Fwd: PNAS Table of Contents for 20 January 2015; Vol. 112, No. 3

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Proceedings of the National Academy of Sciences 20 January 2015; Vol. 112, No. 3 This Week in PNAS In This Issue PNAS 100th Anniversary Article Perspective Identifying strains that contribute to complex diseases through the study of microbial inheritance Jeremiah J. Faith, Jean-Frédéric Colombel, and Jeffrey I. Gordon Letters (Online Only) Mammalian extinction in ancient Egypt, similarities with the southern Levant Guy Bar-Oz, Ella Tsahar, Ido Izhaki, and Simcha Lev-Yadun Ancient Egypt's fluctuating fauna: Ecological events or cultural constructs? Linda Evans Reply to Evans and Bar-Oz et al.: Recovering ecological pattern and process in Ancient Egypt Justin D. Yeakel, Mathias M. Pires, Lars Rudolf, Nathaniel J. Dominy, Paul L. Koch, Paulo R. Guimarães Jr., and Thilo Gross Inner Workings Inner Workings: Malnutrition, gutted  Elie Dolgin An over-the-shoulder look at scientists at work. Commentaries Impact synthesis of the RNA bases Andro C. Rios Geography and personality: Why do different neighborhoods have different vibes? Shigehiro Oishi Reconstructing pathogen evolution from the ruins Sean-Paul Nuccio and Andreas J. Bäumler PNAS Plus Significance Statements PNAS Plus Significance Statements Brief statements written by the authors about the significance of their papers. Feature Article High-energy chemistry of formamide: A unified mechanism of nucleobase formation  Martin Ferus, David Nesvorný, Jiří Šponer, Petr Kubelík, Regina Michalčíková, Violetta Shestivská, Judit E. Šponer, and Svatopluk Civiš Physical Sciences Applied Mathematics Finding long chains in kidney exchange using the traveling salesman problem Ross Anderson, Itai Ashlagi, David Gamarnik, and Alvin E. Roth Applied Physical Sciences Percolation transition in dynamical traffic network with evolving critical bottlenecks Daqing Li, Bowen Fu, Yunpeng Wang, Guangquan Lu, Yehiel Berezin, H. Eugene Stanley, and Shlomo Havlin Fermi surface reconstruction and multiple quantum phase transitions in the antiferromagnet CeRhIn5 Lin Jiao, Ye Chen, Yoshimitsu Kohama, David Graf, E. D. Bauer, John Singleton, Jian-Xin Zhu, Zongfa Weng, Guiming Pang, Tian Shang, Jinglei Zhang, Han-Oh Lee, Tuson Park, Marcelo Jaime, J. D. Thompson, Frank Steglich, Qimiao Si, and H. Q. Yuan Astronomy Crowd science user contribution patterns and their implications Henry Sauermann and Chiara Franzoni Chemistry Tissue-based metabolic labeling of polysialic acids in living primary hippocampal neurons Kyungtae Kang, Sunghoon Joo, Ji Yu Choi, Sujeong Geum, Seok-Pyo Hong, Seung-Yeul Lee, Yong Ho Kim, Seong-Min Kim, Myung-Han Yoon, Yoonkey Nam, Kyung-Bok Lee, Hee-Yoon Lee, and Insung S. Choi High-energy chemistry of formamide: A unified mechanism of nucleobase formation  Martin Ferus, David Nesvorný, Jiří Šponer, Petr Kubelík, Regina Michalčíková, Violetta Shestivská, Judit E. Šponer, and Svatopluk Civiš Semilocal density functional obeying a strongly tightened bound for exchange Jianwei Sun, John P. Perdew, and Adrienn Ruzsinszky Multiaddressable molecular rectangles with reversible host–guest interactions: Modulation of pH-controlled guest release and capture Alan Kwun-Wa Chan, Wai Han Lam, Yuya Tanaka, Keith Man-Chung Wong, and Vivian Wing-Wah Yam Imaging local electric fields