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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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新发HIV/AIDS患者抑郁心理干预效果及其与CD_(4)^(+)T细胞计数的关系研究

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中国全科医学 2024年第32期27卷 4009-4014页

作者：刘云卢和丽邹卿袁也丰广东省广州市民政局精神病院精神心理科 510430 南昌大学第二附属医院心身医学科江西省南昌市330006 南昌大学第一附属医院心身医学科江西省南昌市330006

背景HIV/AIDS与抑郁症相关,抑郁症加大HIV相关认知紊乱(HAND)风险,并降低患者抗逆转录病毒治疗(ART)依从性,加剧HIV传播风险。国内研究较少报道新发HIV/AIDS患者(PLWHA)抑郁心理干预效果及与CD_(4)^(+)T细胞计数相关性。目的探究新发PL... 详细信息

背景HIV/AIDS与抑郁症相关,抑郁症加大HIV相关认知紊乱(HAND)风险,并降低患者抗逆转录病毒治疗(ART)依从性,加剧HIV传播风险。国内研究较少报道新发HIV/AIDS患者(PLWHA)抑郁心理干预效果及与CD_(4)^(+)T细胞计数相关性。目的探究新发PLWHA抑郁心理干预效果及与CD_(4)^(+)T细胞计数相关性,为AIDS临床诊疗提供参考。方法2020年4月—2022年6月采用方便取样方法在江西省ART定点医院抽取新发PLWHA抑郁患者,患者确诊后立即启动ART及心理干预,干预总周期为12周。在干预前后采用汉密尔顿抑郁量表(HAMD)、汉密尔顿焦虑量表(HAMA)进行评估,并检测CD_(4)^(+)T细胞计数进行分析。结果共纳入新发PLWHA抑郁患者200例,有效随访178例,有效率为89.0%。178例PLWHA抑郁患者轻中度88例(49.4%)、重度90例(50.6%),伴焦虑者173例(97.2%)。患者CD_(4)^(+)T细胞计数均值在干预前为(346.39±156.87)个/μL,干预后为(421.93±149.61)个/μL。干预后,新发PLWHA抑郁患者CD_(4)^(+)T细胞计数高于干预前(t_(配对)=10.971,P<0.05),HAMD、HAMA总分及各因子评分均低于干预前(P<0.05)。干预前,HAMD总分与CD_(4)^(+)T细胞计数分级(以500个/μL为分界值)呈负相关(r_(s)=-0.157,P=0.036)、与HAMA总分呈正相关(r_(s)=0.764,P<0.001)。干预后,HAMD总分与干预后CD_(4)^(+)T细胞计数呈负相关(r_(s)=-0.150,P=0.046)、与HAMA总分呈强正相关(r_(s)=0.939,P<0.001)。干预前,新发PLWHA抑郁患者CD_(4)^(+)T细胞计数<500个/μL者HAMD、HAMA总分高于CD_(4)^(+)T细胞计数≥500个/μL者(P<0.05)。结论新发PLWHA抑郁严重程度与CD_(4)^(+)T细胞计数相关,经专业心理干预能显著改善。

关键词：获得性免疫缺陷综合征 HIV感染 CD_(4)^(+)T细胞计数抑郁焦虑

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Impaired Autophagy in Hilar Mossy Cells of the Dentate Gyrus and Its Implication in Schizophrenia

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Journal of Genetics and Genomics 2015年第1期42卷 1-8页

作者： yefeng yuan Hao Wang Zongbo Wei Wei Li State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental BiologyChinese Academy of Sciences University of Chinese Academy of Sciences Center of Alzheimer's Disease Beijing Institute for Brain Disorders

