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Exploring noncoding variants in genetic diseases:from detection to functional insights

Journal of Genetics and Genomics 2024年第2期51卷 111-132页

作者： Ke Wu Fengxiao Bu Yang Wu Gen Zhang Xin Wang shunmin he Mo-Fang Liu Runsheng Chen Huijun Yuan Institute of Rare Diseases West China Hospital of Sichuan UniversityChengduSichuan 610041China Key Laboratory of Systems health Science of Zhejiang Province School of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouZhejiang 310024China Key Laboratory of RNA Biology Center for Big Data Research in HealthInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China State Key Laboratory of Molecular Biology State Key Laboratory of Cell BiologyShanghai Key Laboratory of Molecular AndrologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai 200031China

Previous studies on genetic diseases predominantly focused on protein-coding variations, overlooking the vast noncoding regions in the human genome. The development of high-throughput sequencing technologies and functional genomics tools has enabled the systematic identification of functional noncoding variants. These variants can impact gene expression, regulation, and chromatin conformation, thereby contributing to disease pathogenesis. Understanding the mechanisms that underlie the impact of noncoding variants on genetic diseases is indispensable for the development of precisely targeted therapies and the implementation of personalized medicine strategies. The intricacies of noncoding regions introduce a multitude of challenges and research opportunities. In this review, we introduce a spectrum of noncoding variants involved in genetic diseases, along with research strategies and advanced technologies for their precise identification and in-depth understanding of the complexity of the noncoding genome. We will delve into the research challenges and propose potential solutions for unraveling the genetic basis of rare and complex diseases.

关键词： Noncoding variation Genetic disease Research approach Challenge

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胰头肿块型慢性胰腺炎的临床诊治:附2例报告

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中国普通外科杂志 2024年第9期33卷 1536-1541页

作者：贺舜民严安汪东文樊巍巍罗东李志强涂广平余枭中国人民武装警察部队湖南省总队医院外一科湖南长沙410006 中南大学湘雅三医院肝胆胰外科Ⅱ 湖南长沙410013

背景与目的:胰头肿块型慢性胰腺炎(MFCP)是一种特殊类型的慢性胰腺炎,其临床和影像学特征与胰腺导管腺癌(PDAC)相似,容易导致诊断混淆,其治疗决策也十分棘手,致使患者延误准确、有效治疗。鉴于此,本文对该病临床特点和治疗决策进行分析... 详细信息

背景与目的:胰头肿块型慢性胰腺炎(MFCP)是一种特殊类型的慢性胰腺炎,其临床和影像学特征与胰腺导管腺癌(PDAC)相似,容易导致诊断混淆,其治疗决策也十分棘手,致使患者延误准确、有效治疗。鉴于此,本文对该病临床特点和治疗决策进行分析总结,以期提高此类慢性胰腺炎的诊断和治疗能力,为临床治疗提供有价值的参考。方法:回顾性分析2例典型胰头MFCP患者临床资料,并复习相关文献。结果:2例患者均因长期反复腹痛、腹胀后加重入院,影像学检查均显示胰头肿块。经多学科团队会诊后,2例患者均行胰十二指肠切除术,术后病理回报均为胰腺良性病变。术后均恢复顺利,随访期间未再出现腹痛发作,均可进行正常生活与工作。结论:CT和MRI等多模态影像学检查及实验室指标在MFCP与PDAC鉴别诊断中的关键作用。外科治疗在MFCP管理中占据重要地位,尤其在病理学未明确排除PDAC之前,高度怀疑恶性肿块情况下,手术治疗既能治疗早期肿瘤,又能防止胰腺功能进一步退化。因此,对于胰头MFCP,应综合患者各方面因素,选择最佳治疗方案,是减少复发和并发症发生的风险、提高患者生活品质的关键。

关键词：胰腺炎慢性胰腺肿瘤诊断鉴别胰十二指肠切除术

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机器人与腹腔镜下胰腺肿瘤剜除术疗效与安全性比较

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中国普通外科杂志 2024年第9期33卷 1430-1439页