produced upon synchrotron X-ray exposure Christopher M. Dettmar, Justin A. Newman, Scott J. Toth, Michael Becker, Robert F. Fischetti, and Garth J. Simpson Earth, Atmospheric, and Planetary Sciences Groundwater sapping as the cause of irreversible desertification of Hunshandake Sandy Lands, Inner Mongolia, northern China  Xiaoping Yang, Louis A. Scuderi, Xulong Wang, Louis J. Scuderi, Deguo Zhang, Hongwei Li, Steven Forman, Qinghai Xu, Ruichang Wang, Weiwen Huang, and Shixia Yang Atmospheric record in the Hadean Eon from multiple sulfur isotope measurements in Nuvvuagittuq Greenstone Belt (Nunavik, Quebec) Emilie Thomassot, Jonathan O'Neil, Don Francis, Pierre Cartigny, and Boswell A. Wing Engineering Programmable motion of DNA origami mechanisms Alexander E. Marras, Lifeng Zhou, Hai-Jun Su, and Carlos E. Castro Physics Theory of point contact spectroscopy in correlated materials  Wei-Cheng Lee, Wan Kyu Park, Hamood Z. Arham, Laura H. Greene, and Philip Phillips Statistics Inference for dynamic and latent variable models via iterated, perturbed Bayes maps Edward L. Ionides, Dao Nguyen, Yves Atchadé, Stilian Stoev, and Aaron A. King Social Sciences Economic Sciences Finding long chains in kidney exchange using the traveling salesman problem Ross Anderson, Itai Ashlagi, David Gamarnik, and Alvin E. Roth Environmental Sciences Percolation transition in dynamical traffic network with evolving critical bottlenecks Daqing Li, Bowen Fu, Yunpeng Wang, Guangquan Lu, Yehiel Berezin, H. Eugene Stanley, and Shlomo Havlin Psychological and Cognitive Sciences Geographically varying associations between personality and life satisfaction in the London metropolitan area  Markus Jokela, Wiebke Bleidorn, Michael E. Lamb, Samuel D. Gosling, and Peter J. Rentfrow Social status modulates prosocial behavior and egalitarianism in preschool children and adults Ana Guinote, Ioanna Cotzia, Sanpreet Sandhu, and Pramila Siwa Social Sciences Crowd science user contribution patterns and their implications Henry Sauermann and Chiara Franzoni Biological Sciences Biochemistry Tissue-based metabolic labeling of polysialic acids in living primary hippocampal neurons Kyungtae Kang, Sunghoon Joo, Ji Yu Choi, Sujeong Geum, Seok-Pyo Hong, Seung-Yeul Lee, Yong Ho Kim, Seong-Min Kim, Myung-Han Yoon, Yoonkey Nam, Kyung-Bok Lee, Hee-Yoon Lee, and Insung S. Choi Cdc45 (cell division cycle protein 45) guards the gate of the Eukaryote Replisome helicase stabilizing leading strand engagement Tatjana Petojevic, James J. Pesavento, Alessandro Costa, Jingdan Liang, Zhijun Wang, James M. Berger, and Michael R. Botchan Flies expand the repertoire of protein structures that bind ice Koli Basu, Laurie A. Graham, Robert L. Campbell, and Peter L. Davies Biophysics and Computational Biology Modulation of folding energy landscape by charge–charge interactions: Linking experiments with computational modeling Franco O. Tzul, Katrina L. Schweiker, and George I. Makhatadze Programmable motion of DNA origami mechanisms Alexander E. Marras, Lifeng Zhou, Hai-Jun Su, and Carlos E. Castro Trigger loop folding determines transcription rate of Escherichia coli's RNA polymerase  Yara X. Mejia, Evgeny Nudler, and Carlos Bustamante Protein design algorithms predict viable resistance to an experimental antifolate Stephanie M. Reeve, Pablo Gainza, Kathleen M. Frey, Ivelin Georgiev, Bruce R. Donald, and