Schizophrenia （SCZ） is a complex disease that has been regarded as a neurodevelopmental, synaptic or epigenetic disorder. Here we provide evidence that neurodegeneration is implicated in SCZ. The DTNBP1 （dystrobrevin-binding protein 1） gene encodes dysbindin-1 and is a leading susceptibility gene of SCZ. We previously reported that the dysbindin-lC isoform regulates the survival of the hilar glutamatergic mossy cells in the dentate gyms, which controls the adult hippocampal neurogenesis. However, the underlying mechanism of hilar mossy cell loss in the dysbindin-l-deficient sandy （sdy） mice （a mouse model of SCZ） is unknown. In this study, we did not observe the apoptotic signals in the hilar mossy cells of the sdy mice by using the TUNEL assay and immunostaining of cleaved caspase-3 or necdin, a dysbindin-1- and p53-interacting protein required for neuronal survival. However, we found that the steady-state level of LC3- II, a marker of autophagosomes, was decreased in the hippocampal formation in the mice lacking dysbindin-lC. Furthermore, we observed a significant reduction of the cytosolic LC3-II puncta in the mossy cells of sdy mice. In addition, overexpression of dysbindin- 1C, but not 1A, in cultured cells increased LC3-II level and the LC3 puncta in the transfected cells. These results suggest that dysbindin- 1C deficiency causes impaired autophagy, which is likely implicated in the pathogenesis of SCZ.

关键词： Dysbindin-1 Mossy cell Neurodegeneration Autophagy Schizophrenia

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Back propagation artificial neural network for community Alzheimer's disease screening in China

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Neural Regeneration Research 2013年第3期8卷 270-276页

作者： Jun Tang Lei Wu Helang Huang Jiang Feng yefeng yuan Yueping Zhou Peng Huang Yan Xu Chao Yu Department of Epidemiology Public Health InstituteNanchang University Department of Chemistry Public Health InstituteNanchang University Department of Psychosomatic Medicine First Affiliated Hospital of Nanchang University

AIzheimer＇s disease patients diagnosed with the Chinese Classification of Mental Disorders diagnostic criteria were selected from the community through on-site sampling. Levels of macro and trace elements were measured in blood samples using an atomic absorption method, and neurotransmitters were measured using a radioimmunoassay method. SPSS 13.0 was used to establish a database, and a back propagation artificial neural network for Alzheimer＇s disease prediction was simulated using Clementine 12.0 software. With scores of activities of daily living, creatinine, 5-hydroxytryptamine, age, dopamine and aluminum as input variables, the results revealed that the area under the curve in our back propagation artificial neural network was 0.929 （95% confidence interval： 0.868-0.968）, sensitivity was 90.00%, specificity was 95.00%, and accuracy was 92.50%. The findings indicated that the results of back propagation artificial neural network established based on the above six variables were satisfactory for screening and diagnosis of Alzheimer＇s disease in patients selected from the community.

关键词： neural regeneration clinical practice artificial neural network Alzheimer's disease mathematicalmodel community trace elements neurotransmitters grant-supported paper neuroregeneration

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The origin and evolution of Earth's nitrogen

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National Science Review 2024年第6期11卷 56-75页

作者： yuan Li State Key Laboratory of Isotope Geochemistry Guangzhou Institute of GeochemistryChinese Academy of Sciences Bayerisches Geoinstitut Universit?t Bayreuth

Nitrogen is a vital element for life on Earth. Its cycling between the surface(atmosphere + crust) and the mantle has a profound influence on the atmosphere and climate. However, our understanding of the origin and evolution of Earth's nitrogen is still incomplete. This review presents an overview of the current understanding of Earth's nitrogen budget and the isotope composition of different reservoirs, laboratory constraints on deep nitrogen geochemistry, and our understanding of the origin of Earth's nitrogen and the deep nitrogen cycle through plate subduction and volcanism. The Earth may have acquired its nitrogen heterogeneously during the main accretion phase, initially from reduced, enstatite-chondrite-like impactors,and subsequently from increasingly oxidized impactors and minimal CI-chondrite-like materials. Like Earth's surface, the mantle and core are also significant nitrogen reservoirs. The nitrogen abundance and isotope composition of these three reservoirs may have been fundamentally established during the main accretion phase and have been insignificantly modified afterwards by the deep nitrogen cycle, although there is a net nitrogen ingassing into Earth's mantle in modern subduction zones. However, it is estimated that the early atmosphere of Earth may have contained ～1.4 times the present-day atmospheric nitrogen(PAN),with ～0.4 PAN being sequestered into the crust via biotic nitrogen fixation. In order to gain a better understanding of the origin and evolution of Earth's nitrogen, directions for future research are suggested.

