PNAS Table of Contents for November 5, 2019; Vol. 116, No. 45

[PNAS] [Cozzarelli Prize Nominations](/cgi/adclick/?ad=54441&adclick=true&url=https%3A%2F%2Fwww.pnas.org%2Fpage%2Fabout%2Fcozzarelli-prize)   [November 5, 2019; Vol. 116, No. 45]( ) This Week in PNAS [In This Issue]( --------------------------------------------------------------- News Feature [News Feature: Quantum effects enter the macroworld]( Stephen Ornes An in-depth look at trending science issues. --------------------------------------------------------------- Retrospective [Thomas Bruice (1925–2019)]( Stephen J. Benkovic --------------------------------------------------------------- Commentaries [Watching a virus grow]( Bogdan Dragnea [Resolving a piece of the archaeal lipid puzzle]( Ann Pearson [Insight into promoter clearance by RNA polymerase II]( Donal S. Luse [Epigenetic targeting of DNA repair in lung cancer]( Benjamin H. Lok and Charles M. Rudin [Are individual differences in human brain organization measured with functional MRI meaningful?]( Mark D’Esposito --------------------------------------------------------------- Letters [Communicating racial segregation: Abstract versus concrete]( Tomasz Stepinski and Anna Dmowska [Reply to Stepinski and Dmowska: Segregation beyond scale and across space: Arbitrary versus objective analysis]( Madalina Olteanu, Julien Randon-Furling, and William A. V. Clark [How does transcranial alternating current stimulation entrain single-neuron activity in the primate brain?]( Ahmad Khatoun, Boateng Asamoah, and Myles Mc Laughlin [Reply to Khatoun et al.: Speculation about brain stimulation must be constrained by observation]( Matthew R. Krause, Pedro G. Vieira, Bennett A. Csorba, Praveen K. Pilly, and Christopher C. Pack --------------------------------------------------------------- Brief Report [Assortative mixing and resource inequality enhance collective welfare in sharing networks]( Hirokazu Shirado, George Iosifidis, and Nicholas A. Christakis --------------------------------------------------------------- Physical Sciences Applied Mathematics [Data-driven discovery of coordinates and governing equations]( Kathleen Champion, Bethany Lusch, J. Nathan Kutz, and Steven L. Brunton Applied Physical Sciences [Universal behavior of cascading failures in interdependent networks]( Dongli Duan, Changchun Lv, Shubin Si, Zhen Wang, Daqing Li, Jianxi Gao, Shlomo Havlin, H. Eugene Stanley, and Stefano Boccaletti [Evolution of superconductivity in K2−xFe4+ySe5: Spectroscopic studies of X-ray absorption and emission]( H. T. Wang, Anirudha Ghosh, C. H. Wang, S. H. Hsieh, Y. C. Shao, J. W. Chiou, C. L. Chen, C. W. Pao, J. F. Lee, Y. S. Liu, Y. D. Chuang, J. H. Guo, M. K. Wu, and W. F. Pong [Tunable corrugated patterns in an active nematic sheet]( Anis Senoussi, Shunnichi Kashida, Raphael Voituriez, Jean-Christophe Galas, Ananyo Maitra, and André Estevez-Torres Biophysics and Computational Biology [Asymmetric base-pair opening drives helicase unwinding dynamics]( Francesco Colizzi, Cibran Perez-Gonzalez, Remi Fritzen, Yaakov Levy, Malcolm F. White, J. Carlos Penedo, and Giovanni Bussi [Nanomechanical properties of steric zipper globular structures]( Neta Lester-Zer, Mnar Ghrayeb, and Liraz Chai [Measurements of the self-assembly kinetics of individual viral capsids around their RNA genome]( Rees F. Garmann, Aaron M. Goldfain, and Vinothan N. Manoharan Chemistry [Atomic-level engineering and imaging of polypeptoid crystal lattices]( Sunting Xuan, Xi Jiang, Ryan K. Spencer, Nan K. Li, David Prendergast, Nitash P. Balsara, and Ronald N. Zuckermann Earth, Atmospheric, and Planetary Sciences [Rapid ocean acidification and protracted Earth system recovery followed the end-Cretaceous Chicxulub