作者：李志强孙吉春涂广平谢双溪刘云飞汪东文贺舜民余枭中南大学湘雅三医院肝胆胰Ⅱ外科湖南长沙410013 中国人民武装警察部队湖南省总队医院外一科湖南长沙410006

背景与目的:微创外科时代,胰腺肿瘤剜除术(PTE)在胰腺良性肿瘤或低度恶性肿瘤治疗中的作用越来越受到关注,尤其是达芬奇机器人有着视野放大倍数更高、器械操作更灵活等优势,可为PTE的安全实施提供保障,然而,机器人胰腺肿瘤剜除术(RPTE)... 详细信息

背景与目的:微创外科时代,胰腺肿瘤剜除术(PTE)在胰腺良性肿瘤或低度恶性肿瘤治疗中的作用越来越受到关注,尤其是达芬奇机器人有着视野放大倍数更高、器械操作更灵活等优势,可为PTE的安全实施提供保障,然而,机器人胰腺肿瘤剜除术(RPTE)是否优于腹腔镜胰腺肿瘤剜除术(LPTE)目前尚未定论,因此,本研究就此方面进行探讨。方法:收集中南大学湘雅三医院2020年4月—2024年5月手术治疗的38例良性肿瘤或低度恶性肿瘤患者的临床资料,其中18例行RPTE (RPTE组),20例行LPTE (LPTE组)。比较两组患者的相关临床指标,并进一步对两组中胰头部肿瘤和胰颈体尾部肿瘤患者的临床指标进行亚组比较。结果:全组平均手术时间为125.00 min,平均术中出血量为67.89 mL,无C级胰瘘发生,B级胰瘘、术后出血和再入院发生率分别为39.5%、21.1%和18.4%,术后住院时间平均为11.44 d。整体上,RPTE组手术时间和术中出血量少于LPTE组(均P0.05)。亚组分析结果显示,在胰头部肿瘤患者中,RPTE组手术时间、术中出血量和术后出血发生率均少于LPTE组(均P0.05);在胰颈体尾部肿瘤患者中,RPTE组手术时间、术中出血量均少于LPTE组(均P0.05)。结论:微创下PTE治疗胰腺良性肿瘤或低度恶性肿瘤是安全的,与LPTE相比,RPTE可明显缩短手术时间,减少术中出血量,且在减少术后并发症等方面显示出一定优势,尤其是对于胰头部肿瘤患者。然而,本研究的结论尚需更大样本前瞻性研究证实。

关键词：胰腺肿瘤机器人手术腹腔镜

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Comprehensive landscape of resistance mechanisms for neoadjuvant therapy in esophageal squamous cell carcinoma by single-cell transcriptomics

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Signal Transduction and Targeted Therapy 2023年第9期8卷 3920-3922页

作者： Yushang Yang Yanguo Li Haopeng Yu Zhenyu Ding Longqi Chen Xiaoxi Zeng shunmin he Qi Liao Yi Zhao Yong Yuan Department of Thoracic Surgery West China HospitalSichuan UniversityChengduSichuanChina Zhejiang Key Laboratory of Pathophysiology Health Science CenterNingbo UniversityNingboZhejiangChina West China Biomedical Big Data Center West China HospitalSichuan UniversityChengduSichuanChina

Dear Editor,Preoperative neoadjuvant therapy combined with surgical resection is the standard treatment for locally advanced esopha-geal squamous cell carcinoma(ESCC).However,more than half of patients having a partial response to neoadjuvant therapy,which is considered as a therapy-resistant phenotype and the mechan-ism is still *** heterogeneity of the ESCC with surgery alone therapy were characterized by single-cell RNA sequencing(scRNA-seq)previously,but few report was about ESCC patients with neoadjuvant therapy.1 It is emergent to illustrate the comprehensive hallmarks of neoadjuvant therapy-resistance in ESCC at single cell level.

