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COSINE:A web server for clonal and subclonal structure inference and evolution in cancer genomics

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Zoological Research 2022年第1期43卷 75-77页

作者： Xi-Guo Yuan Yuan Zhao Yang Guo lin-mei ge Wei Liu Shi-Yu Wen Qi Li Zhang-Bo Wan Pei-Na Zheng Tao Guo Zhi-Da Li Martin Peifer Yu-Peng Cun School of Computer Science and Technology Xidian UniversityXi'anShaanxi 710071China iFlora Bioinformatics Center Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingYunan 650201China Yuxi Rongjian Information Technology Co. Ltd.YuxiYunan 653100China Center for Molecular Medicine Cologne(CMMC) University of CologneCologne 50931Germany Pediatric Research Institute Ministry of Education Key Laboratory of Child Development and DisordersNational Clinical Research Center for Child Health and DisordersChina International Science and Technology Cooperation Base of Child Development and Critical DisordersChongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory DisordersChildren’s Hospital of Chongqing Medical UniversityChongqing 400014China

Cancer cell genomes originate from single-cell mutation with sequential clonal and subclonal expansion of somatic mutation acquisition during pathogenesis,thus exhibiting a Darwinian evolutionary process(gerstung et al.,2020;Nik-Zainal et al.,2012).Through next-generation sequencing of tumor tissue,this evolutionary process can be characterized by statistical modelling,which can identify the clonal state,somatic mutation order,and evolutionary process(gerstung et al.,2020;Mcgranahan&Swanton,2017).Inference of clonal and subclonal structure from bulk or single-cell tumor genomic sequencing data has a huge impact on studying cancer *** state and mutation order can provide detailed insight into tumor origin and future *** the past decade,various methods for subclonal reconstruction using bulk tumor sequencing data have been ***,these methods had different programming languages and data input formats,which limited their use and ***,we established a web server for Clonal and Subclonal Structure Inference and Evolution(COSINE)of cancer genomic data,which incorporated twelve popular subclonal reconstruction *** deconstructed each method to provide a detailed workflow of single processing steps with a user-friendly *** the best of our knowledge,this is the first web server providing online subclonal inference based on the integration of most popular subclonal reconstruction *** is freely accessible at ***.

关键词： .net server COSINE

Multi-model ensemble learning for battery state-of-health estimation:Recent advances and perspectives

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Journal of Energy Chemistry 2025年第1期100卷 739-759页

作者： Chuanping lin Jun Xu Delong Jiang Jiayang Hou Ying Liang Zhongyue Zou Xuesong mei State Key Laboratory for Manufacturing Systems Engineering Xi'an Jiaotong University Shaanxi Key Laboratory of Intelligent Robots School of Mechanical Engineering Xi'an Jiaotong University Department of Electrical Engineering and Automation Luoyang Institute of Science and Technology School of Mechanical Engineering Hangzhou Dianzi University

The burgeoning market for lithium-ion batteries has stimulated a growing need for more reliable battery performance monitoring. Accurate state-of-health(SOH) estimation is critical for ensuring battery operational performance. Despite numerous data-driven methods reported in existing research for battery SOH estimation, these methods often exhibit inconsistent performance across different application scenarios. To address this issue and overcome the performance limitations of individual data-driven models,integrating multiple models for SOH estimation has received considerable attention. Ensemble learning(EL) typically leverages the strengths of multiple base models to achieve more robust and accurate outputs. However, the lack of a clear review of current research hinders the further development of ensemble methods in SOH estimation. Therefore, this paper comprehensively reviews multi-model ensemble learning methods for battery SOH estimation. First, existing ensemble methods are systematically categorized into 6 classes based on their combination strategies. Different realizations and underlying connections are meticulously analyzed for each category of EL methods, highlighting distinctions, innovations, and typical applications. Subsequently, these ensemble methods are comprehensively compared in terms of base models, combination strategies, and publication trends. Evaluations across 6 dimensions underscore the outstanding performance of stacking-based ensemble methods. Following this, these ensemble methods are further inspected from the perspectives of weighted ensemble and diversity, aiming to inspire potential approaches for enhancing ensemble performance. Moreover, addressing challenges such as base model selection, measuring model robustness and uncertainty, and interpretability of ensemble models in practical applications is emphasized. Finally, future research prospects are outlined, specifically noting that deep learning ensemble is poised to advance ens

