Fwd: PNAS Table of Contents for 26 November 2013; Vol. 110, No. 48

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Proceedings of the National Academy of Sciences 26 November 2013; Vol. 110, No. 48 This Week in PNAS In This Issue Letters (Online Only) Oxygen isotope anomaly not present in water vapor from Alert, Canada Martin F. Miller Reply to Miller: Concerning the oxygen isotope anomaly observed in water vapor from Alert, Canada, and its stratospheric source Ying Lin, Robert N. Clayton, Lin Huang, Noboru Nakamura, and James R. Lyons Alternative explanation for indole-induced antibiotic tolerance in Salmonella Jessica M. A. Blair, Axel Cloeckaert, Kunihiko Nishino, and Laura J. V. Piddock Reply to Blair et al.: Dose-dependent effects and oxidative stress responses in antibiotic tolerance in Salmonella typhimurium Nicole M. Vega, Kyle R. Allison, Amanda N. Samuels, Mark S. Klempner, and James J. Collins Science and Culture Digital dome J. D. Talasek QnAs QnAs with John Clarke Farooq Ahmed Retrospective Harold Agnew, physicist, atomic bomb Everyman William H. Press Commentaries Thermodynamically inspired classifier for molecular phenotypes of health and disease Marc T. Facciotti HIV provides ample PAMPs for innate immune sensing Benhur Lee Functional reconstitution of a chloride channel bares its soul H. Criss Hartzell and Chelsey Chandler Ruppersburg Local diversity stays about the same, regional diversity increases, and global diversity declines Chris D. Thomas More players in the plant unfolded response Alessandro Vitale PNAS Plus Significance Statements PNAS Plus Significance Statements Brief statements written by the authors about the significance of their papers. Quantitative Geometry Special Feature (Free Online) Introduction Quantitative geometry Assaf Naor Physical Sciences — Computer Sciences Near-optimal deterministic algorithms for volume computation via M-ellipsoids Daniel Dadush and Santosh S. Vempala Physical Sciences — Mathematics Homological and homotopical Dehn functions are different  Aaron Abrams, Noel Brady, Pallavi Dani, and Robert Young Fractional Sylvester–Gallai theorems Boaz Barak, Zeev Dvir, Avi Wigderson, and Amir Yehudayoff On the rate of convergence to the asymptotic cone for nilpotent groups and subFinsler geometry Emmanuel Breuillard and Enrico Le Donne Violating the Shannon capacity of metric graphs with entanglement Jop Briët, Harry Buhrman, and Dion Gijswijt Monotonicity and its analytic and geometric implications Tobias Holck Colding and William P. Minicozzi II Quantitative algebraic topology and Lipschitz homotopy Steve Ferry and Shmuel Weinberger A quantitative version of the commutator theorem for zero trace matrices William B. Johnson, Narutaka Ozawa, and Gideon Schechtman Ultrametric skeletons Manor Mendel and Assaf Naor Physical Sciences Applied Physical Sciences Quantifying the dynamic interactions between a clathrin-coated pit and cargo molecules Aubrey V. Weigel, Michael M. Tamkun, and Diego Krapf MRI of the human brain at 130 microtesla  Ben Inglis, Kai Buckenmaier, Paul SanGiorgio, Anders F. Pedersen, Matthew A. Nichols, and John Clarke Three-dimensional textures and defects of soft material layering revealed by thermal sublimation Dong Ki Yoon, Yun Ho Kim, Dae Seok Kim, Seong Dae Oh, Ivan I. Smalyukh, Noel A. Clark, and Hee-Tae Jung Motionless phase stepping in X-ray phase contrast imaging with a compact source  Houxun Miao, Lei Chen, Eric E. Bennett, Nick M. Adamo, Andrew A. Gomella, Alexa M. DeLuca, Ajay Patel, Nicole Y. Morgan, and Han Wen Astronomy Prevalence of