Notatnik Pascala: Fwd: PNAS Early Edition for 23 Jul 2013

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From: <pnas-mailer@alerts.stanford.edu>
Date: Wed, Jul 24, 2013 at 7:04 AM
Subject: PNAS Early Edition for 23 Jul 2013
To: pascal.alter@gmail.com

Proceedings of the National Academy of Sciences

Early Edition articles for 23 July 2013

QnAs

QnAs with Lynn M. Riddiford: Sujata Gupta

QnAs with Ronald DePinho: Prashant Nair

Commentaries

Neutrophils enlist IL-22 to restore order in the gut: Timothy L. Denning and Charles A. Parkos

Drops on soft surfaces learn the hard way: Todd M. Squires

Oncogenic herpesviruses sending mixed signals: D. Michiel Pegtel

Perspectives

The case for distributed irrigation as a development priority in sub-Saharan Africa: Jennifer A. Burney, Rosamond L. Naylor, and Sandra L. Postel

NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers: Ashok Sekhar and Lewis E. Kay

Physical Sciences

Applied Mathematics

Increased transmissibility explains the third wave of infection by the 2009 H1N1 pandemic virus in England OPEN ACCESS ARTICLE: Ilaria Dorigatti, Simon Cauchemez, and Neil M. Ferguson

Applied Physical Sciences

Multiparametric approach for the evaluation of lipid nanoparticles for siRNA delivery: Christopher A. Alabi, Kevin T. Love, Gaurav Sahay, Hao Yin, Kathryn M. Luly, Robert Langer, and Daniel G. Anderson

Universal collapse of stress and wrinkle-to-scar transition in spherically confined crystalline sheets: Gregory M. Grason and Benny Davidovitch

Chemistry

Determining complete electron flow in the cofactor photoreduction of oxidized photolyase OPEN ACCESS ARTICLE: Zheyun Liu, Chuang Tan, Xunmin Guo, Jiang Li, Lijuan Wang, Aziz Sancar, and Dongping Zhong

Dynamic determination of the functional state in photolyase and the implication for cryptochrome OPEN ACCESS ARTICLE: Zheyun Liu, Meng Zhang, Xunmin Guo, Chuang Tan, Jiang Li, Lijuan Wang, Aziz Sancar, and Dongping Zhong

Sulfatase-activated fluorophores for rapid discrimination of mycobacterial species and strains: Kimberly E. Beatty, Monique Williams, Brian L. Carlson, Benjamin M. Swarts, Robin M. Warren, Paul D. van Helden, and Carolyn R. Bertozzi

Testing the diffusing boundary model for the helix–coil transition in peptides OPEN ACCESS ARTICLE: Sabine Neumaier, Andreas Reiner, Maren Büttner, Beat Fierz, and Thomas Kiefhaber

Role of methyl-induced polarization in ion binding: Mariana Rossi, Alexandre Tkatchenko, Susan B. Rempe, and Sameer Varma

Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery: Hernani Leonardo Silvestre, Thomas L. Blundell, Chris Abell, and Alessio Ciulli

Reactivity landscape of pyruvate under simulated hydrothermal vent conditions: Yehor Novikov and Shelley D. Copley

Proton transfer through the water gossamer: Ali Hassanali, Federico Giberti, Jérôme Cuny, Thomas D. Kühne, and Michele Parrinello

Earth, Atmospheric, and Planetary Sciences

Large Pt anomaly in the Greenland ice core points to a cataclysm at the onset of Younger Dryas: Michail I. Petaev, Shichun Huang, Stein B. Jacobsen, and Alan Zindler

Engineering

Synthesizing cognition in neuromorphic electronic systems: Emre Neftci, Jonathan Binas, Ueli Rutishauser, Elisabetta Chicca, Giacomo Indiveri, and Rodney J. Douglas

Environmental Sciences

Resilience of river flow regimes OPEN ACCESS ARTICLE: Gianluca Botter, Stefano Basso, Ignacio Rodriguez-Iturbe, and Andrea Rinaldo

Statistics

Statistical significance of combinatorial regulations OPEN ACCESS ARTICLE: Aika Terada, Mariko Okada-Hatakeyama, Koji Tsuda, and Jun Sese

Inverse Gillespie for inferring stochastic reaction mechanisms from intermittent samples: Ishanu Chattopadhyay, Anna Kuchina, Gürol M. Süel, and Hod Lipson

Social Sciences

Economic Sciences

Advertisements impact the physiological efficacy of a branded drug: Emir Kamenica, Robert Naclerio, and Anup Malani

