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Pathway paradigms revealed from the genetics of inflammatory bowel disease 期刊论文
NATURE, 2020, 578 (7796) : 527-539
作者:  Yu, Kwanha;  Lin, Chia-Ching John;  Hatcher, Asante;  Lozzi, Brittney;  Kong, Kathleen;  Huang-Hobbs, Emmet;  Cheng, Yi-Ting;  Beechar, Vivek B.;  Zhu, Wenyi;  Zhang, Yiqun;  Chen, Fengju;  Mills, Gordon B.;  Mohila, Carrie A.;  Creighton, Chad J.;  Noebels, Jeffrey L.;  Scott, Kenneth L.;  Deneen, Benjamin
收藏  |  浏览/下载:7/0  |  提交时间:2020/07/03

Inflammatory bowel disease (IBD) is a complex genetic disease that is instigated and amplified by the confluence of multiple genetic and environmental variables that perturb the immune-microbiome axis. The challenge of dissecting pathological mechanisms underlying IBD has led to the development of transformative approaches in human genetics and functional genomics. Here we describe IBD as a model disease in the context of leveraging human genetics to dissect interactions in cellular and molecular pathways that regulate homeostasis of the mucosal immune system. Finally, we synthesize emerging insights from multiple experimental approaches into pathway paradigms and discuss future prospects for disease-subtype classification and therapeutic intervention.


This Review examines inflammatory bowel disease in the context of human genetics studies that help to identify pathways that regulate homeostasis of the mucosal immune system and discusses future prospects for disease-subtype classification and therapeutic intervention.


  
Improved protein structure prediction using potentials from deep learning 期刊论文
NATURE, 2020, 577 (7792) : 706-+
作者:  Ma, Runze;  Cao, Duanyun;  Zhu, Chongqin;  Tian, Ye;  Peng, Jinbo;  Guo, Jing;  Chen, Ji;  Li, Xin-Zheng;  Francisco, Joseph S.;  Zeng, Xiao Cheng;  Xu, Li-Mei;  Wang, En-Ge;  Jiang, Ying
收藏  |  浏览/下载:143/0  |  提交时间:2020/07/03

Protein structure prediction can be used to determine the three-dimensional shape of a protein from its amino acid sequence(1). This problem is of fundamental importance as the structure of a protein largely determines its function(2)  however, protein structures can be difficult to determine experimentally. Considerable progress has recently been made by leveraging genetic information. It is possible to infer which amino acid residues are in contact by analysing covariation in homologous sequences, which aids in the prediction of protein structures(3). Here we show that we can train a neural network to make accurate predictions of the distances between pairs of residues, which convey more information about the structure than contact predictions. Using this information, we construct a potential of mean force(4) that can accurately describe the shape of a protein. We find that the resulting potential can be optimized by a simple gradient descent algorithm to generate structures without complex sampling procedures. The resulting system, named AlphaFold, achieves high accuracy, even for sequences with fewer homologous sequences. In the recent Critical Assessment of Protein Structure Prediction(5) (CASP13)-a blind assessment of the state of the field-AlphaFold created high-accuracy structures (with template modelling (TM) scores(6) of 0.7 or higher) for 24 out of 43 free modelling domains, whereas the next best method, which used sampling and contact information, achieved such accuracy for only 14 out of 43 domains. AlphaFold represents a considerable advance in protein-structure prediction. We expect this increased accuracy to enable insights into the function and malfunction of proteins, especially in cases for which no structures for homologous proteins have been experimentally determined(7).