Earth-size planets orbiting Sun-like stars  Erik A. Petigura, Andrew W. Howard, and Geoffrey W. Marcy Chemistry Islet amyloid polypeptide toxicity and membrane interactions Ping Cao, Andisheh Abedini, Hui Wang, Ling-Hsien Tu, Xiaoxue Zhang, Ann Marie Schmidt, and Daniel P. Raleigh Mechanism of IAPP amyloid fibril formation involves an intermediate with a transient β-sheet Lauren E. Buchanan, Emily B. Dunkelberger, Huong Q. Tran, Pin-Nan Cheng, Chi-Cheng Chiu, Ping Cao, Daniel P. Raleigh, Juan J. de Pablo, James S. Nowick, and Martin T. Zanni Impact of reconstituted cytosol on protein stability Mohona Sarkar, Austin E. Smith, and Gary J. Pielak Earth, Atmospheric, and Planetary Sciences Microphysical effects determine macrophysical response for aerosol impacts on deep convective clouds  Jiwen Fan, L. Ruby Leung, Daniel Rosenfeld, Qian Chen, Zhanqing Li, Jinqiang Zhang, and Hongru Yan Engineering Comminution of solids caused by kinetic energy of high shear strain rate, with implications for impact, shock, and shale fracturing Zdeněk P. Bažant and Ferhun C. Caner Distinct biophysical mechanisms of focal adhesion kinase mechanoactivation by different extracellular matrix proteins Jihye Seong, Arash Tajik, Jie Sun, Jun-Lin Guan, Martin J. Humphries, Susan E. Craig, Asha Shekaran, Andrés J. García, Shaoying Lu, Michael Z. Lin, Ning Wang, and Yingxiao Wang Environmental Sciences Exploring network scaling through variations on optimal channel networks Lily A. Briggs and Mukkai Krishnamoorthy Identifying external influences on global precipitation  Kate Marvel and Céline Bonfils Statistics Searching for efficient Markov chain Monte Carlo proposal kernels Ziheng Yang and Carlos E. Rodríguez Revised standards for statistical evidence  Valen E. Johnson Social Sciences Economic Sciences Similarity increases altruistic punishment in humans Thomas Mussweiler and Axel Ockenfels Biological Sciences Agricultural Sciences Host-induced gene silencing of cytochrome P450 lanosterol C14α-demethylase–encoding genes confers strong resistance to Fusarium species  Aline Koch, Neelendra Kumar, Lennart Weber, Harald Keller, Jafargholi Imani, and Karl-Heinz Kogel Applied Biological Sciences Antibody biomarker discovery through in vitro directed evolution of consensus recognition epitopes  John T. Ballew, Joseph A. Murray, Pekka Collin, Markku Mäki, Martin F. Kagnoff, Katri Kaukinen, and Patrick S. Daugherty Hydrogels preserve native phenotypes of valvular fibroblasts through an elasticity-regulated PI3K/AKT pathway Huan Wang, Mark W. Tibbitt, Stephen J. Langer, Leslie A. Leinwand, and Kristi S. Anseth Biochemistry Structural and genetic analyses reveal the protein SepF as a new membrane anchor for the Z ring  Ramona Duman, Shu Ishikawa, Ilkay Celik, Henrik Strahl, Naotake Ogasawara, Paulina Troc, Jan Löwe, and Leendert W. Hamoen Crystal structure of the human eIF4AIII–CWC22 complex shows how a DEAD-box protein is inhibited by a MIF4G domain Gretel Buchwald, Steffen Schüssler, Claire Basquin, Hervé Le Hir, and Elena Conti Impact of reconstituted cytosol on protein stability Mohona Sarkar, Austin E. Smith, and Gary J. Pielak Dysregulation of synaptogenesis genes antecedes motor neuron pathology in spinal muscular atrophy  Zhenxi Zhang, Anna Maria Pinto, Lili Wan, Wei Wang, Michael G. Berg, Isabela Oliva, Larry N. Singh, Christopher Dengler, Zhi Wei, and Gideon Dreyfuss Purified TMEM16A is sufficient to form Ca2+-activated Cl− channels  Hiroyuki Terashima, Alessandra Picollo, and Alessio Accardi Structural and functional insights into the regulation mechanism of