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1 May 11, 2021 u vol. 118 u no. 19 From the Cover e Heat tolerance in Red Sea corals e Range of human diets across time e Resurrecting ancient date palms e Distance perception in bats e Conditional decision-making in pea plants Contents Cover image: Pictured is a coral reef in the Gulf of Aqaba. Romain Savary et al. exposed Stylophora pistillata corals from the Gulf of Aqaba to temperatures ranging from 27 C to 34.5 C for periods ranging from hours to weeks. The authors found that both corals and their symbiotic algae exhibited rapid response and recovery patterns in gene expression when exposed to temperatures up to 32 C. However, when exposed to 34.5 C, corals exhibited minimal recovery, high mortality, and a microbiome dominated by opportunistic bacteria, even though such high temperatures are not anticipated to occur in the Gulf of Aqaba within this century. See the article by Savary et al., e Image credit: Romain Savary. THIS WEEK IN PNAS This week s research highlights eiti In This Issue OPINION Leading scientists discuss current issues e Compound risks and complex emergencies require new approaches to preparedness A. Kruczkiewicz, J. Klopp, J. Fisher, S. Mason, S. McClain, N. M. Sheekh, R. Moss, R. M. Parks, and C. Braneon COMMENTARIES e Energy landscapes of fast-folding proteins pushing the limits of atomic force microscope (AFM) pulling Abhigyan Sengupta and Matthias Rief See companion article, e , in vol. 118, issue 12 e A tale of two receptors: Bmp heterodimers recruit two type I receptors but use the kinase activity of only one Jan Christian See companion article, e , in vol. 118, issue 15 e To eat, or not to eat, that is the question: Neural stem cells escape phagocytosis in autism with macrocephaly Simon T. Schafer and Fred H. Gage See companion article, e , in vol. 118, issue 15 e Inequalities in jail incarceration across the life course Kristin Turney See companion article, e , in vol. 118, issue 16 LETTERS e e Why it makes sense that increased PM 2.5 was correlated with anthropogenic combustion-derived water Philip K. Hopke and Qili Dai Reply to Hopke and Dai: The correlation between PM 2.5 and combustion-derived water is unlikely driven by local residential coal combustion Meng Xing, Weiguo Liu, Xia Li, Qiyuan Wang, Jie Tian, Xiaofei Li, Xuexi Tie, Guohui Li, Junji Cao, and Huiming Bao Free online through the PNAS open access option. PNAS u May 11, 2021 u vol. 118 u no. 19 u iii vii

2 e e AIS-based profiling of fishing vessels falls short as a proof of concept for identifying forced labor at sea Wilf Swartz, Andrés M. Cisneros-Montemayor, Gerald G. Singh, Patrick Boutet, and Yoshitaka Ota Reply to Swartz et al.: Challenges and opportunities for identifying forced labor using satellite-based fishing vessel monitoring Gavin G. McDonald, Christopher Costello, Jennifer Bone, Reniel B. Cabral, Valerie Farabee, Timothy Hochberg, David Kroodsma, Tracey Mangin, Kyle C. Meng, and Oliver Zahn BRIEF REPORT e DNA-inspired nanomaterials for enhanced endosomal escape Jinhyung Lee, Ian Sands, Wuxia Zhang, Libo Zhou, and Yupeng Chen PHYSICAL SCIENCES e e e e e e e e APPLIED PHYSICAL SCIENCES Hydraulic and electric control of cell spheroids Charlie Duclut, Jacques Prost, and Frank Jülicher Essential role of papillae flexibility in nectar capture