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A simple dynamic model explains the diversity of island birds worldwide 期刊论文
NATURE, 2020
作者:  Li, Junxue;  Wilson, C. Blake;  Cheng, Ran;  Lohmann, Mark;  Kavand, Marzieh;  Yuan, Wei;  Aldosary, Mohammed;  Agladze, Nikolay;  Wei, Peng;  Sherwin, Mark S.;  Shi, Jing
收藏  |  浏览/下载:13/0  |  提交时间:2020/07/03

Colonization, speciation and extinction are dynamic processes that influence global patterns of species richness(1-6). Island biogeography theory predicts that the contribution of these processes to the accumulation of species diversity depends on the area and isolation of the island(7,8). Notably, there has been no robust global test of this prediction for islands where speciation cannot be ignored(9), because neither the appropriate data nor the analytical tools have been available. Here we address both deficiencies to reveal, for island birds, the empirical shape of the general relationships that determine how colonization, extinction and speciation rates co-vary with the area and isolation of islands. We compiled a global molecular phylogenetic dataset of birds on islands, based on the terrestrial avifaunas of 41 oceanic archipelagos worldwide (including 596 avian taxa), and applied a new analysis method to estimate the sensitivity of island-specific rates of colonization, speciation and extinction to island features (area and isolation). Our model predicts-with high explanatory power-several global relationships. We found a decline in colonization with isolation, a decline in extinction with area and an increase in speciation with area and isolation. Combining the theoretical foundations of island biogeography(7,8) with the temporal information contained in molecular phylogenies(10) proves a powerful approach to reveal the fundamental relationships that govern variation in biodiversity across the planet.


Using a global molecular phylogenetic dataset of birds on islands, the sensitivity of island-specific rates of colonization, speciation and extinction to island features (area and isolation) is estimated.


  
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).