关键词： neoadjuvant squamous esophageal

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SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling

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Genomics, Proteomics & Bioinformatics 2021年第4期19卷 602-610页

作者： Yanyan Li Honghong Zhou Xiaomin Chen Yu Zheng Quan Kang Di Hao Lili Zhang Tingrui Song Huaxia Luo Yajing Hao Runsheng Chen Peng Zhang shunmin he College of Life Sciences University of Chinese Academy of Sciences.Beijing 100049China Key Laboratory of RNA Biology Center for Big Data Research in HealthInstitute of BiophysicsChinese Academy of Sciences.Beijing 100101China University of Chinese Academy of Sciences.Beijing 100049 China Department of Cellular and Molecular Medicine University of California.San DiegoLa JollaCA 92093USA Guangdong Geneway Decoding Bio-Tech Co.Ltd Foshan 528316.China

Small proteins specifically refer to proteins consisting of less than 100 amino acids translated from small open reading frames(s ORFs),which were usually missed in previous genome *** significance of small proteins has been revealed in current years,along with the discovery of their diverse ***,systematic annotation of small proteins is still *** Prot was specially developed to provide valuable information on small proteins for scientific *** we present the update of Sm Prot,which emphasizes reliability of translated s ORFs,genetic variants in translated s ORFs,disease-specific s ORF translation events or sequences,and remarkably increased data *** components such as non-ATG translation initiation,function,and new sources are also *** Prot incorporated638,958 unique small proteins curated from 3,165,229 primary records,which were computationally predicted from 419 ribosome profiling(Ribo-seq)datasets or collected from literature and other sources from 370 cell lines or tissues in 8 species(Homo sapiens,Mus musculus,Rattus norvegicus,Drosophila melanogaster,Danio rerio,Saccharomyces cerevisiae,Caenorhabditis elegans,and Escherichia coli).In addition,small protein families identified from human microbiomes were also *** datasets in Sm Prot are free to access,and available for browse,search,and bulk downloads at http://***/SmProt/.

关键词： Ribosome profiling Small open reading frame Upstream open reading frame Variants Disease

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Identification and functional analysis of noval non coding RNAs in Xenopus

Identification and functional analysis of noval non coding R...

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生命的分子机器及其调控网络——2012年全国生物化学与分子生物学学术大会

作者： Xiumei Wang shunmin he Ying Liu Rongqiao he 中国科学院生物物理研究所中国科学院动物研究所

Noncoding RNAs(ncRNAs) are one of the major components of the brain ***,the roles of many ncRNAs are unclear,and the regulation of ncRNA expression is even much less *** analyzing more than 50 thousands of non-coding transcripts identified from the human fetal brain,high sequence conservation was found in the flank-ing 5’ or 3’ of the genomic loci of the *** applied the genome of Xenopus tropicalis to search for ncRNA candidates adjacent with the conserved genomic ***-fold ananlysis showed the similar second structure of ncRNAs in the brain of human fetus and xenopus and Xenc034 had a conserved sequence of tRNA and a stem-loop structure like *** the RT-PCR verification of four predicted ncRNAs

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Genomes of 12 fig wasps provide insights into the adaptation of pollinators to fig syconia

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Journal of Genetics and Genomics 2021年第3期48卷 225-236页

作者： Jinhua Xiao Xianqin Wei Yi Zhou Zhaozhe Xin Yunheng Miao Hongxia Hou Jiaxing Li Dan Zhao Jing Liu Rui Chen Liming Niu Guangchang Ma Wenquan Zhen shunmin he Jianxia Wang Xunfan Wei Weihao Dou Zhuoxiao Sui Haikuan Zhang Shilai Xing Miao Shi Dawei Huang Institute of Entomology College of Life SciencesNankai UniversityTianjin 300071China Institute of Zoology Chinese Academy of SciencesBeijing 100101China Environment and Plant Protection Institute Chinese Academy of Tropical Agricultural SciencesHaikou 571101China Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation College of Marine SciencesBeibu Gulf UniversityQinzhou 535011China Institute of Biophysics Chinese Academy of SciencesBeijing 100101China Berry Genomics Corporation Beijing 102206China

