PNAS Table of Contents for December 26, 2018; Vol. 115, No. 52

[PNAS] [See the PNAS Teaching Resources Portal](/cgi/adclick/?ad=53400&adclick=true&url=http%3A%2F%2Fteachingresources.pnas.org%2F)   [December 26, 2018; Vol. 115, No. 52]( ) This Week in PNAS [In This Issue]( --------------------------------------------------------------- Reviewer Acknowledgment (Online Only) [Acknowledgment of Reviewers, 2018]( --------------------------------------------------------------- Letters (Online Only) [Unraveling the blue paradox: Incomplete analysis yields incorrect conclusions about Phoenix Islands Protected Area closure]( Quentin Hanich, Randi Rotjan, Transform Aqorau, Megan Bailey, Brooke Campbell, Noella Gray, Rebecca Gruby, John Hampton, Yoshitaka Ota, Hannah Parris, Chris Reid, U. Rashid Sumaila, and Wilf Swartz [Reply to Hanich et al.: Alternate explanations for the blue paradox do not withstand statistical scrutiny]( Grant R. McDermott, Kyle C. Meng, Gavin G. McDonald, and Christopher J. Costello [Role of HHV-6 subtypes in accelerating EAE progression]( Hamid Zahednasab, Hossein Keyvani, Sajad Karampour, and Mohammad Hossein Harirchian [Reply to Zahednasab et al.: HHV-6 and marmoset EAE]( Emily C. Leibovitch and Steven Jacobson --------------------------------------------------------------- Science and Culture [Science and Culture: Journal entries, maps, and photos help ecologists reconstruct ecosystems of the past]( Carolyn Beans How science intersects with culture. --------------------------------------------------------------- QnAs [QnAs with David Baker]( Prashant Nair --------------------------------------------------------------- Commentaries [Moving beyond forensic monitoring to understand and manage impacts of hydraulic fracturing for oil and gas development]( David A. Dzombak [Rethinking pneumonia: A paradigm shift with practical utility]( Rishi Chanderraj and Robert P. Dickson [Regulating behavior with the flip of a translational switch]( Efraín Ceh-Pavia and Carrie L. Partch [Subterranean clues to the future of our planetary magnetic shield]( John A. Tarduno --------------------------------------------------------------- PNAS Plus Significance Statements [PNAS Plus Significance Statements]( Brief statements written by the authors about the significance of their papers. --------------------------------------------------------------- Physical Sciences Applied Physical Sciences [Electrostatic effects, band distortions, and superconductivity in twisted graphene bilayers]( Francisco Guinea and Niels R. Walet Biophysics and Computational Biology [Exploiting correlated molecular-dynamics networks to counteract enzyme activity–stability trade-off]( Haoran Yu and Paul A. Dalby [Integral feedback control is at the core of task allocation and resilience of insect societies]( Thomas Schmickl and Istvan Karsai [Cofactors are essential constituents of stable and seeding-active tau fibrils]( Yann Fichou, Yanxian Lin, Jennifer N. Rauch, Michael Vigers, Zhikai Zeng, Madhur Srivastava, Timothy J. Keller, Jack H. Freed, Kenneth S. Kosik, and Songi Han [Combined molecular dynamics and neural network method for predicting protein antifreeze activity]( Daniel J. Kozuch, Frank H. Stillinger, and Pablo G. Debenedetti Chemistry [Yeast require redox switching in DNA primase]( Elizabeth O’Brien, Lauren E. Salay, Esther A. Epum, Katherine L. Friedman, Walter J. Chazin, and Jacqueline K. Barton Earth, Atmospheric, and Planetary Sciences [Climate network percolation reveals the expansion