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DVsc:An Automated Framework for Efficiently Detecting Viral Infection from Single-cell Transcriptomics Data

Genomics, Proteomics & Bioinformatics 2024年第2期22卷 189-200页

作者： Fei leng Song Mei Xiaolin Zhou Xuanshi Liu Yefeng Yuan Wenjian Xu Chongyi Hao Ruolan Guo Chanjuan Hao Wei Li Peng Zhang Beijing Key Laboratory for Genetics of Birth Defects Beijing Pediatric Research Institute/MOE Key Laboratory of Major Diseases in Children/Rare Disease CenterBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijing 100045China Institute of Biomedical Engineering University of TorontoTorontoM5S 3G9Canada

Single-cell RNA sequencing(scRNA-seq)has emerged as a valuable tool for studying cellular heterogeneity in various fields,particularly in virological *** studying the viral and cellular transcriptomes,the dynamics of viral infection can be investigated at a single-cell ***,limited studies have been conducted to investigate whether RNA transcripts from clinical samples contain substantial amounts of viral RNAs,and a specific computational framework for efficiently detecting viral reads based on scRNA-seq data has not been ***,we introduce DVsc,an open-source framework for precise quantitative analysis of viral infection from single-cell transcriptomics *** applied to approximately 200 diverse clinical samples that were infected by more than 10 different viruses,DVsc demonstrated high accuracy in systematically detecting viral infection across a wide array of cell *** innovative bioinformatics pipeline could be crucial for addressing the potential effects of surreptitiously invading viruses on certain illnesses,as well as for designing novel medicines to target viruses in specific host cell subsets and evaluating the efficacy of *** supports the FASTQ format as an input and is compatible with multiple single-cell sequencing ***,it could also be applied to sequences from bulk RNA sequencing *** is available at http://62.***.32.33:5000/DVsc.

关键词： Single-cell RNA sequencing Viral transcriptome Cellular transcriptome Viral infection Quantitative analysis Bulk RNA sequencing

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MetaPINNs:Predicting soliton and rogue wave of nonlinear PDEs via the improved physics-informed neural networks based on meta-learned optimization

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Chinese Physics B 2024年第2期33卷 96-107页

作者：郭亚楠曹小群宋君强冷洪泽 College of Meteorology and Oceanography National University of Defense TechnologyChangsha 410073China College of Computer National University of Defense TechnologyChangsha 410073China Naval Aviation University Huludao 125001China

Efficiently solving partial differential equations(PDEs)is a long-standing challenge in mathematics and physics *** recent years,the rapid development of artificial intelligence technology has brought deep learning-based methods to the forefront of research on numerical methods for partial differential *** them,physics-informed neural networks(PINNs)are a new class of deep learning methods that show great potential in solving PDEs and predicting complex physical *** the field of nonlinear science,solitary waves and rogue waves have been important research *** this paper,we propose an improved PINN that enhances the physical constraints of the neural network model by adding gradient information *** addition,we employ meta-learning optimization to speed up the training *** apply the improved PINNs to the numerical simulation and prediction of solitary and rogue *** evaluate the accuracy of the prediction results by error *** experimental results show that the improved PINNs can make more accurate predictions in less time than that of the original PINNs.

关键词： physics-informed neural networks gradient-enhanced loss function meta-learned optimization nonlinear science

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Natural medicine can substitute antibiotics in animal husbandry:protective effects and mechanisms of rosewood essential oil against Salmonella infection

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Chinese Journal of Natural Medicines 2024年第9期22卷 785-796页

作者： WANG Lanqiao FANG Juan WANG Heng ZHANG Baoyu WANG Nan YAO Xinyu LI He QIU Jiazhang DENG Xuming leng Bingfeng WANG Jianfeng TAN Wenxi ZHANG Qiaoling State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Key Laboratory for Zoonosis Research of the Ministry of EducationInstitute of Zoonosisand College of Veterinary MedicineJilin UniversityChangchun 130062China Shenzhen Beichen Biotech Co. Ltd.Shenzhen 518057China Department of Obstetrics and Gynecology The Second Hospital of Jilin UniversityChangchun 130041China

