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A gas-to-particle conversion mechanism helps to explain atmospheric particle formation through clustering of iodine oxides 期刊论文
Nature Communications, 2020
作者:  Juan Carlos Gó;  mez Martí;  n;  Thomas R. Lewis;  Mark A. Blitz;  John M. C. Plane;  Manoj Kumar;  Joseph S. Francisco;  Alfonso Saiz-Lopez
收藏  |  浏览/下载：7/0  |  提交时间：2020/09/14
Antitumor activity of a systemic STING-activating non-nucleotide cGAMP mimetic 期刊论文
Science, 2020
作者:  Emily N. Chin;  Chenguang Yu;  Vincent F. Vartabedian;  Ying Jia;  Manoj Kumar;  Ana M. Gamo;  William Vernier;  Sabrina H. Ali;  Mildred Kissai;  Daniel C. Lazar;  Nhan Nguyen;  Laura E. Pereira;  Brent Benish;  Ashley K. Woods;  Sean B. Joseph;  Alan Chu;  Kristen A. Johnson;  Philipp N. Sander;  Francisco Martínez-Peña;  Eric N. Hampton;  Travis S. Young;  Dennis W. Wolan;  Arnab K. Chatterjee;  Peter G. Schultz;  H. Michael Petrassi;  John R. Teijaro;  Luke L. Lairson
收藏  |  浏览/下载：19/0  |  提交时间：2020/08/25
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：142/0  |  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).


  
Determining natal origin for improved management of Atlantic bluefin tuna 期刊论文
FRONTIERS IN ECOLOGY AND THE ENVIRONMENT, 2019, 17 (8) : 439-443
作者:  Rodriguez-Ezpeleta, Naiara;  Diaz-Arce, Natalia;  Walter, John F., III;  Richardson, David E.;  Rooker, Jay R.;  Nottestad, Leif;  Hanke, Alex R.;  Franks, James S.;  Deguara, Simeon;  Lauretta, Matthew, V;  Addis, Piero;  Varela, Jose Luis;  Fraile, Igaratza;  Goni, Nicolas;  Abid, Noureddine;  Alemany, Francisco;  Oray, Isik K.;  Quattro, Joseph M.;  Sow, Fambaye N.;  Itoh, Tomoyuki;  Karakulak, F. Saadet;  Pascual-Alayon, Pedro J.;  Santos, Miguel N.;  Tsukahara, Yohei;  Lutcavage, Molly;  Fromentin, Jean-Marc;  Arrizabalaga, Haritz
收藏  |  浏览/下载：11/0  |  提交时间：2019/11/27
Nitrosative stress drives heart failure with preserved ejection fraction 期刊论文
NATURE, 2019, 568 (7752) : 351-+
作者:  Schiattarella, Gabriele G.;  Altamirano, Francisco;  Tong, Dan;  French, Kristin M.;  Villalobos, Elisa;  Kim, Soo Young;  Luo, Xiang;  Jiang, Nan;  May, Herman I.;  Wang, Zhao V.;  Hill, Theodore M.;  Mammen, Pradeep P. A.;  Huang, Jian;  Lee, Dong I.;  Hahn, Virginia S.;  Sharma, Kavita;  Kass, David A.;  Lavandero, Sergio;  Gillette, Thomas G.;  Hill, Joseph A.
收藏  |  浏览/下载：17/0  |  提交时间：2019/11/27
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  
Ion pair particles at the air-water interface 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2017, 114 (47) : 12401-12406
作者:  Kumar, Manoj;  Francisco, Joseph S.