by bees Amandine Lechantre, Ayrton Draux, Hoa-Ai Béatrice Hua, Denis Michez, Pascal Damman, and Fabian Brau Microswimmers learning chemotaxis with genetic algorithms Benedikt Hartl, Maximilian Hübl, Gerhard Kahl, and Andreas Zöttl Density-independent plasmons for terahertzstable topological metamaterials Jianfeng Wang, Xuelei Sui, Wenhui Duan, Feng Liu, and Bing Huang ASTRONOMY AI-assisted superresolution cosmological simulations Yin Li, Yueying Ni, Rupert A. C. Croft, Tiziana Di Matteo, Simeon Bird, and Yu Feng BIOPHYSICS AND COMPUTATIONAL BIOLOGY Membrane fusion and drug delivery with carbon nanotube porins Nga T. Ho, Marc Siggel, Karen V. Camacho, Ramachandra M. Bhaskara, Jacqueline M. Hicks, Yun-Chiao Yao, Yuliang Zhang, Jürgen Köfinger, Gerhard Hummer, and Aleksandr Noy Delineating the heterogeneity of matrixdirected differentiation toward soft and stiff tissue lineages via single-cell profiling Shlomi Brielle, Danny Bavli, Alex Motzik, Yoav Kan-Tor, Xue Sun, Chen Kozulin, Batia Avni, Oren Ram, and Amnon Buxboim CHEMISTRY Ultrafast X-ray scattering offers a structural view of excited-state charge transfer Haiwang Yong, Xuan Xu, Jennifer M. Ruddock, Brian Stankus, Andrés Moreno Carrascosa, Nikola Zotev, Darren Bellshaw, Wenpeng Du, Nathan Goff, Yu Chang, Sébastien Boutet, Sergio Carbajo, Jason E. Koglin, Mengning Liang, Joseph S. Robinson, Adam Kirrander, Michael P. Minitti, and Peter M. Weber e e e e e e e e e e Image-charge effects on ion adsorption near aqueous interfaces Chang Yun Son and Zhen-Gang Wang Molecular dynamics reveals formation path of benzonitrile and other molecules in conditions relevant to the interstellar medium Jeeno Jose, Alon Zamir, and Tamar Stein COMPUTER SCIENCES Belief polarization in a complex world: A learning theory perspective Nika Haghtalab, Matthew O. Jackson, and Ariel D. Procaccia EARTH, ATMOSPHERIC, AND PLANETARY SCIENCES Anatomy of strike-slip fault tsunami genesis Ahmed Elbanna, Mohamed Abdelmeguid, Xiao Ma, Faisal Amlani, Harsha S. Bhat, Costas Synolakis, and Ares J. Rosakis Rules of formation of H C N O compounds at high pressure and the fates of planetary ices Lewis J. Conway, Chris J. Pickard, and Andreas Hermann ENGINEERING Reversed-engineered human alveolar lung-on-a-chip model Di Huang, Tingting Liu, Junlong Liao, Sushila Maharjan, Xin Xie, Montserrat Pérez, Ingrid Anaya, Shiwei Wang, Alan Tirado Mayer, Zhixin Kang, Weijia Kong, Valerio Luca Mainardi, Carlos Ezio Garciamendez-Mijares, Germán García Martínez, Matteo Moretti, Weijia Zhang, Zhongze Gu, Amir M. Ghaemmaghami, and Yu Shrike Zhang Automated, multiparametric monitoring of respiratory biomarkers and vital signs in clinical and home settings for COVID-19 patients Xiaoyue Ni, Wei Ouyang, Hyoyoung Jeong, Jin-Tae Kim, Andreas Tzaveils, Ali Mirzazadeh, Changsheng Wu, Jong Yoon Lee, Matthew Keller, Chaithanya K. Mummidisetty, Manish Patel, Nicholas Shawen, Joy Huang, Hope Chen, Sowmya Ravi, Jan-Kai Chang, KunHyuck Lee, Yixin Wu, Ferrona Lie, Youn J. Kang, Jong Uk Kim, Leonardo P. Chamorro, Anthony R. Banks, Ankit Bharat, Arun Jayaraman, Shuai Xu, and John A. Rogers Compliant 3D frameworks instrumented with strain sensors for characterization of millimeter-scale engineered muscle tissues Hangbo Zhao, Yongdeok Kim, Heling Wang, Xin Ning, Chenkai Xu, Judy Suh, Mengdi Han, Gelson J. Pagan- Diaz, Wei Lu, Haibo