Amy C. Anderson Antimalarial 4(1H)-pyridones bind to the Qi site of cytochrome bc1  Michael J. Capper, Paul M. O'Neill, Nicholas Fisher, Richard W. Strange, Darren Moss, Stephen A. Ward, Neil G. Berry, Alexandre S. Lawrenson, S. Samar Hasnain, Giancarlo A. Biagini, and Svetlana V. Antonyuk Cell Biology Single-molecule tracking of small GTPase Rac1 uncovers spatial regulation of membrane translocation and mechanism for polarized signaling Sulagna Das, Taofei Yin, Qingfen Yang, Jingqiao Zhang, Yi I. Wu, and Ji Yu VEGFR3 does not sustain retinal angiogenesis without VEGFR2 Georgia Zarkada, Krista Heinolainen, Taija Makinen, Yoshiaki Kubota, and Kari Alitalo In vivo, Argonaute-bound microRNAs exist predominantly in a reservoir of low molecular weight complexes not associated with mRNA Gaspare La Rocca, Scott H. Olejniczak, Alvaro J. González, Daniel Briskin, Joana A. Vidigal, Lee Spraggon, Raymond G. DeMatteo, Megan R. Radler, Tullia Lindsten, Andrea Ventura, Thomas Tuschl, Christina S. Leslie, and Craig B. Thompson Loss of autophagy causes a synthetic lethal deficiency in DNA repair  Emma Y. Liu, Naihan Xu, Jim O'Prey, Laurence Y. Lao, Sanket Joshi, Jaclyn S. Long, Margaret O'Prey, Daniel R. Croft, Florian Beaumatin, Alice D. Baudot, Michaela Mrschtik, Mathias Rosenfeldt, Yaou Zhang, David A. Gillespie, and Kevin M. Ryan K-Ras4A splice variant is widely expressed in cancer and uses a hybrid membrane-targeting motif Frederick D. Tsai, Mathew S. Lopes, Mo Zhou, Helen Court, Odis Ponce, James J. Fiordalisi, Jessica J. Gierut, Adrienne D. Cox, Kevin M. Haigis, and Mark R. Philips Developmental Biology Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo  Max V. Staller, Ben J. Vincent, Meghan D. J. Bragdon, Tara Lydiard-Martin, Zeba Wunderlich, Javier Estrada, and Angela H. DePace Calcium waves occur as Drosophila oocytes activate Taro Kaneuchi, Caroline V. Sartain, Satomi Takeo, Vanessa L. Horner, Norene A. Buehner, Toshiro Aigaki, and Mariana F. Wolfner Ecology Inference for dynamic and latent variable models via iterated, perturbed Bayes maps Edward L. Ionides, Dao Nguyen, Yves Atchadé, Stilian Stoev, and Aaron A. King Plant functional traits and the multidimensional nature of species coexistence Nathan J. B. Kraft, Oscar Godoy, and Jonathan M. Levine Evolution Deep conservation of wrist and digit enhancers in fish  Andrew R. Gehrke, Igor Schneider, Elisa de la Calle-Mustienes, Juan J. Tena, Carlos Gomez-Marin, Mayuri Chandran, Tetsuya Nakamura, Ingo Braasch, John H. Postlethwait, José Luis Gómez-Skarmeta, and Neil H. Shubin Adaptive simplification and the evolution of gecko locomotion: Morphological and biomechanical consequences of losing adhesion  Timothy E. Higham, Aleksandra V. Birn-Jeffery, Clint E. Collins, C. Darrin Hulsey, and Anthony P. Russell Adaptive introgression in an African malaria mosquito coincident with the increased usage of insecticide-treated bed nets Laura C. Norris, Bradley J. Main, Yoosook Lee, Travis C. Collier, Abdrahamane Fofana, Anthony J. Cornel, and Gregory C. Lanzaro Dried whole-plant Artemisia annua slows evolution of malaria drug resistance and overcomes resistance to artemisinin  Mostafa A. Elfawal, Melissa J. Towler, Nicholas G. Reich, Pamela J. Weathers, and Stephen M. Rich Genetics Uncoupling lifespan and healthspan in Caenorhabditis elegans longevity mutants Ankita Bansal, Lihua