and weakening of the tropical component under global warming]( Jingfang Fan, Jun Meng, Yosef Ashkenazy, Shlomo Havlin, and Hans Joachim Schellnhuber [Trends and patterns in the contributions to cumulative radiative forcing from different regions of the world]( D. M. Murphy and A. R. Ravishankara [Speleothem record of geomagnetic South Atlantic Anomaly recurrence]( Ricardo I. F. Trindade, Plinio Jaqueto, Filipe Terra-Nova, Daniele Brandt, Gelvam A. Hartmann, Joshua M. Feinberg, Becky E. Strauss, Valdir F. Novello, Francisco W. Cruz, Ivo Karmann, Hai Cheng, and R. Lawrence Edwards [Pliocene and Eocene provide best analogs for near-future climates]( K. D. Burke, J. W. Williams, M. A. Chandler, A. M. Haywood, D. J. Lunt, and B. L. Otto-Bliesner [Pervasive iron limitation at subsurface chlorophyll maxima of the California Current]( Shane L. Hogle, Christopher L. Dupont, Brian M. Hopkinson, Andrew L. King, Kristen N. Buck, Kelly L. Roe, Rhona K. Stuart, Andrew E. Allen, Elizabeth L. Mann, Zackary I. Johnson, and Katherine A. Barbeau Engineering [Effective design principles for leakless strand displacement systems]( Boya Wang, Chris Thachuk, Andrew D. Ellington, Erik Winfree, and David Soloveichik [Quantifying single-cell secretion in real time using resonant hyperspectral imaging]( José Juan-Colás, Ian S. Hitchcock, Mark Coles, Steven Johnson, and Thomas F. Krauss [Continuous-range tunable multilayer frequency-selective surfaces using origami and inkjet printing]( Syed Abdullah Nauroze, Larissa S. Novelino, Manos M. Tentzeris, and Glaucio H. Paulino Environmental Sciences [Termite mounds mitigate half of termite methane emissions]( Philipp A. Nauer, Lindsay B. Hutley, and Stefan K. Arndt Physics [Approaching the adiabatic timescale with machine learning]( Bryce M. Henson, Dong K. Shin, Kieran F. Thomas, Jacob A. Ross, Michael R. Hush, Sean S. Hodgman, and Andrew G. Truscott --------------------------------------------------------------- Social Sciences Economic Sciences [Robust forecast aggregation]( Itai Arieli, Yakov Babichenko, and Rann Smorodinsky Psychological and Cognitive Sciences [Right temporal alpha oscillations as a neural mechanism for inhibiting obvious associations]( Caroline Di Bernardi Luft, Ioanna Zioga, Nicholas M. Thompson, Michael J. Banissy, and Joydeep Bhattacharya [High-capacity preconscious processing in concurrent groupings of colored dots]( Peng Sun, Charles Chubb, Charles E. Wright, and George Sperling [Dominance rank-associated gene expression is widespread, sex-specific, and a precursor to high social status in wild male baboons]( Amanda J. Lea, Mercy Y. Akinyi, Ruth Nyakundi, Peter Mareri, Fred Nyundo, Thomas Kariuki, Susan C. Alberts, Elizabeth A. Archie, and Jenny Tung [People use less information than they think to make up their minds]( Nadav Klein and Ed O’Brien Social Sciences [Persistence of false paradigms in low-power sciences]( George A. Akerlof and Pascal Michaillat Sustainability Science [Resource extraction and infrastructure threaten forest cover and community rights]( Anthony J. Bebbington, Denise Humphreys Bebbington, Laura Aileen Sauls, John Rogan, Sumali Agrawal, César Gamboa, Aviva Imhof, Kimberly Johnson, Herman Rosa, Antoinette Royo, Tessa Toumbourou, and Ricardo Verdum --------------------------------------------------------------- Biological Sciences Anthropology [Dominance rank-associated gene expression is widespread, sex-specific, and a precursor to high social status in wild male baboons]( Amanda J. Lea, Mercy