Li, Wubin Bai, Onur Aydin, Yoonseok Park, Jiaojiao Wang, Yao Yao, Yishan He, M. Taher A. Saif, Yonggang Huang, Rashid Bashir, and John A. Rogers Strategic placement of an obstacle suppresses droplet break up in the hopper flow of a microfluidic soft crystal Alison D. Bick, Jian Wei Khor, Ya Gai, and Sindy K. Y. Tang ENVIRONMENTAL SCIENCES The aryl hydrocarbon receptor suppresses immunity to oral squamous cell carcinoma through immune checkpoint regulation Jessica E. Kenison, Zhongyan Wang, Kangkang Yang, Megan Snyder, Francisco J. Quintana, and David H. Sherr iv u Contents

3 e SOCIAL SCIENCES e e e e e BIOLOGICAL SCIENCES e e e e MATHEMATICS Constructing Turing complete Euler flows in dimension 3 Robert Cardona, Eva Miranda, Daniel Peralta-Salas, and Francisco Presas ECONOMIC SCIENCES Belief polarization in a complex world: A learning theory perspective Nika Haghtalab, Matthew O. Jackson, and Ariel D. Procaccia Interacting regional policies in containing a disease Arun G. Chandrasekhar, Paul Goldsmith-Pinkham, Matthew O. Jackson, and Samuel Thau ENVIRONMENTAL SCIENCES A global carbon and nitrogen isotope perspective on modern and ancient human diet Michael I. Bird, Stefani A. Crabtree, Jordahna Haig, Sean Ulm, and Christopher M. Wurster PSYCHOLOGICAL AND COGNITIVE SCIENCES One-trial perceptual learning in the absence of conscious remembering and independent of the medial temporal lobe Larry R. Squire, Jennifer C. Frascino, Charlotte S. Rivera, Nadine C. Heyworth, and Biyu J. He Cognitive impairment after focal brain lesions is better predicted by damage to structural than functional network hubs Justin Reber, Kai Hwang, Mark Bowren, Joel Bruss, Pratik Mukherjee, Daniel Tranel, and Aaron D. Boes AGRICULTURAL SCIENCES Insects defend against fungal infection by employing micrornas to silence virulence-related genes Yan Wang, Chunlai Cui, Guandong Wang, Yifei Li, and Sibao Wang ANTHROPOLOGY A global carbon and nitrogen isotope perspective on modern and ancient human diet Michael I. Bird, Stefani A. Crabtree, Jordahna Haig, Sean Ulm, and Christopher M. Wurster BIOCHEMISTRY Integrative analysis reveals unique structural and functional features of the Smc5/6 complex You Yu, Shibai Li, Zheng Ser, Tanmoy Sanyal, Koyi Choi, Bingbing Wan, Huihui Kuang, Andrej Sali, Alex Kentsis, Dinshaw J. Patel, and Xiaolan Zhao Galectin-3 N-terminal tail prolines modulate cell activity and glycan-mediated oligomerization/phase separation Zihan Zhao, Xuejiao Xu, Hairong Cheng, Michelle C. Miller, Zhen He, Hongming Gu, Zhongyu Zhang, Avraham Raz, Kevin H. Mayo, Guihua Tai, and Yifa Zhou e e e e e e e e e e e e e SIK2 orchestrates actin-dependent host response upon Salmonella infection Marcel Hahn, Adriana Covarrubias-Pinto, Lina Herhaus, Shankha Satpathy, Kevin Klann, Keith B. Boyle, Christian Münch, Krishnaraj Rajalingam, Felix Randow, Chunaram Choudhary, and Ivan Dikic Cleavage of Braun s lipoprotein Lpp from the bacterial peptidoglycan by a paralog of L,D-transpeptidases, LdtF Raj Bahadur, Pavan Kumar Chodisetti, and Manjula Reddy Physical tuning of galectin-3 signaling Shaheen A. Farhadi, Renjie Liu, Matthew W. Becker, Edward A. Phelps, and Gregory A. Hudalla An interpreted atlas of biosynthetic gene clusters from 1,000 fungal genomes Matthew T. Robey, Lindsay K. Caesar, Milton T. Drott, Nancy P. Keller, and Neil