Fwd: PNAS Early Edition for 7 Jan 2015

---------- Forwarded message ----------
From: <pnas-mailer@alerts.stanford.edu>
Date: Thu, Jan 8, 2015 at 8:07 AM
Subject: PNAS Early Edition for 7 Jan 2015
To: pascal.alter@gmail.com

Proceedings of the National Academy of Sciences Early Edition articles for 7 January 2015 Letters (Online Only) Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks Ge Tan, Manuel Gil, Ari P. Löytynoja, Nick Goldman, and Christophe Dessimoz Reply to Tan et al.: Differences between real and simulated proteins in multiple sequence alignments Kieran Boyce, Fabian Sievers, and Desmond G. Higgins Retrospectives Donald F. Steiner MD, 1930–2014: Discoverer of proinsulin Louis H. Philipson, Graeme Bell, and Kenneth S. Polonsky Max Birnstiel 1933–2014: Gene pioneer Michael Grunstein and Adrian Bird Profile Profile of Brian Charlesworth Jennifer Viegas Commentaries Reconstructing pathogen evolution from the ruins Sean-Paul Nuccio and Andreas J. Bäumler Impact synthesis of the RNA bases Andro C. Rios Perspectives A chemiosmotic mechanism of symport H. Ronald Kaback A generation at risk: Young investigators and the future of the biomedical workforce  Ronald J. Daniels 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 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 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 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 Semilocal density functional obeying a strongly tightened bound for exchange Jianwei Sun, John P. Perdew, and Adrienn Ruzsinszky Earth, Atmospheric, and Planetary Sciences 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 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 Attenuation of sinking particulate organic carbon flux through the mesopelagic ocean Chris M. Marsay, Richard J. Sanders, Stephanie A. Henson, Katsiaryna Pabortsava, Eric P. Achterberg, and Richard S. Lampitt 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 Anthropology Variation in Rapa Nui (Easter Island) land use indicates production and population peaks prior to European contact Christopher M. Stevenson, Cedric O. Puleston, Peter M. Vitousek, Oliver A. Chadwick, Sonia Haoa, and Thegn N. Ladefoged Economic Sciences Finding long chains in kidney exchange using the traveling salesman problem Ross Anderson, Itai Ashlagi, David Gamarnik, and Alvin E. Roth Psychological and Cognitive Sciences Social status modulates prosocial behavior and egalitarianism in preschool children and adults Ana Guinote, Ioanna Cotzia, Sanpreet Sandhu, and Pramila Siwa Social Sciences Cohort of birth modifies the association between FTO genotype and BMI  James Niels Rosenquist, Steven F. Lehrer, A. James O'Malley, Alan M. Zaslavsky, Jordan W. Smoller, and Nicholas A. Christakis Crowd science user contribution patterns and their implications Henry Sauermann and Chiara Franzoni Biological Sciences Biochemistry A chemiosmotic mechanism of symport H. Ronald Kaback 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 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 Programmable motion of DNA origami mechanisms Alexander E. Marras, Lifeng Zhou, Hai-Jun Su, and Carlos E. Castro Cell Biology 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 VEGFR3 does not sustain retinal angiogenesis without VEGFR2 Georgia Zarkada, Krista Heinolainen, Taija Makinen, Yoshiaki Kubota, and Kari Alitalo 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 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 Developmental Biology 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 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 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 Environmental Sciences Attenuation of sinking particulate organic carbon flux through the mesopelagic ocean Chris M. Marsay, Richard J. Sanders, Stephanie A. Henson, Katsiaryna Pabortsava, Eric P. Achterberg, and Richard S. Lampitt Evolution 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 Experimental replacement of an obligate insect symbiont Nancy A. Moran and Yueli Yun 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 Genetics Cohort of birth modifies the association between FTO genotype and BMI  James Niels Rosenquist, Steven F. Lehrer, A. James O'Malley, Alan M. Zaslavsky, Jordan W. Smoller, and Nicholas A. Christakis 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 Uncoupling lifespan and healthspan in Caenorhabditis elegans longevity mutants Ankita Bansal, Lihua J. Zhu, Kelvin Yen, and Heidi A. Tissenbaum 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 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 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 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 Insulin-independent regulation of hepatic triglyceride synthesis by fatty acids  Daniel F. Vatner, Sachin K. Majumdar, Naoki Kumashiro, Max C. Petersen, Yasmeen Rahimi, Arijeet K. Gattu, Mitchell Bears, João-Paulo G. Camporez, Gary W. Cline, Michael J. Jurczak, Varman T. Samuel, and Gerald I. Shulman 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 A generation at risk: Young investigators and the future of the biomedical workforce  Ronald J. Daniels 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 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 Independent role for presynaptic FMRP revealed by an FMR1 missense mutation associated with intellectual disability and seizures  Leila K. Myrick, Pan-Yue Deng, Hideharu Hashimoto, Young Mi Oh, Yongcheol Cho, Mickael J. Poidevin, Joshua A. Suhl, Jeannie Visootsak, Valeria Cavalli, Peng Jin, Xiaodong Cheng, Stephen T. Warren, and Vitaly A. Klyachko Novel neural circuit mechanism for visual edge detection Charles F. Stevens 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 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 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 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 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 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 Psychological and Cognitive Sciences Context-dependent categorical perception in a songbird Robert F. Lachlan and Stephen Nowicki 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 Open Access From the Cover Inaugural Article Classic Cozzarelli Prize Winner Front Matter This message was sent to pascal.alter@gmail.com. (....) Customer Service * 425 Broadway St * Redwood City, CA 94063 * U.S.A. Copyright © 2015 by the National Academy of Sciences