Y. Akinyi, Ruth Nyakundi, Peter Mareri, Fred Nyundo, Thomas Kariuki, Susan C. Alberts, Elizabeth A. Archie, and Jenny Tung Biochemistry [Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel]( Haidai Hu, Kenichi Ataka, Anaïs Menny, Zaineb Fourati, Ludovic Sauguet, Pierre-Jean Corringer, Patrice Koehl, Joachim Heberle, and Marc Delarue [Yeast require redox switching in DNA primase]( Elizabeth O’Brien, Lauren E. Salay, Esther A. Epum, Katherine L. Friedman, Walter J. Chazin, and Jacqueline K. Barton [Cofactors are essential constituents of stable and seeding-active tau fibrils]( Yann Fichou, Yanxian Lin, Jennifer N. Rauch, Michael Vigers, Zhikai Zeng, Madhur Srivastava, Timothy J. Keller, Jack H. Freed, Kenneth S. Kosik, and Songi Han [Modulation of HIF-2α PAS-B domain contributes to physiological responses]( Zhihui Feng, Xuan Zou, Yaomin Chen, Hanzhi Wang, Yingli Duan, and Richard K. Bruick [Ubiquitin-dependent switch during assembly of the proteasomal ATPases mediated by Not4 ubiquitin ligase]( Xinyi Fu, Vladyslava Sokolova, Kristofor J. Webb, William Old, and Soyeon Park Biophysics and Computational Biology [Effective design principles for leakless strand displacement systems]( Boya Wang, Chris Thachuk, Andrew D. Ellington, Erik Winfree, and David Soloveichik [Exploiting correlated molecular-dynamics networks to counteract enzyme activity–stability trade-off]( Haoran Yu and Paul A. Dalby [Eigenvector centrality for characterization of protein allosteric pathways]( Christian F. A. Negre, Uriel N. Morzan, Heidi P. Hendrickson, Rhitankar Pal, George P. Lisi, J. Patrick Loria, Ivan Rivalta, Junming Ho, and Victor S. Batista [Molecular basis for the acid-initiated uncoating of human enterovirus D68]( Yue Liu, Ju Sheng, Arno L. W. van Vliet, Geeta Buda, Frank J. M. van Kuppeveld, and Michael G. Rossmann [Quantifying single-cell secretion in real time using resonant hyperspectral imaging]( José Juan-Colás, Ian S. Hitchcock, Mark Coles, Steven Johnson, and Thomas F. Krauss [Combined molecular dynamics and neural network method for predicting protein antifreeze activity]( Daniel J. Kozuch, Frank H. Stillinger, and Pablo G. Debenedetti [MicroED structures of HIV-1 Gag CTD-SP1 reveal binding interactions with the maturation inhibitor bevirimat]( Michael D. Purdy, Dan Shi, Jakub Chrustowicz, Johan Hattne, Tamir Gonen, and Mark Yeager [Crystal structure of the human NK1 tachykinin receptor]( Jie Yin, Karen Chapman, Lindsay D. Clark, Zhenhua Shao, Dominika Borek, Qingping Xu, Junmei Wang, and Daniel M. Rosenbaum [Cryo-EM structure of the native butyrylcholinesterase tetramer reveals a dimer of dimers stabilized by a superhelical assembly]( Miguel Ricardo Leung, Laura S. van Bezouwen, Lawrence M. Schopfer, Joel L. Sussman, Israel Silman, Oksana Lockridge, and Tzviya Zeev-Ben-Mordehai [Experimental accuracy in protein structure refinement via molecular dynamics simulations]( Lim Heo and Michael Feig Cell Biology [Structural–functional interactions of NS1-BP protein with the splicing and mRNA export machineries for viral and host gene expression]( Ke Zhang, Guijun Shang, Abhilash Padavannil, Juan Wang, Ramanavelan Sakthivel, Xiang Chen, Min Kim, Matthew G. Thompson, Adolfo García-Sastre, Kristen W. Lynch, Zhijian J. Chen, Yuh Min Chook, and Beatriz M. A. Fontoura [SREBP-1a–stimulated lipid synthesis is required for macrophage phagocytosis downstream of TLR4-directed mTORC1]( Jae-Ho Lee, Peter Phelan, Minsang Shin, Byung-Chul Oh, Xianlin Han, Seung-Soon Im, and Timothy F. Osborne [Mitotic