impact]( Michael J. Henehan, Andy Ridgwell, Ellen Thomas, Shuang Zhang, Laia Alegret, Daniela N. Schmidt, James W. B. Rae, James D. Witts, Neil H. Landman, Sarah E. Greene, Brian T. Huber, James R. Super, Noah J. Planavsky, and Pincelli M. Hull [GDGT cyclization proteins identify the dominant archaeal sources of tetraether lipids in the ocean]( Zhirui Zeng, Xiao-Lei Liu, Kristen R. Farley, Jeremy H. Wei, William W. Metcalf, Roger E. Summons, and Paula V. Welander [Historical change of El Niño properties sheds light on future changes of extreme El Niño]( Bin Wang, Xiao Luo, Young-Min Yang, Weiyi Sun, Mark A. Cane, Wenju Cai, Sang-Wook Yeh, and Jian Liu [Sustained wood burial in the Bengal Fan over the last 19 My]( Hyejung Lee, Valier Galy, Xiaojuan Feng, Camilo Ponton, Albert Galy, Christian France-Lanord, and Sarah J. Feakins [Metallic iron limits silicate hydration in Earth’s transition zone]( Feng Zhu, Jie Li, Jiachao Liu, Junjie Dong, and Zhenxian Liu Engineering [Living myofibroblast–silicon composites for probing electrical coupling in cardiac systems]( Menahem Y. Rotenberg, Naomi Yamamoto, Erik N. Schaumann, Laura Matino, Francesca Santoro, and Bozhi Tian Physics [Impact of a hydrophobic ion on the early stage of atmospheric aerosol formation]( Linda Feketeová, Paul Bertier, Thibaud Salbaing, Toshiyuki Azuma, Florent Calvo, Bernadette Farizon, Michel Farizon, and Tilmann D. Märk --------------------------------------------------------------- Social Sciences Environmental Sciences [Modeling trade-offs across carbon sequestration, biodiversity conservation, and equity in the distribution of global REDD+ funds]( Ignacio Palomo, Yann Dujardin, Estelle Midler, Manon Robin, María J. Sanz, and Unai Pascual Psychological and Cognitive Sciences [Oscillatory recurrent gated neural integrator circuits (ORGaNICs), a unifying theoretical framework for neural dynamics]( David J. Heeger and Wayne E. Mackey [Visual fixation patterns during economic choice reflect covert valuation processes that emerge with learning]( Sean E. Cavanagh, W. M. Nishantha Malalasekera, Bruno Miranda, Laurence T. Hunt, and Steven W. Kennerley [Modulation of the pupillary response by the content of visual working memory]( Nahid Zokaei, Alexander G. Board, Sanjay G. Manohar, and Anna C. Nobre --------------------------------------------------------------- Biological Sciences Applied Biological Sciences [Quantifying cellulose accessibility during enzyme-mediated deconstruction using 2 fluorescence-tagged carbohydrate-binding modules]( Vera Novy, Kevin Aïssa, Fredrik Nielsen, Suzana K. Straus, Peter Ciesielski, Christopher G. Hunt, and Jack Saddler Biochemistry [Asymmetric base-pair opening drives helicase unwinding dynamics]( Francesco Colizzi, Cibran Perez-Gonzalez, Remi Fritzen, Yaakov Levy, Malcolm F. White, J. Carlos Penedo, and Giovanni Bussi [Nanomechanical properties of steric zipper globular structures]( Neta Lester-Zer, Mnar Ghrayeb, and Liraz Chai [UV light suppression of EAE (a mouse model of multiple sclerosis) is independent of vitamin D and its receptor]( Amy A. Irving, Steven J. Marling, Jeremy Seeman, Lori A. Plum, and Hector F. DeLuca [Topological analysis of the gp41 MPER on lipid bilayers relevant to the metastable HIV-1 envelope prefusion state]( Yi Wang, Pavanjeet Kaur, Zhen-Yu J. Sun, Mostafa A. Elbahnasawy, Zahra Hayati, Zhi-Song Qiao, Nhat N. Bui, Camila Chile, Mahmoud L. Nasr, Gerhard Wagner, Jia-Huai Wang, Likai Song, Ellis L. Reinherz, and Mikyung Kim [Invariable stoichiometry of ribosomal proteins in mouse brain tissues with aging]( Susan Amirbeigiarab, Parnian Kiani, Ana Velazquez Sanchez, Christoph Krisp, Andriy Kazantsev, Lars Fester, Hartmut Schlüter, and Zoya Ignatova [The capping enzyme facilitates