关键词： nitrogen isotopes silicate Earth atmosphere magma ocean

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Robustness of the octupole collectivity in 144Ba within the cranking covariant density functional theory in 3D lattice

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Nuclear Science and Techniques 2024年第8期35卷 124-131页

作者： Ze‑Kai Li yuan‑yuan Wang Mathematics and Physics Department North China Electric Power UniversityBeijing 102206China Hebei Key Laboratory of Physics and Energy Technology North China Electric Power UniversityBaoding 071000China

The octupole deformation and collectivity in octupole double-magic nucleus 144Ba are investigated using the Cranking covariant density functional theory in a three-dimensional lattice *** reduced B(E3)transition probability is implemented for the first time in semiclassical approximation based on the microscopically calculated electric octupole *** available data,including the I-ωrelation and electric transitional probabilities B(E2)and B(E3)are well ***,it is shown that the ground state of 144Ba exhibits axial octupole and quadrupole deformations that persist up to high spins(I≈24h).

关键词： Octupole collectivity Cranking covariant density functional theory Rotational spectrum Electric transitional probabilities

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江西省男男性行为者高危性行为心理干预防艾效果

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中国艾滋病性病 2020年第10期26卷 1083-1087页

作者：刘云袁也丰徐茜曾欢南昌市疾病预防控制中心艾滋病性病防制科传染病预防控制国家重点实验室研究基地江西省动物源与媒介生物性传染病重点实验室南昌330038 南昌大学第一附属医院心身医学科南昌330006

目的通过对男男性行为者(MSM)高危性行为实施心理干预后评估艾滋病病毒(HIV)感染风险,了解行为心理干预对艾滋病(AIDS)防治的意义。方法 98例MSM随机分为对照组和干预组,每组49人。干预组在对照组基础上增加心理干预,比较行为心理干预... 详细信息

目的通过对男男性行为者(MSM)高危性行为实施心理干预后评估艾滋病病毒(HIV)感染风险,了解行为心理干预对艾滋病(AIDS)防治的意义。方法 98例MSM随机分为对照组和干预组,每组49人。干预组在对照组基础上增加心理干预,比较行为心理干预后两组HIV传播风险。结果干预前两组HIV知识知晓率和性行为及HIV抗体阳性率等方面差异均无统计意义。干预后,干预组知晓率(69.39%)和安全性行为比例(89.80%)均明显高于干预前(38.78%,24.49%)及对照组(40.82%,14.29%),HIV抗体阴性比例(65.31%)较干预前(69.39%)无明显改变(P> 0.05)但高于对照组(44.90%)(P <0.05),HIV抗体持续阴性比例(94.12%)高于对照组(68.75%)(P <0.05);干预组(83.67%)性伴数≤1人数多于干预前(48.98%)及对照组(20.41%)(P <0.05),引导性伴检测的MSM人数也明显多于对照组(P <0.05)。结论 MSM安全性行为比例不高。接受行为心理干预后,MSM防护意识及行为加强并能在一定的时间内保持HIV抗体持续阴性,HIV传播风险下降;还能促使其协助性伴检测,有利于预防艾滋病。

关键词：男男性行为者艾滋病高危行为心理干预

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新发现HIV感染者吸烟对神经认知功能的影响

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中国艾滋病性病 2023年第12期29卷 1309-1312页

作者：刘云卢和丽邹卿袁也丰广州市民政局精神病院广州510430 南昌大学第二附属医院心身医学科南昌330006 南昌大学第一附属医院心身医学科南昌330006

目的了解新发现HIV感染者吸烟对神经认知功能的影响。方法2020年4月至2021年8月采用方便抽样方法在江西省ART定点医院抽取新发现HIV感染者作为观察组,按照年龄、性别、受教育年限匹配非HIV感染者作为对照组,通过神经心理测验分析新发现... 详细信息