L. Kelleher BIOPHYSICS AND COMPUTATIONAL BIOLOGY Hydraulic and electric control of cell spheroids Charlie Duclut, Jacques Prost, and Frank Jülicher Membrane fusion and drug delivery with carbon nanotube porins Nga T. Ho, Marc Siggel, Karen V. Camacho, Ramachandra M. Bhaskara, Jacqueline M. Hicks, Yun-Chiao Yao, Yuliang Zhang, Jürgen Köfinger, Gerhard Hummer, and Aleksandr Noy Delineating the heterogeneity of matrixdirected differentiation toward soft and stiff tissue lineages via single-cell profiling Shlomi Brielle, Danny Bavli, Alex Motzik, Yoav Kan-Tor, Xue Sun, Chen Kozulin, Batia Avni, Oren Ram, and Amnon Buxboim Structural basis for backtracking by the SARS- CoV-2 replication transcription complex Brandon Malone, James Chen, Qi Wang, Eliza Llewellyn, Young Joo Choi, Paul Dominic B. Olinares, Xinyun Cao, Carolina Hernandez, Edward T. Eng, Brian T. Chait, David E. Shaw, Robert Landick, Seth A. Darst, and Elizabeth A. Campbell Dual nature of human ACE2 glycosylation in binding to SARS-CoV-2 spike Ahmad Reza Mehdipour and Gerhard Hummer The voltage sensor is responsible for ΔpH dependence in H v 1 channels Emerson M. Carmona, Miguel Fernandez, Juan J. Alvear-Arias, Alan Neely, H. Peter Larsson, Osvaldo Alvarez, Jose Antonio Garate, Ramon Latorre, and Carlos Gonzalez Protein structure based gene expression signatures Rayees Rahman, Nicole Zatorski, Jens Hansen, Yuguang Xiong, J. G. Coen van Hasselt, Eric A. Sobie, Marc R. Birtwistle, Evren U. Azeloglu, Ravi Iyengar, and Avner Schlessinger CELL BIOLOGY Tau forms oligomeric complexes on microtubules that are distinct from tau aggregates Melina Theoni Gyparaki, Arian Arab, Elena M. Sorokina, Adriana N. Santiago-Ruiz, Christopher H. Bohrer, Jie Xiao, and Melike Lakadamyali PI(3,4)P 2 -mediated membrane tubulation promotes integrin trafficking and invasive cell migration Zhen Feng and Cheng-han Yu Contents PNAS u May 11, 2021 u vol. 118 u no. 19 u v

4 e e e The N terminus of Orai1 couples to the AKAP79 signaling complex to drive NFAT1 activation by local Ca 2+ entry Pulak Kar, Yu-Ping Lin, Rajesh Bhardwaj, Charles J. Tucker, Gary S. Bird, Matthias A. Hediger, Carina Monico, Nader Amin, and Anant B. Parekh DEVELOPMENTAL BIOLOGY Hindbrain neuropore tissue geometry determines asymmetric cell-mediated closure dynamics in mouse embryos Eirini Maniou, Michael F. Staddon, Abigail R. Marshall, Nicholas D. E. Greene, Andrew J. Copp, Shiladitya Banerjee, and Gabriel L. Galea ECOLOGY Fast and pervasive transcriptomic resilience and acclimation of extremely heat-tolerant coral holobionts from the northern Red Sea Romain Savary, Daniel J. Barshis, Christian R. Voolstra, Anny Cárdenas, Nicolas R. Evensen, Guilhem Banc- Prandi, Maoz Fine, and Anders Meibom EVOLUTION Phylogenomic conflict coincides with rapid morphological innovation Caroline Parins-Fukuchi, Gregory W. Stull, and Stephen A. Smith A simple expression for the strength of selection on recombination generated by interference among mutations Denis Roze The genomes of ancient date palms germinated from 2,000 y old seeds Muriel Gros-Balthazard, Jonathan M. Flowers, Khaled M. Hazzouri, Sylvie Ferrand, Frédérique Aberlenc, Sarah Sallon, and Michael D. Purugganan e e e MEDICAL SCIENCES Immune evasion in HPV head and neck precancer cancer transition is driven by an aneuploid switch involving chromosome 9p loss William