promoter escape and assembly of a follow-on preinitiation complex for reinitiation]( Rina Fujiwara, Nivedita Damodaren, Jeremy E. Wilusz, and Kenji Murakami [Repression of eEF2K transcription by NF-κB tunes translation elongation to inflammation and dsDNA-sensing]( Christopher Bianco, Letitia Thompson, and Ian Mohr Biophysics and Computational Biology [Atomic-level engineering and imaging of polypeptoid crystal lattices]( Sunting Xuan, Xi Jiang, Ryan K. Spencer, Nan K. Li, David Prendergast, Nitash P. Balsara, and Ronald N. Zuckermann [A packing for A-form DNA in an icosahedral virus]( Fengbin Wang, Ying Liu, Zhangli Su, Tomasz Osinski, Guilherme A. P. de Oliveira, James F. Conway, Stefan Schouten, Mart Krupovic, David Prangishvili, and Edward H. Egelman [Structural and functional studies of TBC1D23 C-terminal domain provide a link between endosomal trafficking and PCH]( Wenjie Huang, Zhe Liu, Fan Yang, Huan Zhou, Xin Yong, Xiaoyu Yang, Yifei Zhou, Lijia Xue, Yihong Zhang, Dingdong Liu, Wentong Meng, Wenming Zhang, Xiaohu Zhang, Xiaofei Shen, Qingxiang Sun, Li Li, Cong Ma, Yuquan Wei, Daniel D. Billadeau, Xianming Mo, and Da Jia Cell Biology [DNA methyltransferase inhibitors induce a BRCAness phenotype that sensitizes NSCLC to PARP inhibitor and ionizing radiation]( Rachel Abbotts, Michael J. Topper, Christopher Biondi, Daniel Fontaine, Reena Goswami, Lora Stojanovic, Eun Yong Choi, Lena McLaughlin, Aksinija A. Kogan, Limin Xia, Rena Lapidus, Javed Mahmood, Stephen B. Baylin, and Feyruz V. Rassool [PDZD8 mediates a Rab7-dependent interaction of the ER with late endosomes and lysosomes]( Andrés Guillén-Samander, Xin Bian, and Pietro De Camilli [Graded regulation of cellular quiescence depth between proliferation and senescence by a lysosomal dimmer switch]( Kotaro Fujimaki, Ruoyan Li, Hengyu Chen, Kimiko Della Croce, Hao Helen Zhang, Jianhua Xing, Fan Bai, and Guang Yao Developmental Biology [Dynamics of trophoblast differentiation in peri-implantation–stage human embryos]( Rachel C. West, Hao Ming, Deirdre M. Logsdon, Jiangwen Sun, Sandeep K. Rajput, Rebecca A. Kile, William B. Schoolcraft, R. Michael Roberts, Rebecca L. Krisher, Zongliang Jiang, and Ye Yuan Environmental Sciences [Modeling trade-offs across carbon sequestration, biodiversity conservation, and equity in the distribution of global REDD+ funds]( Ignacio Palomo, Yann Dujardin, Estelle Midler, Manon Robin, María J. Sanz, and Unai Pascual [GenBank is a reliable resource for 21st century biodiversity research]( Matthieu Leray, Nancy Knowlton, Shian-Lei Ho, Bryan N. Nguyen, and Ryuji J. Machida Evolution [Rapid ocean acidification and protracted Earth system recovery followed the end-Cretaceous Chicxulub impact]( Michael J. Henehan, Andy Ridgwell, Ellen Thomas, Shuang Zhang, Laia Alegret, Daniela N. Schmidt, James W. B. Rae, James D. Witts, Neil H. Landman, Sarah E. Greene, Brian T. Huber, James R. Super, Noah J. Planavsky, and Pincelli M. Hull [Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths]( Akito Y. Kawahara, David Plotkin, Marianne Espeland, Karen Meusemann, Emmanuel F. A. Toussaint, Alexander Donath, France Gimnich, Paul B. Frandsen, Andreas Zwick, Mario dos Reis, Jesse R. Barber, Ralph S. Peters, Shanlin Liu, Xin Zhou, Christoph Mayer, Lars Podsiadlowski, Caroline Storer, Jayne E. Yack, Bernhard Misof, and Jesse W. Breinholt [Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination]( Kenneth B. Hoehn, Jason A. Vander Heiden, Julian Q. Zhou, Gerton Lunter, Oliver G. Pybus, and Steven H. Kleinstein [Host–symbiont specificity determined by microbe–microbe competition in an insect gut]( Hideomi Itoh, Seonghan Jang, Kazutaka Takeshita, Tsubasa Ohbayashi, Naomi Ohnishi, Xian-Ying Meng, Yasuo Mitani, and Yoshitomo