收藏  |  浏览/下载：4/0  |  提交时间：2019/11/27
interface  particle  formation  air-water  mechanism  
Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution 期刊论文
NATURE, 2017, 545 (7655) : 446-+
作者:  Abbosh, Christopher;  Birkbak, Nicolai J.;  Wilson, Gareth A.;  Jamal-Hanjani, Mariam;  Constantin, Tudor;  Salari, Raheleh;  Le Quesne, John;  Moore, David A.;  Veeriah, Selvaraju;  Rosenthal, Rachel;  Marafioti, Teresa;  Kirkizlar, Eser;  Watkins, Thomas B. K.;  McGranahan, Nicholas;  Ward, Sophia;  Martinson, Luke;  Riley, Joan;  Fraioli, Francesco;  Al Bakir, Maise;  Gronroos, Eva;  Zambrana, Francisco;  Endozo, Raymondo;  Bi, Wenya Linda;  Fennessy, Fiona M.;  Sponer, Nicole;  Johnson, Diana;  Laycock, Joanne;  Shafi, Seema;  Czyzewska-Khan, Justyna;  Rowan, Andrew;  Chambers, Tim;  Matthews, Nik;  Turajlic, Samra;  Hiley, Crispin;  Lee, Siow Ming;  Forster, Martin D.;  Ahmad, Tanya;  Falzon, Mary;  Borg, Elaine;  Lawrence, David;  Hayward, Martin;  Kolvekar, Shyam;  Panagiotopoulos, Nikolaos;  Janes, Sam M.;  Thakrar, Ricky;  Ahmed, Asia;  Blackhall, Fiona;  Summers, Yvonne;  Hafez, Dina;  Naik, Ashwini;  Ganguly, Apratim;  Kareht, Stephanie;  Shah, Rajesh;  Joseph, Leena;  Quinn, Anne Marie;  Crosbie, Phil A.;  Naidu, Babu;  Middleton, Gary;  Langman, Gerald;  Trotter, Simon;  Nicolson, Marianne;  Remmen, Hardy;  Kerr, Keith;  Chetty, Mahendran;  Gomersall, Lesley;  Fennell, Dean A.;  Nakas, Apostolos;  Rathinam, Sridhar;  Anand, Girija;  Khan, Sajid;  Russell, Peter;  Ezhil, Veni;  Ismail, Babikir;  Irvin-Sellers, Melanie;  Prakash, Vineet;  Lester, Jason F.;  Kornaszewska, Malgorzata;  Attanoos, Richard;  Adams, Haydn;  Davies, Helen;  Oukrif, Dahmane;  Akarca, Ayse U.;  Hartley, John A.;  Lowe, Helen L.;  Lock, Sara;  Iles, Natasha;  Bell, Harriet;  Ngai, Yenting;  Elgar, Greg;  Szallasi, Zoltan;  Schwarz, Roland F.;  Herrero, Javier;  Stewart, Aengus;  Quezada, Sergio A.;  Peggs, Karl S.;  Van Loo, Peter;  Dive, Caroline;  Lin, C. Jimmy;  Rabinowitz, Matthew;  Aerts, Hugo J. W. L.;  Hackshaw, Allan;  Shaw, Jacqui A.;  Zimmermann, Bernhard G.;  Swanton, Charles;  Jamal-Hanjani, Mariam;  Abbosh, Christopher;  Veeriah, Selvaraju;  Shafi, Seema;  Czyzewska-Khan, Justyna;  Johnson, Diana;  Laycock, Joanne;  Bosshard-Carter, Leticia;  Goh, Gerald;  Rosenthal, Rachel;  Gorman, Pat;  Murugaesu, Nirupa;  Hynds, Robert E.;  Wilson, Gareth A.;  Birkbak, Nicolai J.;  Watkins, Thomas B. K.;  McGranahan, Nicholas;  Horswell, Stuart;  Al Bakir, Maise;  Gronroos, Eva;  Mitter, Richard;  Escudero, Mickael;  Stewart, Aengus;  Van Loo, Peter;  Rowan, Andrew;  Xu, Hang;  Turajlic, Samra;  Hiley, Crispin;  Goldman, Jacki;  Stone, Richard Kevin;  Denner, Tamara;  Matthews, Nik;  Elgar, Greg;  Ward, Sophia;  Biggs, Jennifer;  Costa, Marta;  Begum, Sharmin;  Phillimore, Ben;  Chambers, Tim;  Nye, Emma;  Graca, Sofia;  Joshi, Kroopa;  Furness, Andrew;  Ben Aissa, Assma;  Wong, Yien Ning Sophia;  Georgiou, Andy;  Quezada, Sergio A.;  Peggs, Karl S.;  Hartley, John A.;  Lowe, Helen L.;  Herrero, Javier;  Lawrence, David;  Hayward, Martin;  Panagiotopoulos, Nikolaos;  Kolvekar, Shyam;  Falzon, Mary;  Borg, Elaine;  Marafioti, Teresa;  Simeon, Celia;  Hector, Gemma;  Smith, Amy;  Aranda, Marie;  