关键词： Contrastive Learning

Bidirectional regulation of the brain-gut-microbiota axis following traumatic brain injury

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Neural Regeneration Research 2025年第8期20卷 2153-2168页

作者： Xinyu You lin Niu Jiafeng Fu Shining ge Jiangwei Shi Yanjun Zhang Pengwei Zhuang National Key Laboratory of Chinese Medicine Modernization Tianjin University of Traditional Chinese MedicineTianjinChina Haihe Laboratory of Modern Chinese Medicine Tianjin University of Traditional Chinese MedicineTianjinChina First Teaching Hospital of Tianjin University of Traditional Chinese Medicine TianjinChina National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion TianjinChina

Traumatic brain injury is a prevalent disorder of the central nervous *** addition to primary brain parenchymal damage,the enduring biological consequences of traumatic brain injury pose long-term risks for patients with traumatic brain injury;however,the underlying pathogenesis remains unclear,and effective intervention methods are *** dysfunction is a significant consequence of traumatic brain *** the most densely innervated peripheral tissue in the body,the gut possesses multiple pathways for the establishment of a bidirectional“brain-gut axis”with the central nervous *** gut harbors a vast microbial community,and alterations of the gut niche contribute to the progression of traumatic brain injury and its unfavorable prognosis through neuronal,hormonal,and immune pathways.A comprehensive understanding of microbiota-mediated peripheral neuroimmunomodulation mechanisms is needed to enhance treatment strategies for traumatic brain injury and its associated *** comprehensively reviewed alterations in the gut microecological environment following traumatic brain injury,with a specific focus on the complex biological processes of peripheral nerves,immunity,and microbes triggered by traumatic brain injury,encompassing autonomic dysfunction,neuroendocrine disturbances,peripheral immunosuppression,increased intestinal barrier permeability,compromised responses of sensory nerves to microorganisms,and potential effector nuclei in the central nervous system influenced by gut ***,we reviewed the mechanisms underlying secondary biological injury and the dynamic pathological responses that occur following injury to enhance our current understanding of how peripheral pathways impact the outcome of patients with traumatic brain *** review aimed to propose a conceptual model for future risk assessment of central nervous system-related diseases while elucidating novel insights into the bidirectional effec

关键词： traumatic brain injury brain-gut-microbiome axis gut microbiota neuroimmune immunosuppression host defense vagal afferents bacterial infection dorsal root ganglia nociception neural circuitry

Recent progress in the applications of presynaptic dopaminergic positron emission tomography imaging in parkinsonism

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Neural Regeneration Research 2025年第1期20卷 93-106页

作者： Yujie Yang Xinyi Li Jiaying Lu Jingjie ge Mingjia Chen Ruixin Yao mei Tian Jian Wang Fengtao Liu Chuantao Zuo Key Laboratory of Arrhythmias Ministry of EducationDepartment of Medical GeneticsShanghai East HospitalSchool of MedicineTongji UniversityShanghaiChina Department of Neurology National Research Center for Aging and MedicineNational Center for Neurological Disordersand State Key Laboratory of Medical NeurobiologyHuashan HospitalFudan UniversityShanghaiChina Department of Nuclear Medicine&PET Center National Center for Neurological Disordersand National Clinical Research Center for Aging and MedicineHuashan HospitalFudan UniversityShanghaiChina International Human Phenome Institutes(Shanghai) ShanghaiChina Human Phenome Institute Fudan UniversityShanghaiChina