N. William Jr, Xin Zhao, Joy J. Bianchi, Heather Y. Lin, Pan Cheng, J. Jack Lee, Hannah Carter, Ludmil B. Alexandrov, Jim P. Abraham, David B. Spetzler, Steven M. Dubinett, Don W. Cleveland, Webster Cavenee, Teresa Davoli, and Scott M. Lippman Hypoxia-inducible factor-dependent ADAM12 expression mediates breast cancer invasion and metastasis Ru Wang, Ines Godet, Yongkang Yang, Shaima Salman, Haiquan Lu, Yajing Lyu, Qiaozhu Zuo, Yufeng Wang, Yayun Zhu, Chelsey Chen, Jianjun He, Daniele M. Gilkes, and Gregg L. Semenza Biallelic splicing variants in the nucleolar 60S assembly factor RBM28 cause the ribosomopathy ANE syndrome Carson J. Bryant, Cláudia F. Lorea, Hiram Larangeira de Almeida Jr, Letícia Weinert, Leonardo Vedolin, Filippo Pinto e Vairo, and Susan J. Baserga Dysregulation of Amphiregulin stimulates the pathogenesis of cystic lymphangioma Naofumi Yoshida, Seiji Yamamoto, Takeru Hamashima, Noriko Okuno, Naruho Okita, Shinjiro Horikawa, Masao Hayashi, Thanh Chung Dang, Quang Linh Nguyen, Koichi Nishiyama, Teruhiko Makino, Yoko Ishii, Kei Tomihara, Tadamichi Shimizu, Masabumi Shibuya, Makoto Noguchi, and Masakiyo Sasahara e e e e e e e IMMUNOLOGY AND INFLAMMATION The aryl hydrocarbon receptor suppresses immunity to oral squamous cell carcinoma through immune checkpoint regulation Jessica E. Kenison, Zhongyan Wang, Kangkang Yang, Megan Snyder, Francisco J. Quintana, and David H. Sherr Toll9 from Bombyx mori functions as a pattern recognition receptor that shares features with Toll-like receptor 4 from mammals Ruonan Zhang, Xiaofeng Li, Jie Zhang, Yanjun Li, Yuan Wang, Yuhang Song, Feifei Ren, Huiyu Yi, Xiaojuan Deng, Yangjin Zhong, Yang Cao, Michael R. Strand, Xiao-Qiang Yu, and Wanying Yang Intranasal vaccination with influenza HA/GO-PEI nanoparticles provides immune protection against homoand heterologous strains Chunhong Dong, Ye Wang, Gilbert X. Gonzalez, Yao Ma, Yufeng Song, Shelly Wang, Sang-Moo Kang, Richard W. Compans, and Bao-Zhong Wang Pharmacological modulation of T cell immunity results in long-term remission of autoimmune arthritis Yi-Shu Huang, Wen-Yi Tseng, Felix I. L. Clanchy, Louise M. Topping, Joy Ogbechi, Kay McNamee, Dany Perocheau, Nien-Yi Chiang, Peter Ericsson, Anette Sundstedt, Zhong-Tian Xue, Leif G. Salford, Hans-Olov Sjögren, Trevor W. Stone, Hsi-Hsien Lin, Shue-Fen Luo, and Richard O. Williams e e e e e MICROBIOLOGY Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice Phillip Pymm, Amy Adair, Li-Jin Chan, James P. Cooney, Francesca L. Mordant, Cody C. Allison, Ester Lopez, Ebene R. Haycroft, Matthew T. O Neill, Li Lynn Tan, Melanie H. Dietrich, Damien Drew, Marcel Doerflinger, Michael A. Dengler, Nichollas E. Scott, Adam K. Wheatley, Nicholas A. Gherardin, Hariprasad Venugopal, Deborah Cromer, Miles P. Davenport, Raelene Pickering, Dale I. Godfrey, Damian F. J. Purcell, Stephen J. Kent, Amy W. Chung, Kanta Subbarao, Marc Pellegrini, Alisa Glukhova, and Wai-Hong Tham ICAM-1 induced rearrangements of capsid and genome prime rhinovirus 14 for activation and uncoating Dominik Hrebík, Tibor Füzik, Mária Gondová, Lenka Smerdová, Athanassios Adamopoulos, Ondrej Sedo, Zbynek Zdráhal, and Pavel Plevka NEUROSCIENCE One-trial perceptual learning in the absence of conscious remembering and independent of the medial temporal lobe Larry R. Squire, Jennifer C. Frascino, Charlotte S. Rivera, Nadine C. Heyworth, and Biyu J. He Cognitive impairment after focal brain lesions is better predicted by damage to structural than functional network hubs Justin Reber, Kai Hwang, Mark Bowren, Joel Bruss, Pratik Mukherjee, Daniel Tranel, and Aaron D. Boes vi u Contents