J. Zhu, Kelvin Yen, and Heidi A. Tissenbaum Control of stem cell self-renewal and differentiation by the heterochronic genes and the cellular asymmetry machinery in Caenorhabditis elegans Omid F. Harandi and Victor R. Ambros Immunology and Inflammation Inflammation-sensitive super enhancers form domains of coordinately regulated enhancer RNAs  Nasun Hah, Chris Benner, Ling-Wa Chong, Ruth T. Yu, Michael Downes, and Ronald M. Evans Temperature-dependent innate defense against the common cold virus limits viral replication at warm temperature in mouse airway cells  Ellen F. Foxman, James A. Storer, Megan E. Fitzgerald, Bethany R. Wasik, Lin Hou, Hongyu Zhao, Paul E. Turner, Anna Marie Pyle, and Akiko Iwasaki Structure of FcγRI in complex with Fc reveals the importance of glycan recognition for high-affinity IgG binding Jinghua Lu, Jonathan Chu, Zhongcheng Zou, Nels B. Hamacher, Mark W. Rixon, and Peter D. Sun Medical Sciences Examination of HER3 targeting in cancer using monoclonal antibodies Nadège Gaborit, Ali Abdul-Hai, Maicol Mancini, Moshit Lindzen, Sara Lavi, Orith Leitner, Lucile Mounier, Myriam Chentouf, Sai Dunoyer, Manjusha Ghosh, Christel Larbouret, Thierry Chardès, Hervé Bazin, André Pèlegrin, Michael Sela, and Yosef Yarden A KIR B centromeric region present in Africans but not Europeans protects pregnant women from pre-eclampsia Annettee Nakimuli, Olympe Chazara, Susan E. Hiby, Lydia Farrell, Stephen Tukwasibwe, Jyothi Jayaraman, James A. Traherne, John Trowsdale, Francesco Colucci, Emma Lougee, Robert W. Vaughan, Alison M. Elliott, Josaphat Byamugisha, Pontiano Kaleebu, Florence Mirembe, Neda Nemat-Gorgani, Peter Parham, Paul J. Norman, and Ashley Moffett Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity  Mona Meyer, Jüri Reimand, Xiaoyang Lan, Renee Head, Xueming Zhu, Michelle Kushida, Jane Bayani, Jessica C. Pressey, Anath C. Lionel, Ian D. Clarke, Michael Cusimano, Jeremy A. Squire, Stephen W. Scherer, Mark Bernstein, Melanie A. Woodin, Gary D. Bader, and Peter B. Dirks Microbiology Single-cell, real-time detection of oxidative stress induced in Escherichia coli by the antimicrobial peptide CM15 Heejun Choi, Zhilin Yang, and James C. Weisshaar Terpene synthases are widely distributed in bacteria  Yuuki Yamada, Tomohisa Kuzuyama, Mamoru Komatsu, Kazuo Shin-ya, Satoshi Omura, David E. Cane, and Haruo Ikeda Patterns of genome evolution that have accompanied host adaptation in Salmonella   Gemma C. Langridge, Maria Fookes, Thomas R. Connor, Theresa Feltwell, Nicholas Feasey, Bryony N. Parsons, Helena M. B. Seth-Smith, Lars Barquist, Anna Stedman, Tom Humphrey, Paul Wigley, Sarah E. Peters, Duncan J. Maskell, Jukka Corander, Jose A. Chabalgoity, Paul Barrow, Julian Parkhill, Gordon Dougan, and Nicholas R. Thomson Clofazimine shortens the duration of the first-line treatment regimen for experimental chemotherapy of tuberculosis Sandeep Tyagi, Nicole C. Ammerman, Si-Yang Li, John Adamson, Paul J. Converse, Rosemary V. Swanson, Deepak V. Almeida, and Jacques H. Grosset Neuroscience Genetic dissection of pheromone processing reveals main olfactory system-mediated social behaviors in mice  Tomohiko Matsuo, Tatsuya Hattori, Akari Asaba, Naokazu Inoue, Nobuhiro Kanomata, Takefumi Kikusui, Reiko Kobayakawa, and Ko Kobayakawa Acceleration of conduction velocity linked to clustering of nodal components precedes