Fwd: PNAS Early Edition for 18 Jun 2015

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Subject: PNAS Early Edition for 18 Jun 2015
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Proceedings of the National Academy of Sciences Early Edition articles for 18 June 2015 Editorial Impact, not impact factor Inder M. Verma Letters (Online Only) Improving efficacy of the combination between antiangiogenic and chemotherapy: Time for mathematical modeling support Joseph Ciccolini, Sébastien Benzekry, Bruno Lacarelle, Dominique Barbolosi, and Fabrice Barlési Reply to Ciccolini et al.: Using mathematical modeling to predict response to antiangiogenic therapy in cancer patients Dan G. Duda, Rebecca S. Heist, Dushyant V. Sahani, Triantafyllos Stylianopoulos, Jeffrey A. Engelman, and Rakesh K. Jain Correlation does not equal causation: Questioning the Great Cahokia Flood Sarah E. Baires, Melissa R. Baltus, and Meghan E. Buchanan Reply to Baires et al.: Shifts in Mississippi River flood regime remain a contributing factor to Cahokia's emergence and decline Samuel E. Munoz, Kristine E. Gruley, David A. Fike, Sissel Schroeder, and John W. Williams Attenuation of dengue (and other RNA viruses) with codon pair recoding can be explained by increased CpG/UpA dinucleotide frequencies Peter Simmonds, Fiona Tulloch, David J. Evans, and Martin D. Ryan Reply to Simmonds et al.: Codon pair and dinucleotide bias have not been functionally distinguished Bruce Futcher, Oleksandr Gorbatsevych, Sam H. Shen, Charles B. Stauft, Yutong Song, Bingyin Wang, Janet Leatherwood, Justin Gardin, Alisa Yurovsky, Steffen Mueller, and Eckard Wimmer Commentaries Discovery of another anti-HIV protein in the search for the CD8+ cell anti-HIV Factor Jay A. Levy African mammals, foodwebs, and coexistence David Tilman and Elizabeth T. Borer The Dynamics of Change in Multiethnic Societies Special Feature (free online) Early Bronze Age migrants and ethnicity in the Middle Eastern mountain zone Mitchell S. Rothman Physical Sciences Applied Mathematics Iterative experiment design guides the characterization of a light-inducible gene expression circuit Jakob Ruess, Francesca Parise, Andreas Milias-Argeitis, Mustafa Khammash, and John Lygeros Applied Physical Sciences Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes Edouard Hannezo, Bo Dong, Pierre Recho, Jean-François Joanny, and Shigeo Hayashi Chemistry Influence of support morphology on the bonding of molecules to nanoparticles Chi Ming Yim, Chi L. Pang, Diego R. Hermoso, Coinneach M. Dover, Christopher A. Muryn, Francesco Maccherozzi, Sarnjeet S. Dhesi, Rubén Pérez, and Geoff Thornton Amorphous oxide alloys as interfacial layers with broadly tunable electronic structures for organic photovoltaic cells Nanjia Zhou, Myung-Gil Kim, Stephen Loser, Jeremy Smith, Hiroyuki Yoshida, Xugang Guo, Charles Song, Hosub Jin, Zhihua Chen, Seok Min Yoon, Arthur J. Freeman, Robert P. H. Chang, Antonio Facchetti, and Tobin J. Marks Mapping fast protein folding with multiple-site fluorescent probes Maxim B. Prigozhin, Shu-Han Chao, Shahar Sukenik, Taras V. Pogorelov, and Martin Gruebele Earth, Atmospheric, and Planetary Sciences High-dose vitamin D3 reduces deficiency caused by low UVB exposure and limits HIV-1 replication in urban Southern Africans  Anna K. Coussens, Celeste E. Naude, Rene Goliath, George Chaplin, Robert J. Wilkinson, and Nina G. Jablonski Extreme ecosystem instability suppressed tropical dinosaur dominance for 30 million years Jessica H. Whiteside, Sofie Lindström, Randall B. Irmis, Ian J. Glasspool, Morgan F. Schaller, Maria Dunlavey, Sterling J. Nesbitt, Nathan D. Smith, and Alan H. Turner Engineering Rescaling of metal oxide nanocrystals for energy storage having high capacitance and energy density with robust cycle life Hyung Mo Jeong, Kyung Min Choi, Tao Cheng, Dong Ki Lee, Renjia