Aniba rosaeodora essential oil(RO) has been traditionally used in natural medicine as a substitute for antibiotics due to its notable antidepressant and antibacterial properties. Salmonella, a prevalent pathogen in foodborne illnesses, presents a major challenge to current antibiotic treatments. However, the antibacterial efficacy and mechanisms of action of RO against Salmonella spp. remain underexplored. This study aims to elucidate the chemical composition of RO, evaluate its antibacterial activity and mechanisms against Salmonella in vitro, and further delineate its anti-inflammatory mechanisms in vivo during Salmonella infection. Gas chromatography-mass spectrometry(GC-MS) was utilized to characterize the chemical constituents of RO. The antibacterial activity of RO was assessed using minimal inhibitory concentration(MIC) and time-kill assays. Various biochemical assays were employed to uncover the potential bactericidal mechanisms. Additionally, mouse and chick models of Salmonella infection were established to investigate the prophylactic effects of RO treatment. RO exhibited significant antibacterial activity against both Gram-positive and Gram-negative bacteria, with an MIC of 4 mg·mL^(-1) for Salmonella spp. RO treatment resulted in bacterial damage through the disruption of lipid and purine metabolism. Moreover, RO reduced injury and microbial colonization in infected mice and chicks. RO treatment also modulated the host inflammatory response by inhibiting proinflammatory pathways. In conclusion, our findings demonstrate that RO is effective against Salmonella infection, highlighting its potential as an alternative to antibiotics for antibacterial therapy.

关键词： Rosewood essential oil Salmonella Aniba rosaeodora Antibacterial effect Anti-inflammation Anti-infection

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Nonlinearly induced entanglement in dissipatively coupled optomechanical system

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Chinese Physics B 2024年第6期33卷 255-260页

作者：杨文全冷轩程泂张闻钊 Department of Physics Ningbo UniversityNingbo 315211China

Nonlinearly induced steady-state photon–phonon entanglement of a dissipative coupled system is studied in the bistable regime. Quantum dynamical characteristics are analysed by solving the mean-field and fluctuation equations of the system. It is shown that dissipative coupling can induce bistable behaviour for the effective dissipation of the *** suitable parameters, one of the steady states significantly reduces the dissipative effect of the system. Consequently,a larger steady-state entanglement can be achieved compared to linear dynamics. Furthermore, the experimental feasibility of the parameters is analysed. Our results provide a new perspective for the implementation of steady-state optomechanical entanglement.

关键词： entanglement optomechanical system dissipatively coupling

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Brain-wide activation involved in 15 mA transcranial alternating current stimulation in patients with first-episode major depressive disorder

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General Psychiatry 2024年第2期37卷 265-273页

作者： Jie Wang Wenfeng Zhao Huang Wang Haixia leng Qing Xue Mao Peng Baoquan Min Xiukun Jin Liucen Tan Keming Gao Hongxing Wang Songjiang Hospital and Songjiang Research Institute Shanghai Key Laboratory of Emotions and Affective DisordersShanghai Jiao Tong University School of MedicineShanghaiChina Institute of Neuroscience and Brain Diseases Xiangyang Central HospitalAffiliated Hospital of Hubei University of Arts and ScienceXiangyangHubeiChina Division of Neuropsychiatry and Psychosomatics Department of NeurologyXuanwu Hospital of Capital Medical UniversityBeijingChina Electroconvulsive Therapy University Hospitals Cleveland Medical CenterClevelandOhioUSA Department of Psychiatry Case Western Reserve University School of MedicineClevelandOhioUSA Institute of Sleep and Consciousness Disorders Center of EpilepsyBeijing Institute for Brain DisordersCapital Medical UniversityBeijingChina Institute of Special Medical Sciences School of Forensic MedicineShanxi Medical UniversityTaiyuanShanxiChina

Background Although 15 mA transcranial alternating current stimulation(tACS)has a therapeutic effect on depression,the activations of brain structures in humans accounting for this tACS configuration remain largely *** To investigate which intracranial brain structures are engaged in the tACS at 77.5 Hz and 15 mA,delivered via the forehead and the mastoid electrodes in the human *** Actual human head models were built using the magnetic resonance imagings of eight outpatient volunteers with drug-naïve,first-episode major depressive disorder and then used to perform the electric field distributions with SimNIBS *** The electric field distributions of the sagittal,coronal and axial planes showed that the bilateral frontal lobes,bilateral temporal lobes,hippocampus,cingulate,hypothalamus,thalamus,amygdala,cerebellum and brainstem were visibly stimulated by the 15 mA tACS *** Brain-wide activation,including the cortex,subcortical structures,cerebellum and brainstem,is involved in the 15 mA tACS intervention for first-episode major depressive *** results indicate that the simultaneous involvement of multiple brain regions is a possible mechanism for its effectiveness in reducing depressive symptoms.