Figs and fig pollinators are one of the few classic textbook examples of obligate pollination *** specific dependence of fig pollinators on the relatively safe living environment with sufficient food sources in the enclosed fig syconia implies that they are vulnerable to habitat ***,there is still no extensive genomic evidence to reveal the evolutionary footprint of this long-term mutually beneficial symbiosis in fig *** fig syconia,there are also non-pollinator *** non-pollinator species differ in their evolutionary and life histories from *** conducted comparative analyses on 11 newly sequenced fig wasp genomes and one previously published *** pollinators colonized the figs approximately 66.9 million years ago,consistent with the origin of host *** with nonpollinators,many more genes in pollinators were subject to relaxed *** genes were absent in pollinators in response to environmental stress and immune *** had more streamlined gene repertoires in the innate immune system,chemosensory toolbox,and detoxification *** results provide genomic evidence for the differentiation between pollinators and *** data suggest that owing to the long-term adaptation to the fig,some genes related to functions no longer required are absent in pollinators.

关键词： Phylogenetics Natural selection Immunity Chemosensory Adaptive evolution

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Study on Paleoearthquakes of the Eastern Liupanshan Piedmont Fault Zone

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Earthquake Research in China 1999年第4期13卷 69-77页

作者： Xiang Hongfa, Yasutaka Ikeda, Zhang Wanxia, Zhang Bingliang, Guo shunmin, and he HonglinInstitute of Geology, CSB, Beijing 100029, China Tokyo University, Tokyo 113, Japan

Based on trench excavation and detailed field investigation, the authors have ascertained that 6 paleoearthquake events have occurred in the Haizixia area of the Eastern Liupanshan Piedmont fault zone since 46Ka B.P. The recurrence time of 6 events were about 15000a, 20250a, 14750a, 12150a, 8550a and 4000a B.P., respectively, the recurrence intervals were about 15000a, 5500a, 2600a, 3600a and 4550a, respectively. According to M-D empirical relations, the vertical dislocation of events 1 and 2 corresponded to the dislocation of the earthquake with M8.0; the vertical dislocation of events 3-6, was corresponded to the dislocation of earthquakes with M6.5~7.5.

关键词： Paleoearthquake recurrence interval Liupanshan.

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“城市”的重启:改革开放初期报纸之上海

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都市文化研究 2019年第1期 26-41页

作者：何顺民淮阴师范学院复旦大学

本文以改革开放初期地方报纸积极介入的"上海病"、为"海派"正名、"洋奴"之辩的媒介讨论为经验材料,针对中国当前城市化进程中城市文化如何传承与创新的现实议题,返观历史,探讨抽象层面的城市文化精神与实体都市空间如何产生关联的问题... 详细信息

本文以改革开放初期地方报纸积极介入的"上海病"、为"海派"正名、"洋奴"之辩的媒介讨论为经验材料,针对中国当前城市化进程中城市文化如何传承与创新的现实议题,返观历史,探讨抽象层面的城市文化精神与实体都市空间如何产生关联的问题。本文认为,承载体制使命的地方大众媒介在特定时刻借由"上海病""海派文化""洋奴"之辩的讨论,"移动"了上海独特的历史文化讯息,重新连接历史和当下,长期隐伏于市民日常生活中的"空间"意识,通过上海历史、文化专家之口"隐隐约约"浮现,意味着"城市"的重新启动,并对后来的城市规划议题产生了深远的影响。

关键词：报纸城市空间意识海派洋味

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传播姿态的调适:《新闻联播》移动短视频的实践创新

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电视研究 2020年第9期 20-22页

作者：何顺民裴梦茹淮阴师范学院浙江传媒学院

为适应新的传播生态,中央广播电视总台《新闻联播》开启了移动短视频实践创新。新媒体产品《主播说联播》试图嵌入新的传播网络节点维持其社会地位,使国家主流价值的声音通过主持人个性化的表达得以在新传播网络中产生强大影响力。同时... 详细信息

为适应新的传播生态,中央广播电视总台《新闻联播》开启了移动短视频实践创新。新媒体产品《主播说联播》试图嵌入新的传播网络节点维持其社会地位,使国家主流价值的声音通过主持人个性化的表达得以在新传播网络中产生强大影响力。同时,因用户、媒介组织以及政策等多重因素的影响,约束着其传播姿态调适的界限和尺度。

关键词：《新闻联播》《主播说联播》短视频传播姿态

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