Biological Sciences

Applied Biological Sciences

Multiparametric approach for the evaluation of lipid nanoparticles for siRNA delivery: Christopher A. Alabi, Kevin T. Love, Gaurav Sahay, Hao Yin, Kathryn M. Luly, Robert Langer, and Daniel G. Anderson

Reactive nitrogen species regulate autophagy through ATM-AMPK-TSC2–mediated suppression of mTORC1: Durga N. Tripathi, Rajdeep Chowdhury, Laura J. Trudel, Andrew R. Tee, Rebecca S. Slack, Cheryl Lyn Walker, and Gerald N. Wogan

Biochemistry

Cost of rNTP/dNTP pool imbalance at the replication fork OPEN ACCESS ARTICLE: Nina Y. Yao, Jeremy W. Schroeder, Olga Yurieva, Lyle A. Simmons, and Mike E. O'Donnell

Structural and mechanistic insights into VEGF receptor 3 ligand binding and activation: Veli-Matti Leppänen, Denis Tvorogov, Kaisa Kisko, Andrea E. Prota, Michael Jeltsch, Andrey Anisimov, Sandra Markovic-Mueller, Edward Stuttfeld, Kenneth N. Goldie, Kurt Ballmer-Hofer, and Kari Alitalo

Structural and functional insight into an unexpectedly selective N-methyltransferase involved in plantazolicin biosynthesis: Jaeheon Lee, Yue Hao, Patricia M. Blair, Joel O. Melby, Vinayak Agarwal, Brandon J. Burkhart, Satish K. Nair, and Douglas A. Mitchell

Biophysics and Computational Biology

Statistical significance of combinatorial regulations OPEN ACCESS ARTICLE: Aika Terada, Mariko Okada-Hatakeyama, Koji Tsuda, and Jun Sese

Importance of lipid–pore loop interface for potassium channel structure and function: Elwin A. W. van der Cruijsen, Deepak Nand, Markus Weingarth, Alexander Prokofyev, Sönke Hornig, Abhishek Arun Cukkemane, Alexandre M. J. J. Bonvin, Stefan Becker, Raymond E. Hulse, Eduardo Perozo, Olaf Pongs, and Marc Baldus

Determining complete electron flow in the cofactor photoreduction of oxidized photolyase OPEN ACCESS ARTICLE: Zheyun Liu, Chuang Tan, Xunmin Guo, Jiang Li, Lijuan Wang, Aziz Sancar, and Dongping Zhong

Dynamic determination of the functional state in photolyase and the implication for cryptochrome OPEN ACCESS ARTICLE: Zheyun Liu, Meng Zhang, Xunmin Guo, Chuang Tan, Jiang Li, Lijuan Wang, Aziz Sancar, and Dongping Zhong

Testing the diffusing boundary model for the helix–coil transition in peptides OPEN ACCESS ARTICLE: Sabine Neumaier, Andreas Reiner, Maren Büttner, Beat Fierz, and Thomas Kiefhaber

Inverse Gillespie for inferring stochastic reaction mechanisms from intermittent samples: Ishanu Chattopadhyay, Anna Kuchina, Gürol M. Süel, and Hod Lipson

Role of methyl-induced polarization in ion binding: Mariana Rossi, Alexandre Tkatchenko, Susan B. Rempe, and Sameer Varma

Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2′-O-transphosphorylation: Hong Gu, Shuming Zhang, Kin-Yiu Wong, Brian K. Radak, Thakshila Dissanayake, Daniel L. Kellerman, Qing Dai, Masaru Miyagi, Vernon E. Anderson, Darrin M. York, Joseph A. Piccirilli, and Michael E. Harris

Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery: Hernani Leonardo Silvestre, Thomas L. Blundell, Chris Abell, and Alessio Ciulli

Structural insights into the proton pumping by unusual proteorhodopsin from nonmarine bacteria: Ivan Gushchin, Pavel Chervakov, Pavel Kuzmichev, Alexander N. Popov, Ekaterina Round, Valentin Borshchevskiy, Andrii Ishchenko, Lada Petrovskaya, Vladimir Chupin, Dmitry A. Dolgikh, Alexander A. Arseniev, Mikhail Kirpichnikov, and Valentin Gordeliy

Cell Biology

Activation-induced cytidine deaminase (AID) is necessary for the epithelial–mesenchymal transition in mammary epithelial cells: Denise P. Muñoz, Elbert L. Lee, Sachiko Takayama, Jean-Philippe Coppé, Seok-Jin Heo, Dario Boffelli, Javier M. Di Noia, and David I. K. Martin