Nowadays,presynaptic dopaminergic positron emission tomography,which assesses deficiencies in dopamine synthesis,storage,and transport,is widely utilized for early diagnosis and differential diagnosis of *** review provides a comprehensive summary of the latest developments in the application of presynaptic dopaminergic positron emission tomography imaging in disorders that manifest *** conducted a thorough literature search using reputable databases such as PubMed and Web of *** criteria involved identifying peer-reviewed articles published within the last 5 years,with emphasis on their relevance to clinical *** findings from these studies highlight that presynaptic dopaminergic positron emission tomography has demonstrated potential not only in diagnosing and differentiating various Parkinsonian conditions but also in assessing disease severity and predicting ***,when employed in conjunction with other imaging modalities and advanced analytical methods,presynaptic dopaminergic positron emission tomography has been validated as a reliable in vivo *** validation extends to screening and exploring potential neuropathological mechanisms associated with dopaminergic *** summary,the insights gained from interpreting these studies are crucial for enhancing the effectiveness of preclinical investigations and clinical trials,ultimately advancing toward the goals of neuroregeneration in parkinsonian disorders.

关键词： aromatic amino acid decarboxylase brain imaging dopamine transporter Parkinson’s disease parkinsonism positron emission tomography presynaptic dopaminergic function vesicle monoamine transporter type 2

KED-ICP-MS测定天然饮用泉水中的18种元素含量

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食品研究与开发 2016年第16期37卷 151-154页

作者：蒋慧雷宁生黎林钟格梅广西疾病预防控制中心广西南宁530028

建立碰撞反应池-电感耦合等离子体质谱（KED-ICP-MS）测定天然饮用泉水中的K、K、Na、Ca、Mg、Fe、Mn、Cu、Zn、Li、Sr、Se、As、Cd、Ni、Pb、Ba、Cr、Hg等18种元素含量的方法,采集的天然饮用泉水经过酸化处理后,采用碰撞反应池技术进... 详细信息

建立碰撞反应池-电感耦合等离子体质谱（KED-ICP-MS）测定天然饮用泉水中的K、K、Na、Ca、Mg、Fe、Mn、Cu、Zn、Li、Sr、Se、As、Cd、Ni、Pb、Ba、Cr、Hg等18种元素含量的方法,采集的天然饮用泉水经过酸化处理后,采用碰撞反应池技术进行测定,通过通入氦气的碰撞反应来消除分子离子干扰,使得检测结果更加准确。试验表明,测定18种元素的线性相关系数均〉0.999,相对标准偏差为0.39%~4.97%,各元素的加标回收率均在85.4%~115.0%之间,测定各元素的标准参考物质,测定值均在标准值范围内。

关键词：元素电感耦合等离子体质谱天然饮用泉水碰撞反应

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内镜治疗肝外胆管良性狭窄29例

世界华人消化杂志 2010年第9期18卷 950-953页

作者：宫爱霞马静葛林梅冷敬郭世斌孙康孙颖大连医科大学附属第一医院消化科辽宁省大连市116011

目的:探讨内镜在肝外胆管良性狭窄治疗中的作用.方法:回顾性分析29例因梗阻性黄疸入院,均经CT或MRI及实验室检查及其病史确诊为胆管良性狭窄患者临床资料.将肝外胆管狭窄分类比照Bismuth标准分为3型,并评价患者行十二指肠镜乳头肌切开术... 详细信息

目的:探讨内镜在肝外胆管良性狭窄治疗中的作用.方法:回顾性分析29例因梗阻性黄疸入院,均经CT或MRI及实验室检查及其病史确诊为胆管良性狭窄患者临床资料.将肝外胆管狭窄分类比照Bismuth标准分为3型,并评价患者行十二指肠镜乳头肌切开术(EST)或行胆管内支架引流术(ERBD)的治疗效果.结果:29例患者经EST或ERBD治疗,有效率为96.55%.随访患者28例,其中行EST治疗4例,均未复发;放置ERBD24例,8例6mo内复发、8例再狭窄患者中4例为慢性胰腺炎,2例为有胆囊切除史者,占该组11.11%(2/18);其余8例中5例为单支架置入者.结论:肝外胆管良性狭窄的内镜下治疗安全有效,其治疗效果与狭窄的病因和部位有关;狭窄部位长时间、多支架置入,可以减少术后再狭窄率.