5 e e e e e Impaired inhibitory GABAergic synaptic transmission and transcription studied in single neurons by Patch-seq in Huntington s disease Foteini Paraskevopoulou, Poorya Parvizi, Gökçe Senger, Nurcan Tuncbag, Christian Rosenmund, and Ferah Yildirim CAG RNAs induce DNA damage and apoptosis by silencing NUDT16 expression in polyglutamine degeneration Shaohong Peng, Pei Guo, Xiao Lin, Ying An, Kong Hung Sze, Matthew Ho Yan Lau, Zhefan Stephen Chen, Qianwen Wang, Wen Li, Jacquelyne Ka-Li Sun, Sum Yi Ma, Ting-Fung Chan, Kwok-Fai Lau, Jacky Chi Ki Ngo, Kin Ming Kwan, Chun-Ho Wong, Sik Lok Lam, Steven C. Zimmerman, Tiziano Tuccinardi, Zhong Zuo, Ho Yu Au-Yeung, Hei-Man Chow, and Ho Yin Edwin Chan Echolocating bats rely on an innate speed-ofsound reference Eran Amichai and Yossi Yovel Manipulating placebo analgesia and nocebo hyperalgesia by changing brain excitability Yiheng Tu, Georgia Wilson, Joan Camprodon, Darin D. Dougherty, Mark Vangel, Fabrizio Benedetti, Ted J. Kaptchuk, Randy L. Gollub, and Jian Kong PHARMACOLOGY Reversed-engineered human alveolar lung-on-a-chip model Di Huang, Tingting Liu, Junlong Liao, Sushila Maharjan, Xin Xie, Montserrat Pérez, Ingrid Anaya, Shiwei Wang, Alan Tirado Mayer, Zhixin Kang, Weijia Kong, Valerio Luca Mainardi, Carlos Ezio Garciamendez-Mijares, Germán García Martínez, Matteo Moretti, Weijia Zhang, Zhongze Gu, Amir M. Ghaemmaghami, and Yu Shrike Zhang e e e e e PLANT BIOLOGY Conditional sanctioning in a legume Rhizobium mutualism Annet Westhoek, Laura J. Clark, Michael Culbert, Neil Dalchau, Megan Griffiths, Beatriz Jorrin, Ramakrishnan Karunakaran, Raphael Ledermann, Andrzej Tkacz, Isabel Webb, Euan K. James, Philip S. Poole, and Lindsay A. Turnbull Low nitrogen conditions accelerate flowering by modulating the phosphorylation state of FLOWERING BHLH 4 in Arabidopsis Miho Sanagi, Shoki Aoyama, Akio Kubo, Yu Lu, Yasutake Sato, Shogo Ito, Mitsutomo Abe, Nobutaka Mitsuda, Masaru Ohme-Takagi, Takatoshi Kiba, Hirofumi Nakagami, Filip Rolland, Junji Yamaguchi, Takato Imaizumi, and Takeo Sato Phosphorylation-dependent subfunctionalization of the calcium-dependent protein kinase CPK28 Melissa Bredow, Kyle W. Bender, Alexandra Johnson Dingee, Danalyn R. Holmes, Alysha Thomson, Danielle Ciren, Cailun A. S. Tanney, Katherine E. Dunning, Marco Trujillo, Steven C. Huber, and Jacqueline Monaghan SYSTEMS BIOLOGY Identification of EMT signaling cross-talk and gene regulatory networks by single-cell RNA sequencing Abhijeet P. Deshmukh, Suhas V. Vasaikar, Katarzyna Tomczak, Shubham Tripathi, Petra den Hollander, Emre Arslan, Priyanka Chakraborty, Rama Soundararajan, Mohit Kumar Jolly, Kunal Rai, Herbert Levine, and Sendurai A. Mani Network medicine framework for identifying drug-repurposing opportunities for COVID-19 Deisy Morselli Gysi, Ítalo do Valle, Marinka Zitnik, Asher Ameli, Xiao Gan, Onur Varol, Susan Dina Ghiassian, J. J. Patten, Robert A. Davey, Joseph Loscalzo, and Albert-László Barabási Contents PNAS u May 11, 2021 u vol. 118 u no. 19 u vii

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