Zhou, Il Woo Ock, Delia J. Milliron, William A. Goddard III, and Jeung Ku Kang Osborne Reynolds pipe flow: Direct simulation from laminar through gradual transition to fully developed turbulence  Xiaohua Wu, Parviz Moin, Ronald J. Adrian, and Jon R. Baltzer Mathematics Functional organization of the human 4D Nucleome  Haiming Chen, Jie Chen, Lindsey A. Muir, Scott Ronquist, Walter Meixner, Mats Ljungman, Thomas Ried, Stephen Smale, and Indika Rajapakse Physics Opacity and conductivity measurements in noble gases at conditions of planetary and stellar interiors R. Stewart McWilliams, D. Allen Dalton, Zuzana Konôpková, Mohammad F. Mahmood, and Alexander F. Goncharov Statistics Posterior predictive checks to quantify lack-of-fit in admixture models of latent population structure  David Mimno, David M. Blei, and Barbara E. Engelhardt Social Sciences Economic Sciences Nazi indoctrination and anti-Semitic beliefs in Germany Nico Voigtländer and Hans-Joachim Voth Environmental Sciences Green spaces and cognitive development in primary schoolchildren Payam Dadvand, Mark J. Nieuwenhuijsen, Mikel Esnaola, Joan Forns, Xavier Basagaña, Mar Alvarez-Pedrerol, Ioar Rivas, Mónica López-Vicente, Montserrat De Castro Pascual, Jason Su, Michael Jerrett, Xavier Querol, and Jordi Sunyer A century of sprawl in the United States Christopher Barrington-Leigh and Adam Millard-Ball Sustainability Science Political influences on greenhouse gas emissions from US states  Thomas Dietz, Kenneth A. Frank, Cameron T. Whitley, Jennifer Kelly, and Rachel Kelly Quantitative methods of identifying the key nodes in the illegal wildlife trade network Nikkita Gunvant Patel, Chris Rorres, Damien O. Joly, John S. Brownstein, Ray Boston, Michael Z. Levy, and Gary Smith Biological Sciences Anthropology On some genetic consequences of social structure, mating systems, dispersal, and sampling Bárbara R. Parreira and Lounès Chikhi Biochemistry Arginine methylation of HSP70 regulates retinoid acid-mediated RARβ2 gene activation Wei-wei Gao, Rong-quan Xiao, Bing-ling Peng, Huan-teng Xu, Hai-feng Shen, Ming-feng Huang, Tao-tao Shi, Jia Yi, Wen-juan Zhang, Xiao-nan Wu, Xiang Gao, Xiang-zhi Lin, Pieter C. Dorrestein, Michael G. Rosenfeld, and Wen Liu MPE-seq, a new method for the genome-wide analysis of chromatin structure Haruhiko Ishii, James T. Kadonaga, and Bing Ren A universal entropy-driven mechanism for thioredoxin–target recognition Prakash B. Palde and Kate S. Carroll Mediation of donor–acceptor distance in an enzymatic methyl transfer reaction Jianyu Zhang, Heather J. Kulik, Todd J. Martinez, and Judith P. Klinman Biophysics and Computational Biology Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes Edouard Hannezo, Bo Dong, Pierre Recho, Jean-François Joanny, and Shigeo Hayashi Mapping fast protein folding with multiple-site fluorescent probes Maxim B. Prigozhin, Shu-Han Chao, Shahar Sukenik, Taras V. Pogorelov, and Martin Gruebele Analysis of the size dependence of macromolecular crowding shows that smaller is better  Kim A. Sharp Cell Biology Ras-GTP dimers activate the Mitogen-Activated Protein Kinase (MAPK) pathway  Xiaolin Nan, Tanja M. Tamgüney, Eric A. Collisson, Li-Jung Lin, Cameron Pitt, Jacqueline Galeas, Sophia Lewis, Joe W. Gray, Frank McCormick, and Steven Chu Epidermal TRPM8 channel isoform controls the balance between keratinocyte proliferation and differentiation in a cold-dependent manner Gabriel Bidaux, Anne-sophie Borowiec, Dmitri Gordienko, Benjamin Beck, George G. Shapovalov, Loïc Lemonnier, Matthieu Flourakis, Matthieu Vandenberghe, Christian Slomianny, Etienne Dewailly, Philippe Delcourt, Emilie Desruelles, Abigaël Ritaine, Renata Polakowska, Jean Lesage, Mounia Chami, Roman Skryma, and Natalia Prevarskaya A set of NF-κB–regulated microRNAs induces acquired TRAIL resistance in Lung cancer Young-Jun Jeon, Justin