Pds5 promotes and protects cohesin acetylation: Kok-Lung Chan, Thomas Gligoris, William Upcher, Yuki Kato, Katsuhiko Shirahige, Kim Nasmyth, and Frédéric Beckouët

Impaired complex IV activity in response to loss of LRPPRC function can be compensated by mitochondrial hyperfusion: Stéphane G. Rolland, Elisa Motori, Nadin Memar, Jürgen Hench, Stephan Frank, Konstanze F. Winklhofer, and Barbara Conradt

Higd-1a interacts with Opa1 and is required for the morphological and functional integrity of mitochondria: Hyun-Jung An, Geunyoung Cho, Jie-Oh Lee, Sang-Gi Paik, Young Sang Kim, and Hayyoung Lee

Interphase cytofission maintains genomic integrity of human cells after failed cytokinesis: Alka Choudhary, Robert F. Lera, Melissa L. Martowicz, Kim Oxendine, Jennifer J. Laffin, Beth A. Weaver, and Mark E. Burkard

Developmental Biology

Unique insights into maternal mitochondrial inheritance in mice: Shi-Ming Luo, Zhao-Jia Ge, Zhong-Wei Wang, Zong-Zhe Jiang, Zhen-Bo Wang, Ying-Chun Ouyang, Yi Hou, Heide Schatten, and Qing-Yuan Sun

Pattern reorganization occurs independently of cell division during Drosophila wing disc regeneration in situ OPEN ACCESS ARTICLE: Sandra Díaz-García and Antonio Baonza

Ecology

Increased transmissibility explains the third wave of infection by the 2009 H1N1 pandemic virus in England OPEN ACCESS ARTICLE: Ilaria Dorigatti, Simon Cauchemez, and Neil M. Ferguson

Recent burning of boreal forests exceeds fire regime limits of the past 10,000 years: Ryan Kelly, Melissa L. Chipman, Philip E. Higuera, Ivanka Stefanova, Linda B. Brubaker, and Feng Sheng Hu

Context-dependent hierarchies in pigeons: Máté Nagy, Gábor Vásárhelyi, Benjamin Pettit, Isabella Roberts-Mariani, Tamás Vicsek, and Dora Biro

Single pollinator species losses reduce floral fidelity and plant reproductive function: Berry J. Brosi and Heather M. Briggs

Agent-based Bayesian approach to monitoring the progress of invasive species eradication programs OPEN ACCESS ARTICLE: Jonathan M. Keith and Daniel Spring

Evolution

Capturing the mutational landscape of the beta-lactamase TEM-1: Hervé Jacquier, André Birgy, Hervé Le Nagard, Yves Mechulam, Emmanuelle Schmitt, Jérémy Glodt, Beatrice Bercot, Emmanuelle Petit, Julie Poulain, Guilène Barnaud, Pierre-Alexis Gros, and Olivier Tenaillon

Immunology

Paradoxical role of the proto-oncogene Axl and Mer receptor tyrosine kinases in colon cancer: Lidia Bosurgi, Jochem H. Bernink, Victor Delgado Cuevas, Nicola Gagliani, Leonel Joannas, Edward T. Schmid, Carmen J. Booth, Sourav Ghosh, and Carla V. Rothlin

Regulation of adipose tissue T cell subsets by Stat3 is crucial for diet-induced obesity and insulin resistance: Saul J. Priceman, Maciej Kujawski, Shudan Shen, Gregory A. Cherryholmes, Heehyoung Lee, Chunyan Zhang, Laura Kruper, Joanne Mortimer, Richard Jove, Arthur D. Riggs, and Hua Yu

Dietary gluten triggers concomitant activation of CD4⁺ and CD8⁺ αβ T cells and γδ T cells in celiac disease OPEN ACCESS ARTICLE: Arnold Han, Evan W. Newell, Jacob Glanville, Nielsen Fernandez-Becker, Chaitan Khosla, Yueh-hsiu Chien, and Mark M. Davis

Inflammatory monocytes are potent antitumor effectors controlled by regulatory CD4⁺ T cells: Arnaud Pommier, Alexandra Audemard, Aurélie Durand, Renée Lengagne, Arnaud Delpoux, Bruno Martin, Laetitia Douguet, Armelle Le Campion, Masashi Kato, Marie-Françoise Avril, Cédric Auffray, Bruno Lucas, and Armelle Prévost-Blondel