  
Drivers of improved PM2.5 air quality in China from 2013 to 2017 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2019
作者:  Qiang Zhang;  Yixuan Zheng;  Dan Tong;  Min Shao;  Shuxiao Wang;  Yuanhang Zhang;  Xiangde Xu;  Jinnan Wang;  Hong He;  Wenqing Liu;  Yihui Ding;  Yu Lei;  Junhua Li;  Zifa Wang;  Xiaoye Zhang;  Yuesi Wang;  Jing Cheng;  Yang Liu;  Qinren Shi;  Liu Yan;  Guannan Geng;  Chaopeng Hong;  Meng Li;  Fei Liu;  Bo Zheng;  Junji Cao;  Aijun Ding;  Jian Gao;  Qingyan Fu;  Juntao Huo;  Baoxian Liu;  Zirui Liu;  Fumo Yang;  Kebin He;  and Jiming Hao
收藏  |  浏览/下载:12/0  |  提交时间:2019/11/27
clean air actions  PM  emission abatements  air quality improvements  health benefits  
VHL substrate transcription factor ZHX2 as an oncogenic driver in clear cell renal cell carcinoma 期刊论文
SCIENCE, 2018, 361 (6399) : 290-295
作者:  Zhang, Jing;  Wu, Tao;  Simon, Jeremy;  Takada, Mamoru;  Saito, Ryoichi;  Fan, Cheng;  Liu, Xian-De;  Jonasch, Eric;  Xie, Ling;  Chen, Xian;  Yao, Xiaosai;  Teh, Bin Tean;  Tan, Patrick;  Zheng, Xingnan;  Li, Mingjie;  Lawrence, Cortney;  Fan, Jie;  Geng, Jiang;  Liu, Xijuan;  Hu, Lianxin;  Wang, Jun;  Liao, Chengheng;  Hong, Kai;  Zurlo, Giada;  Parker, Joel S.;  Auman, J. Todd;  Perou, Charles M.;  Rathmell, W. Kimryn;  Kim, William Y.;  Kirschner, Marc W.;  Kaelin, William G., Jr.;  Baldwin, Albert S.;  Zhang, Qing
收藏  |  浏览/下载:12/0  |  提交时间:2019/11/27
Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis 期刊论文
SCIENCE, 2018, 361 (6398)
作者:  Griesmann, Maximilian;  Chang, Yue;  Liu, Xin;  Song, Yue;  Haberer, Georg;  Crook, Matthew B.;  Billault-Penneteau, Benjamin;  Lauressergues, Dominique;  Keller, Jean;  Imanishi, Leandro;  Roswanjaya, Yuda Purwana;  Kohlen, Wouter;  Pujic, Petar;  Battenberg, Kai;  Alloisio, Nicole;  Liang, Yuhu;  Hilhorst, Henk;  Salgado, Marco G.;  Hocher, Valerie;  Gherbi, Hassen;  Svistoonoff, Sergio;  Doyle, Jeff J.;  He, Shixu;  Xu, Yan;  Xu, Shanyun;  Qu, Jing;  Gao, Qiang;  Fang, Xiaodong;  Fu, Yuan;  Normand, Philippe;  Berry, Alison M.;  Wall, Luis G.;  Ane, Jean-Michel;  Pawlowski, Katharina;  Xu, Xun;  Yang, Huanming;  Spannagl, Manuel;  Mayer, Klaus F. X.;  Wong, Gane Ka-Shu;  Parniske, Martin;  Delaux, Pierre-Marc;  Cheng, Shifeng
收藏  |  浏览/下载:11/0  |  提交时间:2019/11/27
A selfish genetic element confers non-Mendelian inheritance in rice 期刊论文
SCIENCE, 2018, 360 (6393) : 1130-1132
作者:  Yu, Xiaowen;  Zhao, Zhigang;  Zheng, Xiaoming;  Zhou, Jiawu;  Kong, Weiyi;  Wang, Peiran;  Bai, Wenting;  Zheng, Hai;  Zhang, Huan;  Li, Jing;  Liu, Jiafan;  Wang, Qiming;  Zhang, Long;  Liu, Kai;  Yu, Yang;  Guo, Xiuping;  Wang, Jiulin;  Lin, Qibing;  Wu, Fuqing;  Ren, Yulong;  Zhu, Shanshan;  Zhang, Xin;  Cheng, Zhijun;  Lei, Cailin;  Liu, Shijia;  Liu, Xi;  Tian, Yunlu;  Jiang, Ling;  Ge, Song;  Wu, Chuanyin;  Tao, Dayun;  Wang, Haiyang;  Wan, Jianmin
收藏  |  浏览/下载:20/0  |  提交时间:2019/11/27
Importing food damages domestic environment: Evidence from global soybean trade 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2018, 115 (21) : 5415-5419
作者:  Sun, Jing;  Mooney, Harold;  Wu, Wenbin;  Tang, Huajun;  Tong, Yuxin;  Xu, Zhenci;  Huang, Baorong;  Cheng, Yeqing;  Yang, Xinjun;  Wei, Dan;  Zhang, Fusuo;  Liu, Jianguo
收藏  |  浏览/下载:10/0  |  提交时间:2019/11/27
agriculture  environment  nitrogen  Sustainable Development Goals  telecoupling  
3D charge and 2D phonon transports leading to high out-of-plane ZT in n-type SnSe crystals 期刊论文
SCIENCE, 2018, 360 (6390) : 778-782
作者:  Chang, Cheng;  Wu, Minghui;  He, Dongsheng;  Pei, Yanling;  Wu, Chao-Feng;  Wu, Xuefeng;  Yu, Hulei;  Zhu, Fangyuan;  Wang, Kedong;  Chen, Yue;  Huang, Li;  Li, Jing-Feng;  He, Jiaqing;  Zhao, Li-Dong
收藏  |  浏览/下载:7/0  |  提交时间:2019/11/27
Probing the ultimate plasmon confinement limits with a van der Waals heterostructure 期刊论文
SCIENCE, 2018, 360 (6386) : 291-295
作者:  Alcaraz Iranzo, David;  Nanot, Sebastien;  Dias, Eduardo J. C.;  Epstein, Itai;  Peng, Cheng;  Efetov, Dmitri K.;  Lundeberg, Mark B.;  Parret, Romain;  Osmond, Johann;  Hong, Jin-Yong;  Kong, Jing;  Englund, Dirk R.;  Peres, Nuno M. R.;  Koppens, Frank H. L.
收藏  |  浏览/下载:7/0  |  提交时间:2019/11/27
Comment on "The whole-soil carbon flux in response to warming" 期刊论文
SCIENCE, 2018, 359 (6378) : 878-878
作者:  Xiao, Jing;  Yu, Fangjian;  Zhu, Wanying;  Xu, Chenchao;  Zhang, Kaihang;  Luo, Yiqi;  Tiedje, James M.;  Zhou, Jizhong;  Cheng, Lei
收藏  |  浏览/下载:9/0  |  提交时间:2019/11/27