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AlphaFold2 and its applications in the fields of biology and medicine

Signal Transduction and Targeted Therapy 2023年第4期8卷 1630-1643页

作者： Zhenyu Yang Xiaoxi Zeng Yi Zhao Runsheng Chen West China Biomedical Big Data Center West China HospitalSichuan UniversityChengdu 610041China Key Laboratory of Intelligent Information Processing Advanced Computer Research CenterInstitute of Computing TechnologyChinese Academy of SciencesBeijing 100190China Key Laboratory of RNA Biology Center for Big Data Research in HealthInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China Pingshan Translational Medicine Center Shenzhen Bay LaboratoryShenzhen 518118China

AlphaFold2(AF2)is an artificial intelligence(AI)system developed by DeepMind that can predict three-dimensional(3D)structures of proteins from amino acid sequences with atomic-level accuracy.Protein structure prediction is one of the most challenging problems in computational biology and chemistry,and has puzzled scientists for 50 years.The advent of AF2 presents an unprecedented progress in protein structure prediction and has attracted much attention.Subsequent release of structures of more than 200 million proteins predicted by AF2 further aroused great enthusiasm in the science community,especially in the fields of biology and medicine.AF2 is thought to have a significant impact on structural biology and research areas that need protein structure information,such as drug discovery,protein design,prediction of protein function,et al.Though the time is not long since AF2 was developed,there are already quite a few application studies of AF2 in the fields of biology and medicine,with many of them having preliminarily proved the potential of AF2.To better understand AF2 and promote its applications,we will in this article summarize the principle and system architecture of AF2 as well as the recipe of its success,and particularly focus on reviewing its applications in the fields of biology and medicine.Limitations of current AF2 prediction will also be discussed.

关键词： system fields Fold

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Comorbid conditions related to readmissions of Chinese older patients

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Chinese Medical Journal 2022年第6期135卷 741-743页

作者： Chunyang Li Hyokyoung GHong Zhiye Ying Xiaoxi Zeng Yi Li West China Biomedical Big Data Center West China HospitalSichuan UniversityChengduSichuan 610041China Medical Big Data Center Sichuan UniversityChengduSichuan 610041China Department of Statistics and Probability Michigan State UniversityEast LansingMIUSA Department of Biostatistics School of Public HealthUniversity of MichiganAnn ArborMIUSA

To the Editor:China is the most populated country,and it is aging more quickly than almost any other country in the world.According to Worldometer,[1]the population size of China,as of 2020,is around 1.4 billion,with the proportion of the 60-year olds and older being 17.30%in 2017 and expected to reach 35%in 2050.Older age tended to be closely correlated with multimorbidity.Ward and Schiller[2]reported that 65%of men and 72%of women aged>65 years in the US had at least two chronic conditions in 2010.Accordingly,older adults living with multiple chronic conditions tend to be readmitted after discharge,further leading to increased expenditure and more utilization of medical resources.Many studies have reported higher read mission rates in elderly patients.However,previous studies have focused on investigating the factors that influence read mission for a single disease,rather than for the chronic comorbid conditions in the initial hospitalization and the changes in these conditions from initial hospitalization to read mission among the elderly in China.Furthermore,most studies have focused on Caucasian patients and have been conducted in the US.Little is known about Chinese patients due to the lack of large-scale data.Identifying the common chronic comorbid conditions and the changes in these conditions from initial hospitalization to read mission among older people is important as it will help in the understanding of the chronic conditions leading to avoidable read mission and facilitate the development of efficient intervention strategies for the reduction of read missions.

关键词： conditions among admitted

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Sex-specific association between coffee consumption and incident chronic kidney disease: a population-based analysis of 359,906 participants from the UK Biobank

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Chinese Medical Journal 2022年第12期135卷 1414-1424页

作者： Lei Tang Lina Yang Wenwen Chen Chunyang Li Yu zeng Huazhen Yang Yao Hu Yuanyuan Qu Huan Song Xiaoxi Zeng Ping Fu Division of Nephrology Kidney Research InstituteWest China HospitalSichuan UniversityChengduSichuan 610041China Biomedical Big Data Center of West China Hospital Med-X Center for InformaticsSichuan UniversityChengduSichuan 610041China Center of Pubic Health Sciences Faculty of MedicineUniversity of IcelandReykjavikIceland