CK2 by IP6 and the intrinsically disordered protein Nopp140 Won-Kyu Lee, Sang Hyeon Son, Bong-Suk Jin, Jung-Hyun Na, Soo-Youl Kim, Kook-Han Kim, Eunice EunKyeong Kim, Yeon Gyu Yu, and Hyung Ho Lee Metabolically programmed quality control system for dolichol-linked oligosaccharides Yoichiro Harada, Kazuki Nakajima, Yuki Masahara-Negishi, Hudson H. Freeze, Takashi Angata, Naoyuki Taniguchi, and Tadashi Suzuki Biophysics and Computational Biology Quantifying the dynamic interactions between a clathrin-coated pit and cargo molecules Aubrey V. Weigel, Michael M. Tamkun, and Diego Krapf Distinct biophysical mechanisms of focal adhesion kinase mechanoactivation by different extracellular matrix proteins Jihye Seong, Arash Tajik, Jie Sun, Jun-Lin Guan, Martin J. Humphries, Susan E. Craig, Asha Shekaran, Andrés J. García, Shaoying Lu, Michael Z. Lin, Ning Wang, and Yingxiao Wang Detection of single photons by toad and mouse rods Jürgen Reingruber, Johan Pahlberg, Michael L. Woodruff, Alapakkam P. Sampath, Gordon L. Fain, and David Holcman Prefusion structure of syntaxin-1A suggests pathway for folding into neuronal trans-SNARE complex fusion intermediate Binyong Liang, Volker Kiessling, and Lukas K. Tamm Structural insights into the histone H1-nucleosome complex Bing-Rui Zhou, Hanqiao Feng, Hidenori Kato, Liang Dai, Yuedong Yang, Yaoqi Zhou, and Yawen Bai Single-molecule resolution of protein structure and interfacial dynamics on biomaterial surfaces Sean Yu McLoughlin, Mark Kastantin, Daniel K. Schwartz, and Joel L. Kaar Cell Biology Emergence of spatial structure in the tumor microenvironment due to the Warburg effect Carlos Carmona-Fontaine, Vanni Bucci, Leila Akkari, Maxime Deforet, Johanna A. Joyce, and Joao B. Xavier Overexpression of Twinkle-helicase protects cardiomyocytes from genotoxic stress caused by reactive oxygen species Jaakko L. O. Pohjoismäki, Siôn L. Williams, Thomas Boettger, Steffi Goffart, Johnny Kim, Anu Suomalainen, Carlos T. Moraes, and Thomas Braun Unexpected gain of function for the scaffolding protein plectin due to mislocalization in pancreatic cancer Soo J. Shin, Jeffrey A. Smith, Günther A. Rezniczek, Sheng Pan, Ru Chen, Teresa A. Brentnall, Gerhard Wiche, and Kimberly A. Kelly Serotonin regulates glucose-stimulated insulin secretion from pancreatic β cells during pregnancy Mica Ohara-Imaizumi, Hail Kim, Masashi Yoshida, Tomonori Fujiwara, Kyota Aoyagi, Yukiko Toyofuku, Yoko Nakamichi, Chiyono Nishiwaki, Tadashi Okamura, Toyoyoshi Uchida, Yoshio Fujitani, Kimio Akagawa, Masafumi Kakei, Hirotaka Watada, Michael S. German, and Shinya Nagamatsu Phosphoproteomic characterization of DNA damage response in melanoma cells following MEK/PI3K dual inhibition Donald S. Kirkpatrick, Daisy J. Bustos, Taner Dogan, Jocelyn Chan, Lilian Phu, Amy Young, Lori S. Friedman, Marcia Belvin, Qinghua Song, Corey E. Bakalarski, and Klaus P. Hoeflich The EM structure of the TRAPPIII complex leads to the identification of a requirement for COPII vesicles on the macroautophagy pathway Dongyan Tan, Yiying Cai, Juan Wang, Jinzhong Zhang, Shekar Menon, Hui-Ting Chou, Susan Ferro-Novick, Karin M. Reinisch, and Thomas Walz Developmental Biology Hox5 interacts with Plzf to restrict Shh expression in the developing forelimb Ben Xu, Steven M. Hrycaj, Daniel C. McIntyre, Nicholas C. Baker, Jun K. Takeuchi, Lucie Jeannotte, Zachary B. Gaber, Bennett G. Novitch, and Deneen M. Wellik Establishment of smooth muscle and cartilage juxtaposition in the developing mouse upper airways Elizabeth A. Hines, Mary-Kayt N. Jones, Jamie M. Verheyden, Julie