  
Ultrafast optical pulse shaping using dielectric metasurfaces 期刊论文
SCIENCE, 2019, 364 (6443) : 890-+
作者:  Divitt, Shawn;  Zhu, Wenqi;  Zhang, Cheng;  Lezec, Henri J.;  Agrawal, Amit
收藏  |  浏览/下载:1/0  |  提交时间:2019/11/27
Strongly correlated quantum walks with a 12-qubit superconducting processor 期刊论文
SCIENCE, 2019, 364 (6442) : 753-+
作者:  Yan, Zhiguang;  Zhang, Yu-Ran;  Gong, Ming;  Wu, Yulin;  Zheng, Yarui;  Li, Shaowei;  Wang, Can;  Liang, Futian;  Lin, Jin;  Xu, Yu;  Guo, Cheng;  Sun, Lihua;  Peng, Cheng-Zhi;  Xia, Keyu;  Deng, Hui;  Rong, Hao;  You, J. Q.;  Nori, Franco;  Fan, Heng;  Zhu, Xiaobo;  Pan, Jian-Wei
收藏  |  浏览/下载:17/0  |  提交时间:2019/11/27
Anti-parity-time symmetry in diffusive systems 期刊论文
SCIENCE, 2019, 364 (6436) : 170-+
作者:  Li, Ying;  Peng, Yu-Gui;  Han, Lei;  Miri, Mohammad-Ali;  Li, Wei;  Xiao, Meng;  Zhu, Xue-Feng;  Zhao, Jianlin;  Alu, Andrea;  Fan, Shanhui;  Qiu, Cheng-Wei
收藏  |  浏览/下载:12/0  |  提交时间:2019/11/27
Double-negative-index ceramic aerogels for thermal superinsulation 期刊论文
SCIENCE, 2019, 363 (6428) : 723-+
作者:  Xu, Xiang;  Zhang, Qiangqiang;  Hao, Menglong;  Hu, Yuan;  Lin, Zhaoyang;  Peng, Lele;  Wang, Tao;  Ren, Xuexin;  Wang, Chen;  Zhao, Zipeng;  Wan, Chengzhang;  Fei, Huilong;  Wang, Lei;  Zhu, Jian;  Sun, Hongtao;  Chen, Wenli;  Du, Tao;  Deng, Biwei;  Cheng, Gary J.;  Shakir, Imran;  Dames, Chris;  Fisher, Timothy S.;  Zhang, Xiang;  Li, Hui;  Huang, Yu;  Duan, Xiangfeng
收藏  |  浏览/下载:15/0  |  提交时间:2019/11/27
Untangling the formation and liberation of water in the lunar regolith 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2019, 116 (23) : 11165-11170
作者:  Zhu, Cheng;  Crandall, Parker B.;  Gillis-Davis, Jeffrey J.;  Ishii, Hope A.;  Bradley, John P.;  Corley, Laura M.;  Kaiser, Ralf I.
收藏  |  浏览/下载:7/0  |  提交时间:2019/11/27
solar wind  water  Moon  
E-C coupling structural protein junctophilin-2 encodes a stress-adaptive transcription regulator 期刊论文
SCIENCE, 2018, 362 (6421) : 1375-+
作者:  Guo, Ang;  Wang, Yihui;  Chen, Biyi;  Wang, Yunhao;  Yuan, Jinxiang;  Zhang, Liyang;  Hall, Duane;  Wu, Jennifer;  Shi, Yun;  Thu, Qi;  Chen, Cheng;  Thiel, William H.;  Than, Xin;  Weiss, Robert M.;  Zhan, Fenghuang;  Musselman, Catherine A.;  Pufall, Miles;  Zhu, Weizhong;  Au, Kin Fai;  Hong, Jiang;  Anderson, Mark E.;  Grueter, Chad E.;  Song, Long-Sheng
收藏  |  浏览/下载:11/0  |  提交时间:2019/11/27
Multidecadally resolved polarity oscillations during a geomagnetic excursion 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2018, 115 (36) : 8913-8918
作者:  Chou, Yu-Min;  Jiang, Xiuyang;  Liu, Qingsong;  Hu, Hsun-Ming;  Wu, Chung-Che;  Liu, Jianxing;  Jiang, Zhaoxia;  Lee, Teh-Quei;  Wang, Chun-Chieh;  Song, Yen-Fang;  Chiang, Cheng-Cheng;  Tan, Liangcheng;  Lone, Mahjoor A.;  Pan, Yongxin;  Zhu, Rixiang;  He, Yaoqi;  Chou, Yu-Chen;  Tan, An-Hung;  Roberts, Andrew P.;  Zhao, Xiang;  Shen, Chuan-Chou
收藏  |  浏览/下载:6/0  |  提交时间:2019/11/27
multidecadally resolved polarity oscillations  geomagnetic excursion  abrupt reversal transition  asymmetrical interhemispheric polarity drifts  stalagmite U-Th dating  
A molecular perspective for global modeling of upper atmospheric NH3 from freezing clouds 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2018, 115 (24) : 6147-6152
作者:  Ge, Cui;  Zhu, Chongqin;  Francisco, Joseph S.;  Zeng, Xiao Cheng;  Wang, Jun
收藏  |  浏览/下载:6/0  |  提交时间:2019/11/27
ammonia  molecular dynamics simulation  global model  deep convection  freezing clouds