efficiency of heterogeneous core and design some reasonable resource scheduling strategies.To improve the performance of the system,this paper proposes a combination strategy for a single task and a multi-task scheduling strategy for multiple tasks.The combination strategy consists of two sub-strategies,the first strategy improves the execution efficiency of tasks on the GPU by changing the thread organization structure.The second focuses on the working state of the efficient core and develops more reasonable workload balancing schemes to improve resource utilization of heterogeneous systems.The multi-task scheduling strategy obtains the execution efficiency of heterogeneous cores and global task information through the processing of task samples.Based on this information,an improved ant colony algorithm is used to quickly obtain a reasonable task allocation scheme,which fully utilizes the characteristics of heterogeneous cores.The experimental results show that the combination strategy reduces task execution time by 29.13%on average.In the case of processing multiple tasks,the multi-task scheduling strategy reduces the execution time by up to 23.38%based on the combined strategy.Both strategies can make better use of the resources of heterogeneous systems and significantly reduce the execution time of tasks on heterogeneous systems.

关键词： Heterogeneous computing CPU-GPU Performance Workload balance

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A Survey of Statistical Relationships between Tropical Cyclone Genesis and Convectively Coupled Equatorial Rossby Waves

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Advances in Atmospheric Sciences 2022年第5期39卷 747-762页

作者： Shuguang WANG juan fang Xiaodong TANG Zhe-Min TAN Key Laboratory of Mesoscale Severe Weather(MOE) School of Atmospheric SciencesNanjing UniversityNanjing 210093China

Convectively coupled equatorial Rossby waves(ERW)modulate tropical cyclone activities over tropical oceans.This study presents a survey of the statistical relationship between intraseasonal ERWs and tropical cyclone genesis(TCG)over major global TC basins using four-decade-long outgoing longwave radiation(OLR)and TC best-track datasets.Intraseasonal ERWs are identified from the OLR anomalies using an empirical orthogonal function(EOF)analysis method without imposing equatorial symmetry.We find that westward-propagating ERWs are most significant in four tropical ocean basins over the summer hemisphere and that ERWs exhibit similar northeast-southwest(southeast-northwest)tilted phase lines in the northern(southern)hemisphere,with an appreciable poleward advance of wave energy in most TC basins.The EOF-based ERW indices quantitatively show that ERWs significantly modulate TC genesis.The convectively active(suppressed)phases of ERWs coincide with increased(reduced)TCG occurrences.The TCG modulation by ERWs achieves the maximum where the ERWs propagate through the climatological TCG hotspots.As a result,the total number of TCG occurrences in the TC basins varies significantly according to the ERW phase.The ERW-TCG relationship is significant over the northwestern Pacific Ocean,northeastern Pacific Ocean,and the northern Indian Ocean during the northern summer seasons.In the southern summer season,the ERW-TCG relationship is significant over the southern Indian Ocean,Indonesian-Australia basin,and the southwestern Pacific Ocean.However,ERW activities are weak in the main TC development region of the Atlantic Ocean;and the impact on Atlantic TCG appears to be insignificant.

关键词： tropical cyclone genesis equatorial Rossby waves statistical analysis

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KRT4 suppresses oral squamous cell carcinoma development by reducing ATG4B-mediated autophagy

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BIOCELL 2022年第2期46卷 441-451页

作者： XIAOXU LI YUN WANG juan fang ZHI WANG XIAOAN TAO juan XIA BIN CHENG Guangdong Provincial Key Laboratory of Stomatology Guanghua School of StomatologyHospital of StomatologySun Yat-Sen UniversityGuangzhou510055China

Head and neck squamous cell carcinoma is the sixth most common tumor worldwide,and half of head and neck squamous cell carcinoma patients are with oral squamous cell carcinoma(OSCC).300,000 new cases of OSCC were reported annually.Even with multi-modality treatment,the prognosis of OSCC remains unsatisfactory.Thus,it is urgent to discover novel therapeutic targets for OSCC.Some microarray studies have revealed that Keratin 4(KRT4)is downregulated in OSCC,whereas its role in OSCC development remains unknown.The present study revealed that KRT4 suppressed OSCC progression by inducing cell apoptosis and inhibiting cell invasion.In addition,KRT4 over-expression inhibited autophagy by blocking the interaction of autophagy-related 4B cysteine peptidase(ATG4B)and microtubule-associated protein 1A/1B light chain 3(LC3)to regulate apoptosis and invasion of OSCC.In conclusion,KRT4 played an important role in OSCC development through regulating ATG4B-mediated autophagy and may be a novel therapeutic drug target of OSCC.

关键词： Oral squamous cell carcinoma KRT4 Cancer-suppressive role ATG4B Autophagy

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STTAR: A Traffic- and Thermal-Aware Adaptive Routing for 3D Network-on-Chip Systems

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Computers, Materials & Continua 2022年第9期72卷 5531-5545页

作者： juan fang Yunfei Mao Min Cai Li’ang Zhao Huijie Chen Wei Xiang Faculty of Information Technology Beijing University of TechnologyBeijing100124China La Trobe University MelbourneVIC 3086Australia James Cook University CainsQLD 4878Australia

Since the three-dimensional Network on Chip(3D NoC)uses through-silicon via technology to connect the chips,each silicon layer is conducted through heterogeneous thermal,and 3D NoC system suffers from thermal problems.To alleviate the seriousness of the thermal problem,the distribution of data packets usually relies on traffic information or historical temperature information.However,thermal problems in 3D NoC cannot be solved only based on traffic or temperature information.Therefore,we propose a Score-Based Traffic-and Thermal-Aware Adaptive Routing(STTAR)that applies traffic load and temperature information to routing.First,the STTAR dynamically adjusts the input and output buffer lengths of each router with traffic load information to limit routing resources in overheated areas and control the rate of temperature rise.Second,STTAR adopts a scoring strategy based on temperature and the number of free slots in the buffer to avoid data packets being transmitted to high-temperature areas and congested areas and to improve the rationality of selecting routing output nodes.In our experiments,the proposed scoring Score-Based Traffic-and Thermal-Aware Adaptive Routing(STTAR)scheme can increase the throughput by about 14.98%to 47.90%and reduce the delay by about 10.80%to 35.36%compared with the previous works.

关键词： Buffer allocation thermal 3D NoC routing algorithm

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