myelination Sean A. Freeman, Anne Desmazières, Jean Simonnet, Marie Gatta, Friederike Pfeiffer, Marie Stéphane Aigrot, Quentin Rappeneau, Serge Guerreiro, Patrick Pierre Michel, Yuchio Yanagawa, Gilles Barbin, Peter J. Brophy, Desdemona Fricker, Catherine Lubetzki, and Nathalie Sol-Foulon Novel neural circuit mechanism for visual edge detection Charles F. Stevens Enduring good memories of infant trauma: Rescue of adult neurobehavioral deficits via amygdala serotonin and corticosterone interaction Millie Rincón-Cortés, Gordon A. Barr, Anne Marie Mouly, Kiseko Shionoya, Bestina S. Nuñez, and Regina M. Sullivan Signature of consciousness in the dynamics of resting-state brain activity Pablo Barttfeld, Lynn Uhrig, Jacobo D. Sitt, Mariano Sigman, Béchir Jarraya, and Stanislas Dehaene Targeted ablation of cholinergic interneurons in the dorsolateral striatum produces behavioral manifestations of Tourette syndrome Meiyu Xu, Andrew Kobets, Jung-Chieh Du, Jessica Lennington, Lina Li, Mounira Banasr, Ronald S. Duman, Flora M. Vaccarino, Ralph J. DiLeone, and Christopher Pittenger Physiology Intracellular Cl− as a signaling ion that potently regulates Na+/HCO3− transporters Nikolay Shcheynikov, Aran Son, Jeong Hee Hong, Osamu Yamazaki, Ehud Ohana, Ira Kurtz, Dong Min Shin, and Shmuel Muallem Central role of SIAH inhibition in DCC-dependent cardioprotection provoked by netrin-1/NO Qiang Li, Ping Wang, Keqiang Ye, and Hua Cai Plant Biology Natural diversity in daily rhythms of gene expression contributes to phenotypic variation  Amaury de Montaigu, Antonis Giakountis, Matthew Rubin, Réka Tóth, Frédéric Cremer, Vladislava Sokolova, Aimone Porri, Matthieu Reymond, Cynthia Weinig, and George Coupland DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis Xuehua Zhong, Christopher J. Hale, Minh Nguyen, Israel Ausin, Martin Groth, Jonathan Hetzel, Ajay A. Vashisht, Ian R. Henderson, James A. Wohlschlegel, and Steven E. Jacobsen Epigenetic transitions leading to heritable, RNA-mediated de novo silencing in Arabidopsis thaliana  Donna M. Bond and David C. Baulcombe Translatome analyses capture of opposing tissue-specific brassinosteroid signals orchestrating root meristem differentiation Kristina Vragović, Ayala Sela, Lilach Friedlander-Shani, Yulia Fridman, Yael Hacham, Neta Holland, Elizabeth Bartom, Todd C. Mockler, and Sigal Savaldi-Goldstein Systems Biology Model-driven discovery of underground metabolic functions in Escherichia coli Gabriela I. Guzmán, José Utrilla, Sergey Nurk, Elizabeth Brunk, Jonathan M. Monk, Ali Ebrahim, Bernhard O. Palsson, and Adam M. Feist Corrections (Online Only) Correction for Robertson et al., Assembly and molecular order of two-dimensional peptoid nanosheets through the oil–water interface Correction for Ferus et al., High-energy chemistry of formamide: A unified mechanism of nucleobase formation Correction for Wu et al., Structural basis for substrate specificity and catalysis of human histone acetyltransferase 1 Correction for Jadi and Sejnowski, Cortical oscillations arise from contextual interactions that regulate sparse coding Open Access From the Cover Inaugural Article Classic Cozzarelli Prize Winner Front Matter This message was sent to pascal.alter@gmail.com. (....) Or by mail: Customer Service * 425 Broadway St * Redwood City, CA 94063 * U.S.A. Copyright © 2015 by the National Academy of Sciences