关键词：肝外胆管良性狭窄内镜治疗梗阻性黄疸胆管内支架引流术

Noncoding RNAs:Different roles in tumorigenesis

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Chinese Science Bulletin 2012年第9期57卷 959-965页

作者： lin mei WU Jing SHAN ge School of Life Sciences University of Science and Technology of China Hefei 230026 China School of Life Science and Technology Huazhong University of Science and Technology Wuhan 430074 China

A major portion of the mammalian genome is transcribed to produce large numbers of noncoding RNAs(ncRNAs).During the past decade,the discovery of small RNAs,including the microRNAs(miRNA) and small interfering RNAs(siRNA),has led to important advances in *** breadth of the ncRNA field of study has substantially expanded and many recent results have revealed a range of functions that can be attributed to the miRNAs and other *** example,H19 RNA,HOTAIR RNA,transcribed ultraconserved regions(T-UCRs),natural antisense RNA,transfer RNA and mitochondrial noncoding RNA have been suggested to play important roles in cancers and other diseases as well as in diverse cellular *** this review,we focus on the current status of several classes of ncRNAs associated with cancer with the emphasis on those that are not microRNAs.

关键词：非编码RNA 小分子RNA miRNAs RNA干扰肿瘤反义RNA 哺乳动物核糖核酸

Assessment of the potential toxicity of insecticidal compounds to Peristenus spretus,a parasitoid of mirid bugs

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Journal of Integrative Agriculture 2022年第5期21卷 1424-1435页

作者： ZHAO Man LI Yun-he NIU lin-lin CHEN lin LIANG ge-mei State Key Laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193P.R.China College of Plant Protection Henan Agricultural UniversityZhengzhou 450002P.R.China

With the increased cultivation of Bt crops in China,Apolygus lucorum and other mirid bugs have emerged as important agricultural pests because they are insensitive to the Bt *** addition,the reduction of pesticide applications after planting Bt crops also increases the severity of mirid bug *** spretus is a parasitoid of mirid nymphs,but its sensitivity to Bt proteins is not *** the current study,we developed a dietary exposure assay to assess the effects of Bt proteins(Cry1Ab,Cry1Ac,Cry1F,Cry2Aa,and Cry2Ab)on *** adults using a diet consisting of a 10% honey solution with or without Bt proteins at 400μg g^(-1) *** results showed that the survival and reproduction of *** adults were reduced by the cysteine protease inhibitor E-64(a positive control)but were not affected by any of the five Bt *** activities of digestive,detoxifying,and antioxidant enzymes in *** were also unaffected by diets containing the Cry proteins,but they were significantly affected by the diet containing *** then developed a tritrophic bioassay to determine the effects of the five Bt proteins on *** larvae and *** this assay,*** nymphs fed an artificial diet containing Cry proteins were used as the hosts for *** results of the tri-trophic assay indicated that neither the pupation rate nor the eclosion rate of the *** parasitoids were significantly affected by the presence of high concentrations of Bt proteins in the parasitized *** *** overall results indicate that these two assays can be used to evaluate the toxicity of insecticidal compounds to *** and that the tested Cry proteins are not toxic to ***.

关键词： transgenic crops plant bugs parasitic natural enemy Cry proteins non-target risk assessment

The novel usage of thiourea nitrate in aryl nitration

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Chinese Chemical Letters 2014年第1期25卷 87-89页

作者： ge Meng mei-lin Zheng A-Qun Zheng mei Wang Juan Shi School of Pharmacy Xi’an Jiaotong University School of Science Xi’an Jiaotong University

Thiourea nitrate （TN） was easily prepared from thiourea and nitric acid to explore its use as a new nitration reagent, Nitrations of various aromatic compounds utilizing TN in concentrated sulfuric acid were studied, TN could convert aromatic compounds to the corresponding nitrated derivatives with various abnormal yields under mild conditions. The results suggested that the reaction mechanism might be different from those of traditional nitration reagents.

关键词： Thiourea nitrate Nitration Thiourea Aromatic compounds