Background:The risk for chronic kidney disease(CKD)is influenced by genetic predisposition,sex,and lifestyle.Previous research indicates that coffee is a potentially protective factor in CKD.The current study aims to investigate whether sex disparity exists in the coffee–CKD association,and whether genetic risk of CKD or genetic polymorphisms of caffeine metabolism affect this association.Methods:A total of 359,906 participants from the UK Biobank who were enrolled between 2006 and 2010 were included in this prospective cohort study,which aimed to estimate the hazard ratios for coffee intake and incident CKD using a Cox proportional hazard model.Allele scores of CKD and caffeine metabolism were additionally adjusted for in a subsample with qualified genetic data(n=255,343).Analyses stratified by genetic predisposition,comorbidities,and sex hormones were performed.Tests based on Bayesian model averaging were conducted to ascertain the robustness of the results.Results:Coffee was inversely associated with CKD in a dose-dependent manner.The effects of coffee did not differ across different strata of genetic risk for CKD,but were more evident among slower genetically predicted caffeine metabolizers.Significant sex disparity was observed(P value for interaction=0.013),in that coffee drinking was only associated with the risk reduction of CKD in females.Subgroup analysis revealed that testosterone and sex hormone-binding globulin(SHBG),but not estradiol,modified the coffee–CKD association.Conclusions:In addition to the overall inverse coffee–CKD association that was observed in the general population,we could also establish that a sex disparity existed,in that females were more likely to experience the benefit of the association.Testosterone and SHBG may partly account for the sex disparity.

关键词： Coffee Chronic kidney diseases Genotype Sex

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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 unclear.The 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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Multi-omics approaches identify SF3B3 and SIRT3 as candidate autophagic regulators and druggable targets in invasive breast carcinoma

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Acta Pharmaceutica Sinica B 2021年第5期11卷 1227-1245页

作者： Shouyue Zhang Jin Zhang Yang An Xiaoxi Zeng Ziyi Qin Yuqian Zhao Heng Xu Bo Liu State Key Laboratory of Biotherapy and Cancer Center West China HospitalSichuan UniversityChengdu 610041China Department of Laboratory Medicine State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu 610041China Department of Plastic Surgery Peking University Third HospitalBeijing 100191China Division of Plastic Surgery Brigham and Women's HospitalHarvard Medical SchoolBostonMA 02115USA West China Biomedical Big Data Center West China HospitalSichuan UniversityChengdu 610041China School of Pharmaceutical Sciences Health Science CenterShenzhen UniversityShenzhen 518060China

Autophagy is a critical cellular homeostatic mechanism,and its dysfunction is linked to invasive breast carcinoma(BRCA).Recently,several omics methods have been applied to explore autophagic regulators in BRCA;however,more reliable and robust approaches for identifying crucial regulators and druggable targets remain to be discovered.Thus,we report here the results of multi-omics approaches to identify potential autophagic regulators in BRCA,including gene expression(EXP),DNA methylation(MET)and copy number alterations(CNAs)from The Cancer Genome Atlas(TCGA).Newly identified candidate genes,such as SF3 B3,TRAPPC10,SIRT3,MTERFD1,and FBXO5,were confirmed to be involved in the positive or negative regulation of autophagy in BRCA.SF3 B3 was identified firstly as a negative autophagic regulator,and siRNA/shRNA-SF3 B3 were shown to induce autophagyassociated cell death in in vitro and in vivo breast cancer models.Moreover,a novel small-molecule activator of SIRT3,1-methylbenzylamino amiodarone,was discovered to induce autophagy in vitro and in vivo.Together,these results provide multi-omics approaches to identify some key candidate autophagic regulators,such as the negative regulator SF3 B3 and positive regulator SIRT3 in BRCA,and highlight SF3 B3 and SIRT3 as new druggable targets that could be used to fill the gap between autophagy and cancer drug development.

关键词： Invasive breast carcinoma Multi-omics approach SIRT3 SF3B3 Autophagic regulator Anti-proliferation Migration Druggable target

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覆盖型岩溶土洞形成的临界水流速度数值模拟研究

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水文地质工程地质 2024年第4期51卷 189-196页

作者：陈小茜黄荷朱燕曾斌湖北省生态环境科学研究院湖北武汉　430074 长沙理工大学水利与环境工程学院湖南长沙　410114 中国地质大学（武汉）环境学院湖北武汉　430074

覆盖型岩溶塌陷灾害具有隐蔽性、突发性、不确定性、机理复杂性等特点，致使其预防、治理工作十分困难。覆盖型岩溶塌陷过程中，覆盖层土体形成土洞，土洞发育、扩展直至地表塌陷。现阶段土洞塌陷研究方法多为有限单元法等数值模拟，但... 详细信息