HLA targeting efficiency correlates with human T-cell response magnitude and with mortality from influenza A infection OPEN ACCESS ARTICLE: Tomer Hertz, Christine M. Oshansky, Philippa L. Roddam, John P. DeVincenzo, Miguela A. Caniza, Nebojsa Jojic, Simon Mallal, Elizabeth Phillips, Ian James, M. Elizabeth Halloran, Paul G. Thomas, and Lawrence Corey

Advertisements impact the physiological efficacy of a branded drug: Emir Kamenica, Robert Naclerio, and Anup Malani

Medical Sciences

Macrophage migration inhibitory factor (MIF) is a critical mediator of the innate immune response to Mycobacterium tuberculosis: Rituparna Das, Mi-Sun Koo, Bae Hoon Kim, Shevin T. Jacob, Selvakumar Subbian, Jie Yao, Lin Leng, Rebecca Levy, Charles Murchison, William J. Burman, Christopher C. Moore, W. Michael Scheld, John R. David, Gilla Kaplan, John D. MacMicking, and Richard Bucala

Monovalent antibody design and mechanism of action of onartuzumab, a MET antagonist with anti-tumor activity as a therapeutic agent OPEN ACCESS ARTICLE: Mark Merchant, Xiaolei Ma, Henry R. Maun, Zhong Zheng, Jing Peng, Mally Romero, Arthur Huang, Nai-ying Yang, Merry Nishimura, Joan Greve, Lydia Santell, Yu-Wen Zhang, Yanli Su, Dafna W. Kaufman, Karen L. Billeci, Elaine Mai, Barbara Moffat, Amy Lim, Eileen T. Duenas, Heidi S. Phillips, Hong Xiang, Judy C. Young, George F. Vande Woude, Mark S. Dennis, Dorothea E. Reilly, Ralph H. Schwall, Melissa A. Starovasnik, Robert A. Lazarus, and Daniel G. Yansura

Bispecific antibodies directed to CD4 domain 2 and HIV envelope exhibit exceptional breadth and picomolar potency against HIV-1: Craig S. Pace, Ruijiang Song, Christina Ochsenbauer, Chasity D. Andrews, David Franco, Jian Yu, Deena A. Oren, Michael S. Seaman, and David D. Ho

Exosome-mediated transmission of hepatitis C virus between human hepatoma Huh7.5 cells: Vedashree Ramakrishnaiah, Christine Thumann, Isabel Fofana, Francois Habersetzer, Qiuwei Pan, Petra E. de Ruiter, Rob Willemsen, Jeroen A. A. Demmers, Victor Stalin Raj, Guido Jenster, Jaap Kwekkeboom, Hugo W. Tilanus, Bart L. Haagmans, Thomas F. Baumert, and Luc J. W. van der Laan

Microbiology

Sulfatase-activated fluorophores for rapid discrimination of mycobacterial species and strains: Kimberly E. Beatty, Monique Williams, Brian L. Carlson, Benjamin M. Swarts, Robin M. Warren, Paul D. van Helden, and Carolyn R. Bertozzi

A riboswitch-regulated antisense RNA in Listeria monocytogenes OPEN ACCESS ARTICLE: J. R. Mellin, Teresa Tiensuu, Christophe Bécavin, Edith Gouin, Jörgen Johansson, and Pascale Cossart

Rapid and robust signaling in the CsrA cascade via RNA–protein interactions and feedback regulation: David Nellinger Adamson and Han N. Lim

Homologous 2′,5′-phosphodiesterases from disparate RNA viruses antagonize antiviral innate immunity: Rong Zhang, Babal K. Jha, Kristen M. Ogden, Beihua Dong, Ling Zhao, Ruth Elliott, John T. Patton, Robert H. Silverman, and Susan R. Weiss

Nucleosome maps of the human cytomegalovirus genome reveal a temporal switch in chromatin organization linked to a major IE protein: Einat Zalckvar, Christina Paulus, Desiree Tillo, Alexandra Asbach-Nitzsche, Yaniv Lubling, Carla Winterling, Nicholas Strieder, Katrin Mücke, Felicia Goodrum, Eran Segal, and Michael Nevels

Neuroscience

In vivo synaptic recovery following optogenetic hyperstimulation: Maike Kittelmann, Jana F. Liewald, Jan Hegermann, Christian Schultheis, Martin Brauner, Wagner Steuer Costa, Sebastian Wabnig, Stefan Eimer, and Alexander Gottschalk

Adult pallium transcriptomes surprise in not reflecting predicted homologies across diverse chicken and mouse pallial sectors OPEN ACCESS ARTICLE: T. Grant Belgard, Juan F. Montiel, Wei Zhi Wang, Fernando García-Moreno, Elliott H. Margulies, Chris P. Ponting, and Zoltán Molnár

