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Denoising Autoencoder, A Deep Learning Algorithm, Aids the Identification of A Novel Molecular Signature of Lung Adenocarcinoma

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Genomics, Proteomics & Bioinformatics 2020年第4期18卷 468-480页

作者： Jun Wang Xueying Xie junchao shi Wenjun He Qi Chen Liang Chen Wanjun Gu Tong Zhou Department of Thoracic Surgery Jiangsu Province People’s Hospital and the First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029China State Key Laboratory of Bioelectronics School of Biological Sciences and Medical EngineeringSoutheast UniversityNanjing 210096China Department of Physiology and Cell Biology University of NevadaReno School of MedicineRenoNV 89557USA State Key Lab of Respiratory Disease Guangzhou Medical UniversityGuangzhou 510000China

Precise biomarker development is a key step in disease management. However, most of the published biomarkers were derived from a relatively small number of samples with supervised approaches. Recent advances in unsupervised machine learning promise to leverage very large datasets for making better predictions of disease biomarkers. Denoising autoencoder(DA) is one of the unsupervised deep learning algorithms, which is a stochastic version of autoencoder techniques. The principle of DA is to force the hidden layer of autoencoder to capture more robust features by reconstructing a clean input from a corrupted one. Here, a DA model was applied to analyze integrated transcriptomic data from 13 published lung cancer studies, which consisted of 1916 human lung tissue samples. Using DA, we discovered a molecular signature composed of multiple genes for lung adenocarcinoma(ADC). In independent validation cohorts, the proposed molecular signature is proved to be an effective classifier for lung cancer histological subtypes. Also, this signature successfully predicts clinical outcome in lung ADC, which is independent of traditional prognostic factors. More importantly, this signature exhibits a superior prognostic power compared with the other published prognostic genes. Our study suggests that unsupervised learning is helpful for biomarker development in the era of precision medicine.

关键词： Denoising autoencoder Unsupervised learning Lung cancer Prognosis Molecular signature

Evaluation and Hydrological Application of CMADS Reanalysis Precipitation Data against Four Satellite Precipitation Products in the Upper Huaihe River Basin, China

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Journal of Meteorological Research 2020年第5期34卷 1096-1113页

作者： Shanhu JIANG Ruolan LIU Liliang REN Menghao WANG junchao shi Feng ZHONG Zheng DUAN State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering Hohai UniversityNanjing 210098China Hydrology and Water Resources Monitoring and Forecasting Center Ministry of Water ResourcesBeijing 100053China Department of Physical Geography and Ecosystem Science L und UniversityLund S-22362Sweden

Satellite-and reanalysis-based precipitation products are important data source for precipitation, particularly in areas with a sparse gauge network. Here, five open-access precipitation products, including the newly released China Meteorological Assimilation Driving Datasets for the Soil and Water Assessment Tool(SWAT) model(CMADS)reanalysis dataset and four widely used bias-adjusted satellite precipitation products [SPPs;i.e., Tropical Rainfall Measuring Mission(TRMM) Multisatellite Precipitation Analysis 3B42 Version 7(TMPA 3B42V7), Climate Prediction Center(CPC) morphing technique satellite–gauge blended product(CMORPH-BLD), Climate Hazards Group Infrared Precipitation with Station Data(CHIRPS), and Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks–Climate Data Record(PERSIANN-CDR)], were assessed. These products were first compared with the gauge observed data collected for the upper Huaihe River basin, and then were used as forcing data for streamflow simulation by the Xin’anjiang(XAJ) hydrological model under two scenarios with different calibration procedures. The performance of CMADS precipitation product for the Chinese mainland was also assessed. The results show that:(1) for the statistical assessment, CMADS and CMORPH-BLD perform the best, followed by TMPA 3B42V7, CHIRPS, and PERSIANN-CDR, among which the correlation coefficient(CC) and rootmean-square error(RMSE) values of CMADS are optimal, although it exhibits certain significant negative relative bias(BIAS;-22.72%);(2) CMORPH-BLD performs the best in capturing and detecting rainfall events, while CMADS tends to underestimate heavy and torrential precipitation;(3) for streamflow simulation, the performance of using CMADS as input is very good, with the highest Nash–Sutcliffe efficiency(NSE) values(0.85 and 0.75 for calibration period and validation period, respectively);and(4) CMADS exhibits high accuracy in eastern China while with significant negative BIAS, and the performance declines from southeast to n

关键词： reanalysis precipitation data China Meteorological Assimilation Driving Datasets for the Soil and Water Assessment Tool(SWAT)model(CMADS) satellite precipitation hydrological evaluation Xin’anjiang(XAJ)hydrological model

GRACE observed mass loss in the middle and lower Yangtze basin

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Geodesy and Geodynamics 2019年第2期10卷 157-162页

作者： Jiangjun Ran Natthachet Tangdamrongsub junchao shi Changqing Wang Lihui Wang Xiaoyun Wan Institute of Geodesy and Geophysics Chinese Academy of Sciences School of Engineering University of Newcastle Information Center Ministry of Water Resources Qian Xuesen Laboratory of Space Technology