覆盖型岩溶塌陷灾害具有隐蔽性、突发性、不确定性、机理复杂性等特点，致使其预防、治理工作十分困难。覆盖型岩溶塌陷过程中，覆盖层土体形成土洞，土洞发育、扩展直至地表塌陷。现阶段土洞塌陷研究方法多为有限单元法等数值模拟，但有限单元法无法解决颗粒迁移、土体崩落等岩体大变形问题。在浙江省江山市岩溶塌陷地质条件分析的基础上，利用颗粒流数值模拟方法（PFC）对覆盖型岩溶土洞的形成过程进行了模拟，从微观角度揭示土洞形成过程中特殊土体颗粒的位移、裂纹的发展趋势和系统不平衡力的变化情况等，再现外力作用下岩溶土洞形成的多场变化特征。结果表明：（1）岩溶土洞发育过程可概化为裂纹产生、连通面形成、颗粒剥落3个阶段;（2）岩溶土洞开始发育时，土体颗粒位移曲线、裂纹的贯通程度、不平衡力三者之间具有良好的一致性，且垂直方向扩展速度大于水平速度;（3）覆盖层土体为黏土时初始土洞形成的临界水流速度为0.104 cm/s。研究结果可为岩溶塌陷治理提供参考数据。

关键词：颗粒流覆盖型岩溶塌陷土洞临界水流速度

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《脊柱关节炎靶向药物治疗专家共识》要点解读

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协和医学杂志 2024年第1期15卷 58-67页

作者：杨晓曦田新平李梦涛冷晓梅赵岩曾小峰中国医学科学院北京协和医院风湿免疫科国家皮肤与免疫疾病临床医学研究中心风湿免疫病学教育部重点实验室北京100730 中国医学科学院北京协和医院疑难重症及罕见病国家重点实验室北京100730

脊柱关节炎(spondyloarthritis,SpA)是一组以中轴骨和/或外周关节受累为主的慢性炎症性、致残性风湿免疫病,严重影响患者的身体功能和生活质量。随着靶向药物的临床应用越来越多,其精准且规范应用成为目前关注的重点。遵循共识制订的国... 详细信息

脊柱关节炎(spondyloarthritis,SpA)是一组以中轴骨和/或外周关节受累为主的慢性炎症性、致残性风湿免疫病,严重影响患者的身体功能和生活质量。随着靶向药物的临床应用越来越多,其精准且规范应用成为目前关注的重点。遵循共识制订的国际规范,国家皮肤与免疫疾病临床医学研究中心制定了我国首部《脊柱关节炎靶向药物治疗专家共识》,该共识对13个靶向药物应用过程中的重点问题作出推荐,涵盖了靶向药物治疗SpA的原则、适用人群、用药前筛查、用药时机、药物选择和转换、合并用药、不良反应监测等,并对特殊人群的用药注意事项提出建议,对临床实践具有重要指导意义。

关键词：脊柱关节炎靶向药物治疗专家共识解读

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Prediction of severe preeclampsia in machine learning

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Medicine in Novel Technology and Devices 2022年第3期15卷 148-153页

作者： Xinyuan Zhang Yu Chen Stephen Salerno Yi Li Libin Zhou Xiaoxi Zeng Huafeng Li Department of Applied Mechanics College of Architecture and EnvironmentSichuan Province Biomechanical Engineering LaboratorySichuan UniversityChengdu610065SichuanChina Department of Biostatistics University of MichiganAnn ArborMIUSA Medical Big Data Center Sichuan UniversityChengdu610065SichuanChina Department of Computer Science University of WisconsinMadisonWIUSA West China Second University Hospital Sichuan UniversityChengdu610041China Department of Applied Mechanics Sichuan UniversityChengdu610065SichuanChina

This study aimed to find out the blood data characteristics of patients and explore the correlation between severe preeclampsia and blood index value.Provide assistance for the early attention direction of severe preeclampsia diagnosis and treatment.19,653 pregnant women presenting to the West China Second University Hospital,Sichuan University from January 2017 to April 2019.After screening,a total of 248 patients,124 severe preeclampsia cases,and 124 controls were selected for this study.Forty-three blood examination variables were obtained from routine blood work,hepatic,renal and coagulation function examination.Light gradient boosting machine(light GBM),decision tree and random forest were used for date diving.We randomly divided 35%of the original data as a testing set to conduct internal validation of the performance of the prediction model.The area under receiver operating characteristic curve(AUC)was used as the main score to compare the three methods.Finally,a binary classification light GBM model based on aspartate aminotransferase,direct bilirubin and activated partial thromboplastin time ratio can predict severe preeclampsia with sensitivity of 88.37%,specificity of 77.27%,AUC of 89.74%and positive predictive value of 65.96%.We believe relevant quantifiable indicators can establish an effective prediction model,which can provide guidance for early detection and prevention of severe preeclampsia.