关键词： stimulation involvement activation

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电碳市场背景下典型环境权益产品衔接互认机制及关键技术

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中国电机工程学报 2024年第7期44卷 2558-2577,I0005页

作者：尚楠陈政冷媛南方电网能源发展研究院有限责任公司广东省广州市510663

“碳达峰、碳中和”目标下,我国电力市场、碳市场、绿证市场等在产品属性、价格形成、治理监管等方面的联系日益密切,推动电碳市场背景下典型环境权益产品的联通互认,是推动实现不同市场体系之间充分融合、协同发展的关键桥梁和有力抓... 详细信息

“碳达峰、碳中和”目标下,我国电力市场、碳市场、绿证市场等在产品属性、价格形成、治理监管等方面的联系日益密切,推动电碳市场背景下典型环境权益产品的联通互认,是推动实现不同市场体系之间充分融合、协同发展的关键桥梁和有力抓手。目前,国内电碳环境权益产品尚未形成规范统一的概念定义,暂未出现电碳环境权益产品衔接互认的成熟案例,亦较为缺少密切相关的政策与市场机制设计。该文通过归纳分析国内外主流电碳环境权益产品特点及衔接互认经验,结合我国电力市场、碳市场等市场建设发展现状,剖析当前绿色电力证书、绿色电力消费、非水可再生能源(电力)消纳量、碳排放权、自愿减排量(Chinese certified emission reduction,CCER)等不同类型环境权益产品衔接互认过程中存在的碳排放量核算不准确、减排量重复认证、CCER申领范围不清晰等问题。该文在分析论述已有方案的同时,研究提出一种电碳市场背景下的不同类型环境权益产品的衔接互认体系,包括绿色电力消费与碳排放量的衔接、绿证或非水可再生能源(电力)消纳量与碳排放量的衔接、绿证与CCER的衔接等,并阐述支撑电碳环境权益产品衔接的4大类关键技术,为推动电、碳、绿证等多市场体系之间的协同发展提供决策参考。

关键词：电碳市场环境权益产品衔接互认机制碳排放量绿色电力消费碳排放因子

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天文/惯性组合系统中重力扰动补偿方法

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系统工程与电子技术 2024年第4期46卷 1357-1363页

作者：冷悦钟胜华中科技大学人工智能与自动化学院湖北武汉430074 多谱信息智能处理技术全国重点实验室湖北武汉430074 华中光电技术研究所武汉光电国家研究中心湖北武汉430223

针对重力扰动引起惯性水平基准姿态测量误差进而导致天文/惯性组合导航系统定位精度下降的问题,提出天文/惯性组合系统中的重力扰动补偿方法。首先,基于导航误差模型分析了影响天文/惯性组合导航系统定位精度的主要因素。其次,推导了重... 详细信息

针对重力扰动引起惯性水平基准姿态测量误差进而导致天文/惯性组合导航系统定位精度下降的问题,提出天文/惯性组合系统中的重力扰动补偿方法。首先,基于导航误差模型分析了影响天文/惯性组合导航系统定位精度的主要因素。其次,推导了重力扰动、惯性水平基准姿态测量误差与天文导航定位误差之间的传播机理。然后,研究了重力扰动建模与修正方法,并将重力扰动补偿方法应用于惯性水平基准的导航解算回路中,实现重力扰动的有效补偿。跑车试验结果表明,所提重力扰动补偿方法可以将天文/惯性组合导航系统中定位误差的振荡幅值由1.6 n mile降低至0.5 n mile。

关键词：天文导航系统惯性导航系统组合导航系统重力扰动

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Independent dual beams generated by array element division in integrated optical phased arrays

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Chinese Optics Letters 2024年第7期22卷 35-41页

作者： Guihan Wu Yu Xin Lemeng leng Xiang Ji Shichong Yang Kaifei Tang Quan Luo Hongsheng Luo Jinshan Su Wei Jiang College of Engineering and Applied Sciences Nanjing UniversityNanjing 210023China National Laboratory of Solid-State Microstructures Nanjing 210093China Key Laboratory of Intelligent Optical Sensing and Manipulation Ministry of EducationNanjing UniversityNanjing 210023China Jiangsu Key Laboratory of Artificial Functional Materials Nanjing UniversityNanjing 210023China Key Laboratory of Vibration Signal Capture and Intelligent Processing Yili Normal UniversityIli 835000China

Optical phased arrays(OPAs)have broad application prospects due to their advanced capability in beamforming and *** this work,we achieve independent dual beams in the far field by dividing the array elements of the OPA,with the maximum scanning range reaching 100°.Based on the working principle of OPAs,theoretical considerations of such multibeam generation are presented.A phase data allocation approach for OPAs in the presence of fabrication-induced random phase variation is *** of large ensembles of OPAs with various levels of random residual phase errors have been conducted to help analyze the *** approach can help OPAs realize multi-beams for light detection and ranging(LiDAR).