Kikuchi Genetics [Deletions associated with stabilization of the Top1 cleavage complex in yeast are products of the nonhomologous end-joining pathway]( Jang-Eun Cho and Sue Jinks-Robertson [Long-range Pitx2c enhancer–promoter interactions prevent predisposition to atrial fibrillation]( Min Zhang, Matthew C. Hill, Zachary A. Kadow, Ji Ho Suh, Nathan R. Tucker, Amelia W. Hall, Tien T. Tran, Paul S. Swinton, John P. Leach, Kenneth B. Margulies, Patrick T. Ellinor, Na Li, and James F. Martin Immunology and Inflammation [Combination anti–CTLA-4 plus anti–PD-1 checkpoint blockade utilizes cellular mechanisms partially distinct from monotherapies]( Spencer C. Wei, Nana-Ama A. S. Anang, Roshan Sharma, Miles C. Andrews, Alexandre Reuben, Jacob H. Levine, Alexandria P. Cogdill, James J. Mancuso, Jennifer A. Wargo, Dana Pe’er, and James P. Allison [Aged hind-limb clasping experimental autoimmune encephalomyelitis models aspects of the neurodegenerative process seen in multiple sclerosis]( Lindsay S. Cahill, Monan Angela Zhang, Valeria Ramaglia, Heather Whetstone, Melika Pahlevan Sabbagh, Tae Joon Yi, Laura Woo, Thomas S. Przybycien, Marina Moshkova, Fei Linda Zhao, Olga L. Rojas, Josephine Gomes, Stefanie Kuerten, Jennifer L. Gommerman, John G. Sled, and Shannon E. Dunn [Polymerase III transcription is necessary for T cell priming by dendritic cells]( Marisa Reverendo, Rafael J. Argüello, Christine Polte, Jan Valečka, Voahirana Camosseto, Nathalie Auphan-Anezin, Zoya Ignatova, Evelina Gatti, and Philippe Pierre Medical Sciences [Whole-exome sequencing of cervical carcinomas identifies activating ERBB2 and PIK3CA mutations as targets for combination therapy]( Luca Zammataro, Salvatore Lopez, Stefania Bellone, Francesca Pettinella, Elena Bonazzoli, Emanuele Perrone, Siming Zhao, Gulden Menderes, Gary Altwerger, Chanhee Han, Burak Zeybek, Anna Bianchi, Aranzazu Manzano, Paola Manara, Emiliano Cocco, Natalia Buza, Pei Hui, Serena Wong, Antonella Ravaggi, Eliana Bignotti, Chiara Romani, Paola Todeschini, Laura Zanotti, Franco Odicino, Sergio Pecorelli, Carla Donzelli, Laura Ardighieri, Roberto Angioli, Francesco Raspagliesi, Giovanni Scambia, Jungmin Choi, Weilai Dong, Kaya Bilguvar, Ludmil B. Alexandrov, Dan-Arin Silasi, Gloria S. Huang, Elena Ratner, Masoud Azodi, Peter E. Schwartz, Valentina Pirazzoli, Amy L. Stiegler, Titus J. Boggon, Richard P. Lifton, Joseph Schlessinger, and Alessandro D. Santin [Expert-level detection of acute intracranial hemorrhage on head computed tomography using deep learning]( Weicheng Kuo, Christian Hӓne, Pratik Mukherjee, Jitendra Malik, and Esther L. Yuh [Mutational inactivation of mTORC1 repressor gene DEPDC5 in human gastrointestinal stromal tumors]( Yuzhi Pang, Feifei Xie, Hui Cao, Chunmeng Wang, Meijun Zhu, Xiaoxiao Liu, Xiaojing Lu, Tao Huang, Yanying Shen, Ke Li, Xiaona Jia, Zhang Li, Xufen Zheng, Simin Wang, Yi He, Linhui Wang, Jonathan A. Fletcher, and Yuexiang Wang [Mutations in thyroid hormone receptor α1 cause premature neurogenesis and progenitor cell depletion in human cortical development]( Teresa G. Krieger, Carla M. Moran, Alberto Frangini, W. Edward Visser, Erik Schoenmakers, Francesco Muntoni, Chris A. Clark, David Gadian, Wui K. Chong, Adam Kuczynski, Mehul Dattani, Greta Lyons, Alexandra Efthymiadou, Faraneh Varga-Khadem, Benjamin D. Simons, Krishna Chatterjee, and Frederick J. Livesey Microbiology [Measurements of the self-assembly kinetics of individual viral capsids around their RNA genome]( Rees F. Garmann, Aaron M. Goldfain, and Vinothan N. Manoharan [GDGT cyclization proteins identify the dominant archaeal sources of tetraether lipids in the ocean]( Zhirui Zeng, Xiao-Lei Liu, Kristen R. Farley, Jeremy H. Wei, William W. Metcalf, Roger E. Summons, and