关键词： Preeclampsia Screening Prediction Blood examination Data characteristics

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A button switch inspired duplex hydrogel sensor based on both triboelectric and piezoresistive effects for detecting dynamic and static pressure

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Nanotechnology and Precision Engineering 2022年第2期5卷 12-20页

作者： Zhensheng Chen Jiahao Yu xiaoxi Zhang Haozhe zeng Yunjia Li Jin Wu Kai Tao Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace Northwestern Polytechnical UniversityXi’an 710072China AVIC Xi’an Aircraft Industry Group Company Ltd. Xi’an 710089China School of Electrical Engineering Xi’an Jiaotong UniversityXi’an 710049China State Key Laboratory of Optoelectronic Materials and Technologies and the Guangdong Province Key Laboratory of Display Material and Technology School of Electronics and Information TechnologySun Yat-sen UniversityGuangzhou 510275China

The capability to sense complex pressure variations comprehensively is vital for wearable electronics and flexible human–machine interfaces.In this paper,inspired by button switches,a duplex tactile sensor based on the combination of triboelectric and piezoresistive effects is designed and fabricated.Because of its excellent mechanical strength and electrical stability,a double-networked ionic hydrogel is used as both the conductive electrode and elastic current regulator.In addition,micro-pyramidal patterned polydimethylsiloxane(PDMS)acts as both the friction layer and the encapsulation elastomer,thereby boosting the triboelectric output performance significantly.The duplex hydrogel sensor demonstrates comprehensive sensing ability in detecting the whole stimulation process including the dynamic and static pressures.The dynamic stress intensity(10–300 Pa),the action time,and the static variations(increase and decrease)of the pressure can be identified precisely from the dual-channel signals.Combined with a signal processing module,an intelligent visible door lamp is achieved for monitoring the entire“contact–hold–release–separation”state of the external stimulation,which shows great application potential for future smart robot e-skin and flexible electronics.

关键词： Duplex hydrogel sensor Triboelectric nanogenerator Piezoresistive sensor Dynamic and static sensing

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北方常见绿化树种凋落物添加对城市土壤有机碳组成特征的影响

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植物科学学报 2024年第2期42卷 140-149页

作者：张晓曦田爽曾磊陈灵素张蔓刘凯旋胡嘉伟刘冲延安大学生命科学学院陕西延安716000 陕西省红枣重点实验室(延安大学) 陕西延安716000

本研究将垂柳(Salix babylonica L.)、元宝枫(Acer pictum subsp.mono(Maxim.)H.Ohashi)、银杏(Ginkgo biloba L.)、龙爪槐(Sophora japonica L.var.japonica f.pendula Hort.)、油松(Pinus tabuliformis Carrière)、刺柏(Juniperus formosana Hayata)、侧柏(Platycladus orientalis(L.)Franco)和云杉(Picea asperata Mast.)等8种北方城市常见绿化树种的凋落物与延安市城区受到频繁扰动的表层土壤以2%(凋落物/干土)的比例混合,在模拟自然条件下的土壤容重和含水量的基础上进行120 d的室内培养实验,检测处理后土壤有机碳及其各组分的含量以及相应碳库指数的变化,并分析凋落物化学特性与上述指标的关系。结果显示,8种供试凋落物中,除五角枫和刺柏外的所有凋落物处理均显著提高了土壤总有机碳含量,除五角枫、银杏和刺柏外的凋落物处理显著提高了其稳定组分的含量,而所有凋落物处理普遍显著提高了中等和高活性组分的含量。垂柳、侧柏、云杉和油松凋落物处理显著提高了土壤碳库指数,几乎所有处理均显著提高了土壤有机碳活度指数和碳库管理指数,仅侧柏凋落物处理显著提高了土壤固碳指数。凋落物氮和氨基酸含量与土壤有机碳各组分含量和相关碳库指数总体呈负相关;凋落物总酚和可溶性糖含量以及碳氮比、碳磷比和氮磷比与高活性、低活性和稳定有机碳组分含量呈正相关,其总有机酸、磷、总碳、萜类、酚类含量和碳氮比则与中等活性有机碳组分含量呈正相关。仅从提高土壤有机碳总量及其各组分含量,以及土壤有机碳活性和稳定的角度考虑,侧柏凋落物可作为处理城市土壤的优选材料,其次为垂柳、云杉和油松凋落物。

关键词：土壤有机碳组分凋落物化学特性园林绿化树种土壤生化性质

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