Oscillatory activity in the monkey hippocampus during visual exploration and memory formation: Michael J. Jutras, Pascal Fries, and Elizabeth A. Buffalo

Neuropathic and inflammatory pain are modulated by tuberoinfundibular peptide of 39 residues: Eugene L. Dimitrov, Jonathan Kuo, Kenji Kohno, and Ted B. Usdin

Stimulus-dependent variability and noise correlations in cortical MT neurons: Adrián Ponce-Alvarez, Alexander Thiele, Thomas D. Albright, Gene R. Stoner, and Gustavo Deco

Synthesizing cognition in neuromorphic electronic systems: Emre Neftci, Jonathan Binas, Ueli Rutishauser, Elisabetta Chicca, Giacomo Indiveri, and Rodney J. Douglas

Targeting H3K4 trimethylation in Huntington disease: Malini Vashishtha, Christopher W. Ng, Ferah Yildirim, Theresa A. Gipson, Ian H. Kratter, Laszlo Bodai, Wan Song, Alice Lau, Adam Labadorf, Annie Vogel-Ciernia, Juan Troncosco, Christopher A. Ross, Gillian P. Bates, Dimitri Krainc, Ghazaleh Sadri-Vakili, Steven Finkbeiner, J. Lawrence Marsh, David E. Housman, Ernest Fraenkel, and Leslie M. Thompson

Physiology

Shear stress activation of nuclear receptor PXR in endothelial detoxification: Xiaohong Wang, Xi Fang, Jing Zhou, Zhen Chen, Beilei Zhao, Lei Xiao, Ao Liu, Yi-Shuan J. Li, John Y.-J. Shyy, Youfei Guan, Shu Chien, and Nanping Wang

Ca²⁺ release-activated Ca²⁺ channel blockade as a potential tool in antipancreatitis therapy OPEN ACCESS ARTICLE: Julia V. Gerasimenko, Oleksiy Gryshchenko, Pawel E. Ferdek, Eloise Stapleton, Tania O. G. Hébert, Solomiia Bychkova, Shuang Peng, Malcolm Begg, Oleg V. Gerasimenko, and Ole H. Petersen

Ion channel-kinase TRPM7 is required for maintaining cardiac automaticity: Rajan Sah, Pietro Mesirca, Marjolein Van den Boogert, Jonathan Rosen, John Mably, Matteo E. Mangoni, and David E. Clapham

Plant Biology

Single-particle analysis reveals shutoff control of the Arabidopsis ammonium transporter AMT1;3 by clustering and internalization OPEN ACCESS ARTICLE: Qinli Wang, Yuanyuan Zhao, Wangxi Luo, Ruili Li, Qihua He, Xiaohong Fang, Roberto De Michele, Cindy Ast, Nicolaus von Wirén, and Jinxing Lin

Ultradian metabolic rhythm in the diazotrophic cyanobacterium Cyanothece sp. ATCC 51142: Jan Červený, Maria A. Sinetova, Luis Valledor, Louis A. Sherman, and Ladislav Nedbal

Convergence of auxin and gibberellin signaling on the regulation of the GATA transcription factors GNC and GNL in Arabidopsis thaliana: René Richter, Carina Behringer, Melina Zourelidou, and Claus Schwechheimer

Six-rowed spike4 (Vrs4) controls spikelet determinacy and row-type in barley OPEN ACCESS ARTICLE: Ravi Koppolu, Nadia Anwar, Shun Sakuma, Akemi Tagiri, Udda Lundqvist, Mohammad Pourkheirandish, Twan Rutten, Christiane Seiler, Axel Himmelbach, Ruvini Ariyadasa, Helmy Mohamad Youssef, Nils Stein, Nese Sreenivasulu, Takao Komatsuda, and Thorsten Schnurbusch

Psychological and Cognitive Sciences

Bottlenose dolphins can use learned vocal labels to address each other: Stephanie L. King and Vincent M. Janik

Systems Biology

Intrinsic gray-matter connectivity of the brain in adults with autism spectrum disorder OPEN ACCESS ARTICLE: Christine Ecker, Lisa Ronan, Yue Feng, Eileen Daly, Clodagh Murphy, Cedric E. Ginestet, Michael Brammer, Paul C. Fletcher, Edward T. Bullmore, John Suckling, Simon Baron-Cohen, Steve Williams, Eva Loth, MRC AIMS Consortium, and Declan G. M. Murphy

Corrections