Paula V. Welander [Global selective sweep of a highly inbred genome of the cattle parasite Neospora caninum]( Asis Khan, Ayako Wendy Fujita, Nadine Randle, Javier Regidor-Cerrillo, Jahangheer S. Shaik, Kui Shen, Andrew J. Oler, Mariam Quinones, Sarah M. Latham, Bartholomew D. Akanmori, Sarah Cleaveland, Elizabeth A. Innes, Una Ryan, Jan Šlapeta, Gereon Schares, Luis M. Ortega-Mora, Jitender P. Dubey, Johnathan M. Wastling, and Michael E. Grigg [Developmental competence and antigen switch frequency can be uncoupled in Trypanosoma brucei]( Kirsty R. McWilliam, Alasdair Ivens, Liam J. Morrison, Monica R. Mugnier, and Keith R. Matthews Neuroscience [Oscillatory recurrent gated neural integrator circuits (ORGaNICs), a unifying theoretical framework for neural dynamics]( David J. Heeger and Wayne E. Mackey [Visual fixation patterns during economic choice reflect covert valuation processes that emerge with learning]( Sean E. Cavanagh, W. M. Nishantha Malalasekera, Bruno Miranda, Laurence T. Hunt, and Steven W. Kennerley [Modulation of the pupillary response by the content of visual working memory]( Nahid Zokaei, Alexander G. Board, Sanjay G. Manohar, and Anna C. Nobre [Simple framework for constructing functional spiking recurrent neural networks]( Robert Kim, Yinghao Li, and Terrence J. Sejnowski [During infant maltreatment, stress targets hippocampus, but stress with mother present targets amygdala and social behavior]( Charlis Raineki, Maya Opendak, Emma Sarro, Ashleigh Showler, Kevin Bui, Bruce S. McEwen, Donald A. Wilson, and Regina M. Sullivan [Corticobasal ganglia projecting neurons are required for juvenile vocal learning but not for adult vocal plasticity in songbirds]( Miguel Sánchez-Valpuesta, Yumeno Suzuki, Yukino Shibata, Noriyuki Toji, Yu Ji, Nasiba Afrin, Chinweike Norman Asogwa, Ippei Kojima, Daisuke Mizuguchi, Satoshi Kojima, Kazuo Okanoya, Haruo Okado, Kenta Kobayashi, and Kazuhiro Wada [Arm movements induced by noninvasive optogenetic stimulation of the motor cortex in the common marmoset]( Teppei Ebina, Keitaro Obara, Akiya Watakabe, Yoshito Masamizu, Shin-Ichiro Terada, Ryota Matoba, Masafumi Takaji, Nobuhiko Hatanaka, Atsushi Nambu, Hiroaki Mizukami, Tetsuo Yamamori, and Masanori Matsuzaki [Trait-like variants in human functional brain networks]( Benjamin A. Seitzman, Caterina Gratton, Timothy O. Laumann, Evan M. Gordon, Babatunde Adeyemo, Ally Dworetsky, Brian T. Kraus, Adrian W. Gilmore, Jeffrey J. Berg, Mario Ortega, Annie Nguyen, Deanna J. Greene, Kathleen B. McDermott, Steven M. Nelson, Christina N. Lessov-Schlaggar, Bradley L. Schlaggar, Nico U. F. Dosenbach, and Steven E. Petersen Physiology [Hearing loss mutations alter the functional properties of human P2X2 receptor channels through distinct mechanisms]( Benjamin George, Kenton J. Swartz, and Mufeng Li Plant Biology [The viral F-box protein P0 induces an ER-derived autophagy degradation pathway for the clearance of membrane-bound AGO1]( Simon Michaeli, Marion Clavel, Esther Lechner, Corrado Viotti, Jian Wu, Marieke Dubois, Thibaut Hacquard, Benoît Derrien, Esther Izquierdo, Maxime Lecorbeiller, Nathalie Bouteiller, Julia De Cilia, Véronique Ziegler-Graff, Hervé Vaucheret, Gad Galili, and Pascal Genschik --------------------------------------------------------------- Correction [Correction for Tang et al., Electronic-cigarette smoke induces lung adenocarcinoma and bladder urothelial hyperplasia in mice]( [Cover] --------------------------------------------------------------- This message was sent to {EMAIL}. [Unsubscribe]( from or [edit]( your subscription for this service. Or by mail: Customer Service * 973 University Avenue * Los Gatos, CA 95032 * U.S.A. Copyright © 2019 by the National Academy of Sciences