antipairing of homologous and sex chromosomes via spatial restriction of two haploid sets]( Lisa L. Hua and Takashi Mikawa [Profiling proliferative cells and their progeny in damaged murine hearts]( Kai Kretzschmar, Yorick Post, Marie Bannier-Hélaouët, Andrea Mattiotti, Jarno Drost, Onur Basak, Vivian S. W. Li, Maaike van den Born, Quinn D. Gunst, Danielle Versteeg, Lieneke Kooijman, Stefan van der Elst, Johan H. van Es, Eva van Rooij, Maurice J. B. van den Hoff, and Hans Clevers [TANGO1 and SEC12 are copackaged with procollagen I to facilitate the generation of large COPII carriers]( Lin Yuan, Samuel J. Kenny, Juliet Hemmati, Ke Xu, and Randy Schekman [PCNA-mediated stabilization of E3 ligase RFWD3 at the replication fork is essential for DNA replication]( Yo-Chuen Lin, Yating Wang, Rosaline Hsu, Sumanprava Giri, Susan Wopat, Mariam K. Arif, Arindam Chakraborty, Kannanganattu V. Prasanth, and Supriya G. Prasanth Developmental Biology [Steroidogenic differentiation and PKA signaling are programmed by histone methyltransferase EZH2 in the adrenal cortex]( Mickael Mathieu, Coralie Drelon, Stéphanie Rodriguez, Houda Tabbal, Amandine Septier, Christelle Damon-Soubeyrand, Typhanie Dumontet, Annabel Berthon, Isabelle Sahut-Barnola, Cyril Djari, Marie Batisse-Lignier, Jean-Christophe Pointud, Damien Richard, Gwenneg Kerdivel, Marie-Ange Calméjane, Valentina Boeva, Igor Tauveron, Anne-Marie Lefrançois-Martinez, Antoine Martinez, and Pierre Val Ecology [Pliocene and Eocene provide best analogs for near-future climates]( K. D. Burke, J. W. Williams, M. A. Chandler, A. M. Haywood, D. J. Lunt, and B. L. Otto-Bliesner [Bioenergy cropland expansion may offset positive effects of climate change mitigation for global vertebrate diversity]( Christian Hof, Alke Voskamp, Matthias F. Biber, Katrin Böhning-Gaese, Eva Katharina Engelhardt, Aidin Niamir, Stephen G. Willis, and Thomas Hickler Environmental Sciences [Different iron storage strategies among bloom-forming diatoms]( Robert H. Lampe, Elizabeth L. Mann, Natalie R. Cohen, Claire P. Till, Kimberlee Thamatrakoln, Mark A. Brzezinski, Kenneth W. Bruland, Benjamin S. Twining, and Adrian Marchetti [Pervasive iron limitation at subsurface chlorophyll maxima of the California Current]( Shane L. Hogle, Christopher L. Dupont, Brian M. Hopkinson, Andrew L. King, Kristen N. Buck, Kelly L. Roe, Rhona K. Stuart, Andrew E. Allen, Elizabeth L. Mann, Zackary I. Johnson, and Katherine A. Barbeau [Termite mounds mitigate half of termite methane emissions]( Philipp A. Nauer, Lindsay B. Hutley, and Stefan K. Arndt Evolution [New insights into the evolution of wheat avenin-like proteins in wild emmer wheat (Triticum dicoccoides)]( Yujuan Zhang, Xin Hu, Shahidul Islam, Maoyun She, Yanchun Peng, Zitong Yu, Steve Wylie, Angela Juhasz, Mirza Dowla, Rongchang Yang, Jingjuan Zhang, Xiaolong Wang, Bernard Dell, Xueyan Chen, Eviatar Nevo, Dongfa Sun, and Wujun Ma [Inosine, but none of the 8-oxo-purines, is a plausible component of a primordial version of RNA]( Seohyun Chris Kim, Derek K. O’Flaherty, Lijun Zhou, Victor S. Lelyveld, and Jack W. Szostak [Rapid evolution of a skin-lightening allele in southern African KhoeSan]( Meng Lin, Rebecca L. Siford, Alicia R. Martin, Shigeki Nakagome, Marlo Möller, Eileen G. Hoal, Carlos D. Bustamante, Christopher R. Gignoux, and Brenna M. Henn [Dietary versatility of Early Pleistocene hominins]( Tina Lüdecke, Ottmar Kullmer, Ulrike Wacker, Oliver Sandrock, Jens Fiebig, Friedemann Schrenk, and Andreas Mulch Genetics [Apurinic endonuclease-1 preserves neural genome integrity to maintain homeostasis and thermoregulation and prevent brain tumors]( Lavinia C. Dumitrache, Mikio Shimada, Susanna M. Downing, Young Don Kwak, Yang Li, Jennifer L. Illuzzi, Helen R. Russell, David M. Wilson III, and Peter J. McKinnon [RNA-mediated gene fusion in mammalian cells]( Sachin Kumar Gupta, Liming Luo, and Laising Yen [Nuclear receptor HNF4A transrepresses CLOCK:BMAL1 and modulates tissue-specific circadian networks]( Meng Qu, Tomas Duffy, Tsuyoshi Hirota, and Steve A. Kay [Sex-specific phenotypes of histone H4 point mutants establish dosage compensation as the critical function of H4K16 acetylation in Drosophila]( Ömer Copur, Andrey Gorchakov, Katja Finkl, Mitzi I. Kuroda, and Jürg Müller [Role of gene body methylation in acclimatization and adaptation in a basal metazoan]( Groves Dixon, Yi Liao, Line K. Bay, and Mikhail V. Matz Immunology and Inflammation [Protein kinase p38α signaling in dendritic cells regulates colon inflammation and tumorigenesis]( Tingting Zheng, Baohua Zhang, Ce Chen, Jingyu Ma, Deyun Meng, Jian Huang, Ran Hu, Xinguang Liu, Kinya Otsu, Andrew C. Liu, Huabin Li, Zhinan Yin, and Gonghua Huang [Autoimmunity to hypocretin and molecular mimicry to flu in type 1 narcolepsy]( Guo Luo, Aditya Ambati, Ling Lin, Mélodie Bonvalet, Markku Partinen, Xuhuai Ji, Holden Terry Maecker, and Emmanuel Jean-Marie Mignot [Defective respiration and one-carbon metabolism contribute to impaired naïve T cell activation in aged mice]( Noga Ron-Harel, Giulia Notarangelo, Jonathan M. Ghergurovich, Joao A. Paulo, Peter T. Sage, Daniel Santos, F. Kyle Satterstrom, Steven P. Gygi, Joshua D. Rabinowitz, Arlene H. Sharpe, and Marcia C. Haigis Medical Sciences [Nanotechnology-mediated crossing of two impermeable membranes to modulate the stars of the neurovascular unit for neuroprotection]( Bapurao Surnar, Uttara Basu, Bhabatosh Banik, Anis Ahmad, Brian Marples, Nagesh Kolishetti, and Shanta Dhar [DeltaNp63-dependent super enhancers define molecular identity in pancreatic cancer by an interconnected transcription factor network]( Feda H. Hamdan and Steven A. Johnsen [Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults]( Charles Langelier, Katrina L. Kalantar, Farzad Moazed, Michael R. Wilson, Emily D. Crawford, Thomas Deiss, Annika Belzer, Samaneh Bolourchi, Saharai Caldera, Monica Fung, Alejandra Jauregui, Katherine Malcolm, Amy Lyden, Lillian Khan, Kathryn Vessel, Jenai Quan, Matt Zinter, Charles Y. Chiu, Eric D. Chow, Jenny Wilson, Steve Miller, Michael A. Matthay, Katherine S. Pollard, Stephanie Christenson, Carolyn S. Calfee, and Joseph L. DeRisi [Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue]( Fabio Zanini, Makeda L. Robinson, Derek Croote, Malaya Kumar Sahoo, Ana Maria Sanz, Eliana Ortiz-Lasso, Ludwig Luis Albornoz, Fernando Rosso, Jose G. Montoya, Leslie Goo, Benjamin A. Pinsky, Stephen R. Quake, and Shirit Einav [Improving vaccines against Streptococcus pneumoniae using synthetic glycans]( Paulina Kaplonek, Naeem Khan, Katrin Reppe, Benjamin Schumann, Madhu Emmadi, Marilda P. Lisboa, Fei-Fei Xu, Adam D. J. Calow, Sharavathi G. Parameswarappa, Martin Witzenrath, Claney L. Pereira, and Peter H. Seeberger Microbiology [Human cytomegalovirus US21 protein is a viroporin that modulates calcium homeostasis and protects cells against apoptosis]( Anna Luganini, Giovanna Di Nardo, Luca Munaron, Gianfranco Gilardi, Alessandra Fiorio Pla, and Giorgio Gribaudo [Phototaxis in a wild isolate of the