Anthropogenic architectures have a significant impact to the environment. The Three Gorges Dam(TGD),as the largest dam in the world, is a typical example, and has influenced the mass anomalies transported by the flow downstream in the Yangtze River since June 2003. However, the evidence of TGD influence on downstream mass transportation is not documented. In this study, we analyze the monthly gravity solutions from GRACE to investigate the downstream mass variations of Yangtze River. From our results,the considerable mass loss is detected in the downstream of TGD. By comparing our estimations with the in situ water level data of TGD, we find that the mass variations derived from GRACE at Datong station decreases shortly after the impoundment of TGD. This confirms a strong connection between them.Furthermore, by comparing with the in situ sediment load and river discharge at Yichang and Datong gauging stations, we find that the sediment load data shows a similar mass loss signature while the river discharge of both stations has stay at a relative stable level. This indicates that further study is still needed to understand the mechanism better.

关键词： GRACE Mass loss The Yangtze River basin Sediment load River discharge

Development of mouse preimplantation embryos in space

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National Science Review 2020年第9期7卷 1437-1446页

作者： Xiaohua Lei Yujing Cao Baohua Ma Yunfang Zhang Lina Ning Jingjing Qian Liwen Zhang Yongcun Qu Tao Zhang Dehong Li Qi Chen junchao shi Xudong Zhang Chiyuan Ma Ying Zhang Enkui Duan State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of Sciences University of Chinese Academy of Sciences Shanghai Institute of Technical Physics Chinese Academy of Sciences Division of Ionizing Radiation National Institute of Metrology College of Veterinary Medicine Northwest A&F University/Key Laboratory of Animal BiotechnologyMinistry of Agriculture

The development of life beyond planet Earth is a long-standing quest of the human race, but whether normal mammalian embryonic development can occur in space is still unclear. Here, we show unequivocally that preimplantation mouse embryos can develop in space, but the rate of blastocyst formation and blastocyst quality are compromised. Additionally, the cells in the embryo contain severe DNA damage, while the genome of the blastocysts developed in space is globally hypomethylated with a unique set of differentially methylated regions. The developmental defects, DNA damage and epigenetic abnormalities can be largely mimicked by the treatment with ground-based low-dose radiation. However,the exposure to simulated microgravity alone does not cause major disruptions of embryonic development,indicating that radiation is the main cause for the developmental defects. This work advances the understanding of embryonic development in space and reveals long-term extreme low-dose radiation as a hazardous factor for mammalian reproduction.

关键词： space-flight radiation microgravity preimplantation development DNA damage DNA methylation

Identification and characterization of an ancient class of small RNAs enriched in serum associating with active infection

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Journal of Molecular Cell Biology 2014年第2期8卷 172-174页

作者： Yunfang Zhang Ying Zhang junchao shi He Zhang Zhonghong Cao Xuan Gao Wanhua Ren Yunna Ning Lina Ning Yujing Cao Yongchang Chen Weizhi Ji Zi-jiang Chen Qi Chen Enkui Duan State Key Laboratory of Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China School of Life Sciences Anhui UniversityHefei 230039China University of Chinese Academy of Sciences Beijing 100049China Center for Reproductive Medicine Shandong Provincial HospitalShandong UniversityNational Research Center for Assisted Reproductive Technology and ReproductiveGeneticsKey Laboratory for Reproductive Endocrinology of Ministry of EducationJinan 250021China Department of Infectious Diseases Provincial Hospital Affiliated to Shandong UniversityJinan 250021China Yunnan Key Laboratory of Primate Biomedical Research Kunming 650500China

The identification of novel serum biomarkers holds great value for diagnosing and monitoring disease conditions due to its convenient and non-invasive nature. Recently, great interests have been shed on serum microRNAs (miRNAs), which emerge as promising biomarkers for a variety of diseases including cancer and metabolic disorders (Cortez et al., 2011). Despite the concentrated attention on serum miRNAs, the reports on the existence and diagnostic value of other serum small RNAs remain surprisingly few. In present study, we identify and characterize an ancient class of tRNA-derived small RNAs (tsRNAs) that abundantly and conservatively exist across a wide range of vertebrate species (from fish to human) and demonstrate their sensitive response to body infection in mouse, monkey, and human being.

关键词： MICRORNAS COMPLEXES VESICLES

3例犬炎性乳腺癌的病理学诊断和组织学分级评价

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中国兽医杂志 2024年第1期60卷 15-20页

作者：高蕊石俊超张竞贾茜涵马莹贺文琦陆慧君吉林大学动物医学学院吉林长春130062

为了对3例临床疑似犬炎性乳腺癌的病例进行确诊,本试验采用苏木精-伊红(H.E.)染色对送检肿物进行组织病理学检查,应用全角蛋白(Pan ck)抗体、角蛋白8(CK8)抗体和血管性血友病因子(VWF)抗体进行免疫组织化学染色以判断免疫表型。结果显... 详细信息