Novelli, Marco;  Oukrif, Dahmane;  Akarca, Ayse U.;  Janes, Sam M.;  Thakrar, Ricky;  Forster, Martin D.;  Ahmad, Tanya;  Lee, Siow Ming;  Papadatos-Pastos, Dionysis;  Carnell, Dawn;  Mendes, Ruheena;  George, Jeremy;  Navani, Neal;  Ahmed, Asia;  Taylor, Magali;  Choudhary, Junaid;  Summers, Yvonne;  Califano, Raffaele;  Taylor, Paul;  Shah, Rajesh;  Krysiak, Piotr;  Rammohan, Kendadai;  Fontaine, Eustace;  Booton, Richard;  Evison, Matthew;  Crosbie, Phil A.;  Moss, Stuart;  Idries, Faiza;  Joseph, Leena;  Bishop, Paul;  Chaturvedi, Anshuman;  Quinn, Anne Marie;  Doran, Helen;  Leek, Angela;  Harrison, Phil;  Moore, Katrina;  Waddington, Rachael;  Novasio, Juliette;  Blackhall, Fiona;  Rogan, Jane;  Smith, Elaine;  Dive, Caroline;  Tugwood, Jonathan;  Brady, Ged;  Rothwell, Dominic G.;  Chemi, Francesca;  Pierce, Jackie;  Gulati, Sakshi;  Naidu, Babu;  Langman, Gerald;  Trotter, Simon;  Bellamy, Mary;  Bancroft, Hollie;  Kerr, Amy;  Kadiri, Salma;  Webb, Joanne;  Middleton, Gary;  Djearaman, Madava;  Fennell, Dean A.;  Shaw, Jacqui A.;  Le Quesne, John;  Moore, David A.;  Thomas, Anne;  Walter, Harriet;  Riley, Joan;  Martinson, Luke;  Nakas, Apostolos;  Rathinam, Sridhar;  Monteiro, William;  Marshall, Hilary;  Nelson, Louise;  Bennett, Jonathan;  Primrose, Lindsay;  Anand, Girija;  Khan, Sajid;  Amadi, Anita;  Nicolson, Marianne;  Kerr, Keith;  Palmer, Shirley;  Remmen, Hardy;  Miller, Joy;  Buchan, Keith;  Chetty, Mahendran;  Gomersall, Lesley;  Lester, Jason F.;  Edwards, Alison;  Morgan, Fiona;  Adams, Haydn;  Davies, Helen;  Kornaszewska, Malgorzata;  Attanoos, Richard;  Lock, Sara;  Verjee, Azmina;  MacKenzie, Mairead;  Wilcox, Maggie;  Bell, Harriet;  Iles, Natasha;  Hackshaw, Allan;  Ngai, Yenting;  Smith, Sean;  Gower, Nicole;  Ottensmeier, Christian;  Chee, Serena;  Johnson, Benjamin;  Alzetani, Aiman;  Shaw, Emily;  Lim, Eric;  De Sousa, Paulo;  Barbosa, Monica Tavares;  Bowman, Alex;  Jordan, Simon;  Rice, Alexandra;  Raubenheimer, Hilgardt;  Proli, Chiara;  Cufari, Maria Elena;  Ronquillo, John Carlo;  Kwayie, Angela;  Bhayani, Harshil;  Hamilton, Morag;  Bakar, Yusura;  Mensah, Natalie;  Ambrose, Lyn;  Devaraj, Anand;  Buderi, Silviu;  Finch, Jonathan;  Azcarate, Leire;  Chavan, Hema;  Green, Sophie;  Mashinga, Hillaria;  Nicholson, Andrew G.;  Lau, Kelvin;  Sheaff, Michael;  Schmid, Peter;  Conibear, John;  Ezhil, Veni;  Ismail, Babikir;  Irvin-Sellers, Melanie;  Prakash, Vineet;  Russell, Peter;  Light, Teresa;  Horey, Tracey;  Danson, Sarah;  Bury, Jonathan;  Edwards, John;  Hill, Jennifer;  Matthews, Sue;  Kitsanta, Yota;  Suvarna, Kim;  Fisher, Patricia;  Keerio, Allah Dino;  Shackcloth, Michael;  Gosney, John;  Postmus, Pieter;  Feeney, Sarah;  Asante-Siaw, Julius;  Constantin, Tudor;  Salari, Raheleh;  Sponer, Nicole;  Naik, Ashwini;  Zimmermann, Bernhard G.;  Rabinowitz, Matthew;  Aerts, Hugo J. W. L.;  Dentro, Stefan;  Dessimoz, Christophe
收藏  |  浏览/下载：24/0  |  提交时间：2019/04/09
Elemental sulfur aerosol-forming mechanism 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2017, 114 (5) : 864-869
作者:  Kumar, Manoj;  Francisco, Joseph S.
收藏  |  浏览/下载：5/0  |  提交时间：2019/11/27
sulfur aerosols  catalysis  planetary environment  nonphotochemical  hydrogen sulfide