F. Harvey, and Xin Sun Lkb1/Stk11 regulation of mTOR signaling controls the transition of chondrocyte fates and suppresses skeletal tumor formation Lick Pui Lai, Brendan N. Lilley, Joshua R. Sanes, and Andrew P. McMahon Ecology Global meta-analysis reveals no net change in local-scale plant biodiversity over time  Mark Vellend, Lander Baeten, Isla H. Myers-Smith, Sarah C. Elmendorf, Robin Beauséjour, Carissa D. Brown, Pieter De Frenne, Kris Verheyen, and Sonja Wipf Evolution Gene amplification and microsatellite polymorphism underlie a recent insect host shift Chris Bass, Christoph T. Zimmer, Jacob M. Riveron, Craig S. Wilding, Charles S. Wondji, Martin Kaussmann, Linda M. Field, Martin S. Williamson, and Ralf Nauen Genetics Intrinsic karyotype stability and gene copy number variations may have laid the foundation for tetraploid wheat formation  Huakun Zhang, Yao Bian, Xiaowan Gou, Yuzhu Dong, Sachin Rustgi, Bangjiao Zhang, Chunming Xu, Ning Li, Bao Qi, Fangpu Han, Diter von Wettstein, and Bao Liu Human-specific endogenous retroviral insert serves as an enhancer for the schizophrenia-linked gene PRODH Maria Suntsova, Elena V. Gogvadze, Sergey Salozhin, Nurshat Gaifullin, Fedor Eroshkin, Sergey E. Dmitriev, Natalia Martynova, Kirill Kulikov, Galina Malakhova, Gulnur Tukhbatova, Alexey P. Bolshakov, Dmitry Ghilarov, Andrew Garazha, Alexander Aliper, Charles R. Cantor, Yuri Solokhin, Sergey Roumiantsev, Pavel Balaban, Alex Zhavoronkov, and Anton Buzdin Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing  Uffe Hellsten, Kevin M. Wright, Jerry Jenkins, Shengqiang Shu, Yaowu Yuan, Susan R. Wessler, Jeremy Schmutz, John H. Willis, and Daniel S. Rokhsar Repair of UV photolesions in xeroderma pigmentosum group C cells induced by translational readthrough of premature termination codons Christiane Kuschal, John. J. DiGiovanna, Sikandar G. Khan, Richard A. Gatti, and Kenneth H. Kraemer Synthetic lethality between CCNE1 amplification and loss of BRCA1  Dariush Etemadmoghadam, Barbara A. Weir, George Au-Yeung, Kathryn Alsop, Gillian Mitchell, Joshy George, Australian Ovarian Cancer Study Group, Sally Davis, Alan D. D'Andrea, Kaylene Simpson, William C. Hahn, and David D. L. Bowtell Genetic variants related to gap junctions and hormone secretion influence conception rates in cows Mayumi Sugimoto, Shinji Sasaki, Yusaku Gotoh, Yuuki Nakamura, Yoshito Aoyagi, Takayoshi Kawahara, and Yoshikazu Sugimoto Immunology IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication  Martin R. Jakobsen, Rasmus O. Bak, Annika Andersen, Randi K. Berg, Søren B. Jensen, Tengchuan Jin, Anders Laustsen, Kathrine Hansen, Lars Østergaard, Katherine A. Fitzgerald, T. Sam Xiao, Jacob G. Mikkelsen, Trine H. Mogensen, and Søren R. Paludan Growth hormone prevents the development of autoimmune diabetes Ricardo Villares, Dimitri Kakabadse, Yasmina Juarranz, Rosa P. Gomariz, Carlos Martínez-A, and Mario Mellado Peripheral subnuclear positioning suppresses Tcrb recombination and segregates Tcrb alleles from RAG2 Elizabeth A. W. Chan, Grace Teng, Elizabeth Corbett, Kingshuk Roy Choudhury, Craig H. Bassing, David G. Schatz, and Michael S. Krangel Antitumor activities of agonistic anti-TNFR antibodies require differential FcγRIIB coengagement in vivo Fubin Li and Jeffrey V. Ravetch Medical Sciences Bioavailable copper modulates oxidative phosphorylation and growth of tumors  Seiko Ishida, Pénélope Andreux, Carole Poitry-Yamate, Johan Auwerx, and Douglas Hanahan Mouse model of intrahepatic cholangiocarcinoma validates FIG–ROS as a potent fusion oncogene and