cyanobacterium Synechococcus elongatus]( Yiling Yang, Vinson Lam, Marie Adomako, Ryan Simkovsky, Annik Jakob, Nathan C. Rockwell, Susan E. Cohen, Arnaud Taton, Jingtong Wang, J. Clark Lagarias, Annegret Wilde, David R. Nobles, Jerry J. Brand, and Susan S. Golden [HflXr, a homolog of a ribosome-splitting factor, mediates antibiotic resistance]( Mélodie Duval, Daniel Dar, Filipe Carvalho, Eduardo P. C. Rocha, Rotem Sorek, and Pascale Cossart [Baseplate variability of Vibrio cholerae chemoreceptor arrays]( Wen Yang, Alejandra Alvarado, Timo Glatter, Simon Ringgaard, and Ariane Briegel [Symbiotic unicellular cyanobacteria fix nitrogen in the Arctic Ocean]( Katie Harding, Kendra A. Turk-Kubo, Rachel E. Sipler, Matthew M. Mills, Deborah A. Bronk, and Jonathan P. Zehr Neuroscience [Right temporal alpha oscillations as a neural mechanism for inhibiting obvious associations]( Caroline Di Bernardi Luft, Ioanna Zioga, Nicholas M. Thompson, Michael J. Banissy, and Joydeep Bhattacharya [Translational switching of Cry1 protein expression confers reversible control of circadian behavior in arrhythmic Cry-deficient mice]( Elizabeth S. Maywood, Thomas S. Elliott, Andrew P. Patton, Toke P. Krogager, Johanna E. Chesham, Russell J. Ernst, Václav Beránek, Marco Brancaccio, Jason W. Chin, and Michael H. Hastings [Ventral striatum’s role in learning from gains and losses]( Craig A. Taswell, Vincent D. Costa, Elisabeth A. Murray, and Bruno B. Averbeck [MTSS1/Src family kinase dysregulation underlies multiple inherited ataxias]( Alexander S. Brown, Pratap Meera, Banu Altindag, Ravi Chopra, Emma M. Perkins, Sharan Paul, Daniel R. Scoles, Eric Tarapore, Jessica Magri, Haoran Huang, Mandy Jackson, Vikram G. Shakkottai, Thomas S. Otis, Stefan M. Pulst, Scott X. Atwood, and Anthony E. Oro [Epigenetic regulator UHRF1 inactivates REST and growth suppressor gene expression via DNA methylation to promote axon regeneration]( Young Mi Oh, Marcus Mahar, Eric E. Ewan, Kathleen M. Leahy, Guoyan Zhao, and Valeria Cavalli [Spatiotemporal activation of the C/EBPβ/δ-secretase axis regulates the pathogenesis of Alzheimer’s disease]( Hualong Wang, Xia Liu, Shengdi Chen, and Keqiang Ye [Multilayer network switching rate predicts brain performance]( Mangor Pedersen, Andrew Zalesky, Amir Omidvarnia, and Graeme D. Jackson Physiology [Transgenerational hypocortisolism and behavioral disruption are induced by the antidepressant fluoxetine in male zebrafish Danio rerio]( Marilyn N. Vera-Chang, Antony D. St-Jacques, Rémi Gagné, Chris J. Martyniuk, Carole L. Yauk, Thomas W. Moon, and Vance L. Trudeau Plant Biology [Fluctuating selection on migrant adaptive sodium transporter alleles in coastal Arabidopsis thaliana]( Silvia Busoms, Pirita Paajanen, Sarah Marburger, Sian Bray, Xin-Yuan Huang, Charlotte Poschenrieder, Levi Yant, and David E. Salt [SOG1 activator and MYB3R repressors regulate a complex DNA damage network in Arabidopsis]( Clara Bourbousse, Neeraja Vegesna, and Julie A. Law --------------------------------------------------------------- Corrections (Online Only) [Correction for Kritee et al., Reply to Yan and Akiyama: Nitrous oxide emissions from rice and their mitigation potential depend on the nature of intermittent flooding]( [Correction for Mann, Inner Workings: Hunting for microbial life throughout the solar system]( [Correction Rivas-Carrillo et al., Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations]( [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 © 2018 by the National Academy of Sciences