为了对3例临床疑似犬炎性乳腺癌的病例进行确诊,本试验采用苏木精-伊红(H.E.)染色对送检肿物进行组织病理学检查,应用全角蛋白(Pan ck)抗体、角蛋白8(CK8)抗体和血管性血友病因子(VWF)抗体进行免疫组织化学染色以判断免疫表型。结果显示,3例患犬肿瘤内部形成管状癌、致密癌、筛状癌和粉刺性癌,并伴有淋巴管扩张、肿瘤栓子浸润淋巴管等现象,符合犬炎性乳腺癌的特征;免疫组织化学染色结果证实,肿瘤为腺上皮起源,且淋巴管、血管内存在大量肿瘤栓子。通过病理学分析结合临床表现,3例病例均确诊为犬炎性乳腺癌。根据Pena分级标准,将病例1判定为Ⅲ级炎性乳腺癌,病例2和3判定为Ⅱ级炎性乳腺癌。本试验结果不仅可为犬炎性乳腺癌的病理诊断提供参考,而且为犬炎性乳腺癌临床病例治疗方案的制定和预后评估提供理论依据。

关键词：犬炎性乳腺癌病理组织学免疫组织化学

Cooperation-based sperm clusters mediate sperm oviduct entry and fertilization

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Protein & Cell 2021年第10期12卷 810-817页

作者： Yongcun Qu Qi Chen Shanshan Guo Chiyuan Ma Yonggang Lu junchao shi shichao Liu Tong Zhou Taichi Noda Jingjing Qian Liwen Zhang Xili Zhu Xiaohua Lei Yujing Cao Wei Li Wei Li Nicolas Plachta Martin M.Matzuk Masahito Ikawa Enkui Duan Ying Zhang Hongmei Wang State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Division of Biomedical Sciences School of MedicineUniversity of CaliforniaRiversideCA 92521USA Research Institute for Microbial Diseases Osaka UniversitySuitaOsakaJapan Department of Physiology and Cell Biology Reno School of MedicineUniversity of NevadaRenoNVUSA Institute of Molecular and Cell Biology A*STARSingaporeSin gapore Center for Drug Discovery Department of Pathology and ImmunologyBaylor College of MedicineHoustonTX 77030USA Division of Biology and Biological Engineering California Institute of TechnologyPasadenaCAUSA Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijing 100101China The Key Laboratory of Cell Proliferation and Regulation Biology Ministry of EducationInstitute of Cell BiologyBeijing Normal UniversityBeijing 100875China

Dear Editor,Sperm cooperation has been observed in multiple species(Pizzari and Foster,2008),yet its existenee and benefit for reproductive success in mammals remains underexplored.Here,combining tissue-clearing with deep three-dimensional(3D)imagi ng,we dem on strate that postcopulatory mouse sperm congregate into unidirectional sperm cooperative clusters at the utero-tubal junction(UTJ),a key physical barrier for passage into the oviduct.

关键词： passage media Foster

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ATF3在PHEV感染中的表达及作用

中国兽医学报 2024年第4期44卷 781-786页

作者：陈雨竹王真真焦宇博胡锐杰王改丽石俊超贺文琦陆慧君高丰宋德光兰云刚吉林大学动物医学学院吉林长春130062 吉林省畜牧兽医科学研究院吉林长春130062

为探究转录激活因子3(activating transcription factor 3,ATF3)在猪血凝性脑脊髓炎病毒(porcine hemagglutinating encephalomyelitis virus,PHEV)复制过程中的作用,本研究通过Western blot、qRT-PCR和间接免疫荧光试验检测PHEV感染后ATF3表达水平及亚细胞定位变化,并在干扰ATF3后检测PHEV含量及相关炎性细胞因子变化。结果显示,PHEV感染后,ATF3的表达水平显著上调,同时ATF3从细胞浆转入细胞核中启动下游基因表达;而干扰ATF3后,细胞内炎性因子IFN-β,IFN-γ,IL-6,IL-1β转录水平下调,PHEV含量显著增加。结果表明,PHEV感染后上调ATF3可动态调节神经元中的炎性因子并对机体产生保护作用。

关键词：猪血凝性脑脊髓炎病毒转录激活因子3 炎性因子病毒复制

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《儒林外史》的水路空间叙事与江南书写

明清小说研究 2023年第1期 143-159页

作者：史俊超南京大学文学院江苏第二师范学院文学院

作为与《红楼梦》双峰并峙的清代章回小说,《儒林外史》不但具有出色的讽刺性,而且它的写实风格也颇具特色。江南地区丰富的水网以及运河作为枢纽沟通其中,为小说提供了广阔的叙事空间。水路交通的载体航船成为叙事空间的重要组成部分,... 详细信息

作为与《红楼梦》双峰并峙的清代章回小说,《儒林外史》不但具有出色的讽刺性,而且它的写实风格也颇具特色。江南地区丰富的水网以及运河作为枢纽沟通其中,为小说提供了广阔的叙事空间。水路交通的载体航船成为叙事空间的重要组成部分,许多情节的转换,故事的发生都与之相关。从小说中我们可以看出江南地区山水之间的互动,典型的江南书写也体现了吴敬梓的人生理想和全书主题。

关键词：《儒林外史》水路航船叙事空间江南