therapeutic target  Anna Saborowski, Michael Saborowski, Monika A. Davare, Brian J. Druker, David S. Klimstra, and Scott W. Lowe Foretinib is a potent inhibitor of oncogenic ROS1 fusion proteins Monika A. Davare, Anna Saborowski, Christopher A. Eide, Cristina Tognon, Rebecca L. Smith, Johannes Elferich, Anupriya Agarwal, Jeffrey W. Tyner, Ujwal P. Shinde, Scott W. Lowe, and Brian J. Druker CDK10/cyclin M is a protein kinase that controls ETS2 degradation and is deficient in STAR syndrome Vincent J. Guen, Carly Gamble, Marc Flajolet, Sheila Unger, Aurélie Thollet, Yoan Ferandin, Andrea Superti-Furga, Pascale A. Cohen, Laurent Meijer, and Pierre Colas TREM2 governs Kupffer cell activation and explains belr1 genetic resistance to malaria liver stage infection Lígia Antunes Gonçalves, Lurdes Rodrigues-Duarte, Joana Rodo, Luciana Vieira de Moraes, Isabel Marques, and Carlos Penha-Gonçalves Keratin 16 regulates innate immunity in response to epidermal barrier breach Juliane C. Lessard, Sylvia Piña-Paz, Jeremy D. Rotty, Robyn P. Hickerson, Roger L. Kaspar, Allan Balmain, and Pierre A. Coulombe Microbiology Structure and assembly of an inner membrane platform for initiation of type IV pilus biogenesis  Vijaykumar Karuppiah, Richard F. Collins, Angela Thistlethwaite, Ya Gao, and Jeremy P. Derrick Phosphorylation-dependent derepression by the response regulator HnoC in the Shewanella oneidensis nitric oxide signaling network Lars Plate and Michael A. Marletta Global methylation state at base-pair resolution of the Caulobacter genome throughout the cell cycle Jennifer B. Kozdon, Michael D. Melfi, Khai Luong, Tyson A. Clark, Matthew Boitano, Susana Wang, Bo Zhou, Diego Gonzalez, Justine Collier, Stephen W. Turner, Jonas Korlach, Lucy Shapiro, and Harley H. McAdams Site-2 protease substrate specificity and coupling in trans by a PDZ-substrate adapter protein Jessica S. Schneider, Shilpa P. Reddy, Hock Y. E, Henry W. Evans, and Michael S. Glickman Gene product 0.4 increases bacteriophage T7 competitiveness by inhibiting host cell division Ruth Kiro, Shahar Molshanski-Mor, Ido Yosef, Sara L. Milam, Harold P. Erickson, and Udi Qimron Neuroscience Dynamic faces speed up the onset of auditory cortical spiking responses during vocal detection  Chandramouli Chandrasekaran, Luis Lemus, and Asif A. Ghazanfar Rapid stimulus-evoked astrocyte Ca2+ elevations and hemodynamic responses in mouse somatosensory cortex in vivo Barbara Lykke Lind, Alexey R. Brazhe, Sanne Barsballe Jessen, Florence C. C. Tan, and Martin J. Lauritzen Transmission of multiple system atrophy prions to transgenic mice Joel C. Watts, Kurt Giles, Abby Oehler, Lefkos Middleton, David T. Dexter, Steve M. Gentleman, Stephen J. DeArmond, and Stanley B. Prusiner Fungal-derived semiochemical 1-octen-3-ol disrupts dopamine packaging and causes neurodegeneration Arati A. Inamdar, Muhammad M. Hossain, Alison I. Bernstein, Gary W. Miller, Jason R. Richardson, and Joan Wennstrom Bennett BMP9 ameliorates amyloidosis and the cholinergic defect in a mouse model of Alzheimer's disease Rebecca M. Burke, Timothy A. Norman, Tarik F. Haydar, Barbara E. Slack, Susan E. Leeman, Jan Krzysztof Blusztajn, and Tiffany J. Mellott Differential effects of global versus local testosterone on singing behavior and its underlying neural substrate Beau A. Alward, Jacques Balthazart, and Gregory F. Ball High-affinity olfactory receptor for the death-associated odor cadaverine Ashiq Hussain, Luis R. Saraiva, David M. Ferrero, Gaurav Ahuja, Venkatesh S. Krishna, Stephen D. Liberles, and Sigrun I. Korsching Frequency-specific