目的了解新发现HIV感染者吸烟对神经认知功能的影响。方法2020年4月至2021年8月采用方便抽样方法在江西省ART定点医院抽取新发现HIV感染者作为观察组,按照年龄、性别、受教育年限匹配非HIV感染者作为对照组,通过神经心理测验分析新发现HIV感染者吸烟对神经认知功能的影响。结果共纳入研究对象400例,回收有效问卷338份(观察组170例及对照组168例),问卷有效率84.5%。观察组吸烟率高达57.65%(98/170),神经认知功能(信息处理速度、词语学习、视觉学习等3个神经认知领域)差于对照组(t=-7.306,P=0.000;t=-9.714,P=0.000;t=-8.816,P=0.000)。观察组吸烟者在信息处理速度领域得分低于不吸烟者(t=-2.679,P=0.000),在3个神经认知领域得分低于对照组吸烟者(t=-9.798,P=0.000;t=-8.220,P=0.000;t=-6.554,P=0.000)。结论新发现HIV感染者吸烟会加剧其神经认知功能损害并提高HIV传播风险,应尽早接受ART并同时进行控烟干预。

关键词：艾滋病病毒感染者/艾滋病患者吸烟神经认知功能

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Collective Molecular Machines: Multidimensionality and Reconfigurability

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Nano-Micro Letters 2024年第8期16卷 309-340页

作者： Bin Wang yuan Lu Department of Chemical Engineering Tsinghua UniversityBeijing 100084People’s Republic of China Key Laboratory of Industrial Biocatalysis Ministry of EducationTsinghua UniversityBeijing 100084People’s Republic of China

Molecular machines are key to cellular activity where they are involved in converting chemical and light energy into efficient mechanical *** the last 60 years,designing molecular structures capable of generating unidirectional mechanical motion at the nanoscale has been the topic of intense *** progress has been made,attributed to advances in various fields such as supramolecular chemistry,biology and nanotechnology,and ***,individual molecular machines are only capable of producing nanometer work and generally have only a single *** order to address these problems,collective behaviors realized by integrating several or more of these individual mechanical units in space and time have become a new *** this review,we comprehensively discuss recent developments in the collective behaviors of molecular *** particular,collective behavior is divided into two *** is the appropriate integration of molecular machines to efficiently amplify molecular motions and deformations to construct novel functional *** other is the construction of swarming modes at the supramolecular level to perform nanoscale or microscale *** discuss design strategies for both modes and focus on the modulation of features and ***,in order to address existing challenges,the idea of transferring experience gained in the field of micro/nano robotics is presented,offering prospects for future developments in the collective behavior of molecular machines.

关键词： Molecular machines Collective control Collective behaviors DNA Biomolecular motors

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Global adaptive output-feedback tracking with prescribed performance for uncertain nonlinear systems

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Science China(Information Sciences) 2024年第5期67卷 150-164页

作者： yuan WANG Yungang LIU School of Control Science and Engineering Shandong University

At present, one typical control strategy for guaranteeing transient and steady-state performance is funnel control and prescribed performance control. The strategy features completely discarding the system nonlinearities, even if they are completely known and available. Such an intrinsic feature requires the controller to produce a larger control effect to eliminate the negative impact caused by the high nonlinearities, leading to a conservative controller. In this paper, we fully take advantage of known information on nonlinearities in control design, instead of completely discarding it as done in funnel control. Particularly, we leverage adaptive techniques(i.e., high-gain dynamic compensation) to deal with unknown system nonlinearities. Meanwhile, we integrate the tools of output feedback, tracking control, and the performance *** such, an adaptive output-feedback scheme is developed for global tracking with spatiotemporal performance specifications: arbitrarily given tracking accuracy and accuracy-ensured time. A simulation example supports the developed approach.

关键词： uncertain nonlinear systems output feedback prescribed performance unknown control direction dynamic high gain global tracking

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