关键词： optical phased arrays beamforming phase error calibration array element division

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Characteristics,Distribution Patterns,and Classification of Volcanic Reservoirs in the Huanghua Depression,Bohai Bay Basin,China

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Journal of Earth Science 2024年第5期35卷 1464-1481页

作者： Jian Huang Changqian Ma Shihui Zhang Muyue Xu Da Lou Chongbiao leng Mutian Qin Hongjun Li State Key Laboratory of Geological Processes and Mineral Resources Faculty of Earth SciencesChina University of GeosciencesWuhan 430074China Chongqing Industry Polytechnic College Chongqing 401120China Institute of Geophysics and Geomatics China University of GeosciencesWuhan 430074China Key Laboratory of Tectonics and Petroleum Resources of Ministry of Education China University of GeosciencesWuhan 430074China Dagang Oilfield Company China National Petroleum CorporationTianjin 300280China Hubei Earthquake Agency Wuhan 430071China Yichang Earthquake Monitoring Center Station Yichang 443100China College of Marine Geosciences Ocean University of ChinaQingdao 266000China

Identifying volcanic reservoir types and their distribution patterns in volcanic edifices is important for accurate prediction and exploration of hydrocarbon ***,we analyzed the distribution patterns of different reservoir levels in volcanic edifices,discussed controlling factors,and reclassified reservoir *** was done using core observations,whole-rock geochemistry,and reservoir physical property analysis,combined with logging,drilling,seismic,and oil-gas test *** can be divided into three classes based on their physical *** Mesozoic intermediate and basic rocks formed ClassⅠreservoirs,most lithologies formed ClassⅡreservoirs,and diabase intrusions and tight volcanic rocks formed ClassⅢ*** form in different lithologies in the Huanghua depression due to *** faults deepen the influence of weathering leading to the formation of reservoirs in ***,volcanic rhythms and fractures control the vertical distribution of Cenozoic basaltic *** reservoirs are classified into five types based on the main controlling factors and distribution patterns in volcanic edifices:tectonic-alteration,vesiclefracture,weathered-effusive,weathered-eruptive,and weathered-tectonic *** these,the weathered-eruptive type can easily form ClassⅠreservoirs,making it the best target for *** the weathered-tectonic and vesicle-fracture types tend to develop ClassⅡreservoirs and can be potential *** new classification takes into account the relationship between reservoir levels and their distribution in volcanic edifices,it is more conducive to igneous reservoir prediction in the Huanghua *** study provides a novel idea for the classification and comparative study of igneous reservoirs in petroliferous basins.

关键词： volcanic reservoir types volcanic edifice controlling factors weathering and tectonism Huanghua depression petroleum geology

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β-Receptor blocker enhances the anabolic effect of PTH after osteoporotic fracture

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Bone Research 2024年第2期12卷 302-313页

作者： Jie Huang Tong Wu Yi-Rong Jiang Xuan-Qi Zheng Huan Wang Hao Liu Hong Wang Hui-Jie leng Dong-Wei Fan Wan-Qiong Yuan Chun-Li Song Department of Orthopedics Peking University Third Hospital100191 BeijingChina Beijing Key Laboratory of Spinal Disease 100191 BeijingChina Engineering Research Center of Bone and Joint Precision Medicine 100191 BeijingChina

The autonomic nervous system plays a crucial role in regulating bone metabolism,with sympathetic activation stimulating bone resorption and inhibiting bone *** found that fractures lead to increased sympathetic tone,enhanced osteoclast resorption,decreased osteoblast formation,and thus hastened systemic bone loss in ovariectomized(OVX)***,the combined administration of parathyroid hormone(PTH)and theβ-receptor blocker propranolol dramatically promoted systemic bone formation and osteoporotic fracture healing in OVX *** effect of this treatment is superior to that of treatment with PTH or propranolol *** vitro,the sympathetic neurotransmitter norepinephrine(NE)suppressed PTH-induced osteoblast differentiation and mineralization,which was rescued by ***,NE decreased the PTH-induced expression of Runx2 but enhanced the expression of Rankl and the effect of PTH-stimulated osteoblasts on osteoclastic differentiation,whereas these effects were reversed by ***,PTH increased the expression of the circadian clock gene Bmal1,which was inhibited by NE-βAR ***1 knockdown blocked the rescue effect of propranolol on the NE-induced decrease in PTHstimulated osteoblast *** together,these results suggest that propranolol enhances the anabolic effect of PTH in preventing systemic bone loss following osteoporotic fracture by blocking the negative effects of sympathetic signaling on PTH anabolism.

关键词： blocker metabolism inhibited

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