mechanism links human brain networks for spatial attention Amy L. Daitch, Mohit Sharma, Jarod L. Roland, Serguei V. Astafiev, David T. Bundy, Charles M. Gaona, Abraham Z. Snyder, Gordon L. Shulman, Eric C. Leuthardt, and Maurizio Corbetta Persistence of hippocampal multivoxel patterns into postencoding rest is related to memory Arielle Tambini and Lila Davachi Sleep deprivation increases dorsal nexus connectivity to the dorsolateral prefrontal cortex in humans Oliver G. Bosch, Julia S. Rihm, Milan Scheidegger, Hans-Peter Landolt, Philipp Stämpfli, Janis Brakowski, Fabrizio Esposito, Björn Rasch, and Erich Seifritz ErbB4 reduces synaptic GABAA currents independent of its receptor tyrosine kinase activity Robert M. Mitchell, Megan J. Janssen, Irina Karavanova, Detlef Vullhorst, Katrina Furth, Anthony Makusky, Sanford P. Markey, and Andres Buonanno Serotonin selectively enhances perception and sensory neural responses to stimuli generated by same-sex conspecifics Tara Deemyad, Michael G. Metzen, Yingzhou Pan, and Maurice J. Chacron Pharmacology Exchange protein directly activated by cAMP plays a critical role in bacterial invasion during fatal rickettsioses Bin Gong, Thomas Shelite, Fang C. Mei, Tuha Ha, Yaohua Hu, Guang Xu, Qing Chang, Maki Wakamiya, Thomas G. Ksiazek, Paul J. Boor, Donald H. Bouyer, Vsevolod L. Popov, Ju Chen, David H. Walker, and Xiaodong Cheng Physiology Phosphorylation sites required for regulation of cardiac calcium channels in the fight-or-flight response Ying Fu, Ruth E. Westenbroek, Todd Scheuer, and William A. Catterall Plant Biology Arabidopsis thaliana AHL family modulates hypocotyl growth redundantly by interacting with each other via the PPC/DUF296 domain Jianfei Zhao, David S. Favero, Hao Peng, and Michael M. Neff GmNAC30 and GmNAC81 integrate the endoplasmic reticulum stress- and osmotic stress-induced cell death responses through a vacuolar processing enzyme  Giselle C. Mendes, Pedro A. B. Reis, Iara P. Calil, Humberto H. Carvalho, Francisco J. L. Aragão, and Elizabeth P. B. Fontes Protein kinase and ribonuclease domains of IRE1 confer stress tolerance, vegetative growth, and reproductive development in Arabidopsis  Yan Deng, Renu Srivastava, and Stephen H. Howell Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species Amanda J. Waters, Paul Bilinski, Steven R. Eichten, Matthew W. Vaughn, Jeffrey Ross-Ibarra, Mary Gehring, and Nathan M. Springer Population Biology Searching for efficient Markov chain Monte Carlo proposal kernels Ziheng Yang and Carlos E. Rodríguez Pathogen selection drives nonoverlapping associations between HLA loci  Bridget S. Penman, Ben Ashby, Caroline O. Buckee, and Sunetra Gupta Psychological and Cognitive Sciences Similarity increases altruistic punishment in humans Thomas Mussweiler and Axel Ockenfels Corrections Correction for Petigura et al., Prevalence of Earth-size planets orbiting Sun-like stars Correction for Briët et al., Violating the Shannon capacity of metric graphs with entanglement Correction for Li et al., Mechanism of E-cadherin dimerization probed by NMR relaxation dispersion Correction for Breau et al., A Hox gene controls lateral line cell migration by regulating chemokine receptor expression downstream of Wnt signaling Correction for Jakobsen et al., IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication Open Access From the Cover Inaugural Article Classic Cozzarelli Prize Winner This message was sent to pascal.alter@gmail.com. (....)* 425 Broadway St * Redwood City, CA 94063 * U.S.A. Copyright © 2013 by the National Academy of Sciences