Middleton, Taewan Kim, Alessandro Laganà, Claudia Piovan, Paola Secchiero, Gerard J. Nuovo, Ri Cui, Pooja Joshi, Giulia Romano, Gianpiero Di Leva, Bum-Kyu Lee, Hui-Lung Sun, Yonghwan Kim, Paolo Fadda, Hansjuerg Alder, Michela Garofalo, and Carlo M. Croce Nuclear matrix-associated protein SMAR1 regulates alternative splicing via HDAC6-mediated deacetylation of Sam68  Kiran Kumar Nakka, Nidhi Chaudhary, Shruti Joshi, Jyotsna Bhat, Kulwant Singh, Subhrangsu Chatterjee, Renu Malhotra, Abhijit De, Manas Kumar Santra, F. Jeffrey Dilworth, and Samit Chattopadhyay Self-repairing symmetry in jellyfish through mechanically driven reorganization  Michael J. Abrams, Ty Basinger, William Yuan, Chin-Lin Guo, and Lea Goentoro Developmental Biology Functional organization of the human 4D Nucleome  Haiming Chen, Jie Chen, Lindsey A. Muir, Scott Ronquist, Walter Meixner, Mats Ljungman, Thomas Ried, Stephen Smale, and Indika Rajapakse Ecology Light-driven synchrony of Prochlorococcus growth and mortality in the subtropical Pacific gyre Francois Ribalet, Jarred Swalwell, Sophie Clayton, Valeria Jiménez, Sebastian Sudek, Yajuan Lin, Zackary I. Johnson, Alexandra Z. Worden, and E. Virginia Armbrust Successional dynamics in Neotropical forests are as uncertain as they are predictable Natalia Norden, Héctor A. Angarita, Frans Bongers, Miguel Martínez-Ramos, Iñigo Granzow-de la Cerda, Michiel van Breugel, Edwin Lebrija-Trejos, Jorge A. Meave, John Vandermeer, G. Bruce Williamson, Bryan Finegan, Rita Mesquita, and Robin L. Chazdon Environmental Sciences Green spaces and cognitive development in primary schoolchildren Payam Dadvand, Mark J. Nieuwenhuijsen, Mikel Esnaola, Joan Forns, Xavier Basagaña, Mar Alvarez-Pedrerol, Ioar Rivas, Mónica López-Vicente, Montserrat De Castro Pascual, Jason Su, Michael Jerrett, Xavier Querol, and Jordi Sunyer Evolution Parental care buffers against inbreeding depression in burying beetles Natalie Pilakouta, Seonaidh Jamieson, Jacob A. Moorad, and Per T. Smiseth Mx1 and Mx2 key antiviral proteins are surprisingly lost in toothed whales  Benjamin A. Braun, Amir Marcovitz, J. Gray Camp, Robin Jia, and Gill Bejerano Extreme ecosystem instability suppressed tropical dinosaur dominance for 30 million years Jessica H. Whiteside, Sofie Lindström, Randall B. Irmis, Ian J. Glasspool, Morgan F. Schaller, Maria Dunlavey, Sterling J. Nesbitt, Nathan D. Smith, and Alan H. Turner Genetics Reduction of toxic RNAs in myotonic dystrophies type 1 and type 2 by the RNA helicase p68/DDX5  Karlie Jones, Christina Wei, Benedikt Schoser, Giovanni Meola, Nikolai Timchenko, and Lubov Timchenko Next-generation libraries for robust RNA interference-based genome-wide screens Martin Kampmann, Max A. Horlbeck, Yuwen Chen, Jordan C. Tsai, Michael C. Bassik, Luke A. Gilbert, Jacqueline E. Villalta, S. Chul Kwon, Hyeshik Chang, V. Narry Kim, and Jonathan S. Weissman Immunology and Inflammation Inflammation induces dermal Vγ4+ γδT17 memory-like cells that travel to distant skin and accelerate secondary IL-17–driven responses Francisco Ramírez-Valle, Elizabeth E. Gray, and Jason G. Cyster Medical Sciences COX/mPGES-1/PGE2 pathway depicts an inflammatory-dependent high-risk neuroblastoma subset  Karin Larsson, Anna Kock, Helena Idborg, Marie Arsenian Henriksson, Tommy Martinsson, John I. Johnsen, Marina Korotkova, Per Kogner, and Per-Johan Jakobsson Dysplastic spondylolysis is caused by mutations in the diastrophic dysplasia sulfate transporter gene Tao Cai, Liu Yang, Wanshi Cai, Sen Guo, Ping Yu, Jinchen Li, Xueyu Hu, Ming Yan, Qianzhi Shao, Yan Jin, Zhong Sheng Sun, and Zhuo-Jing Luo High-dose vitamin D3 reduces deficiency caused by low UVB exposure and limits HIV-1 replication in urban Southern Africans  Anna K. Coussens, Celeste E. Naude, Rene Goliath, George Chaplin, Robert J. Wilkinson, and Nina G. Jablonski Deregulation of the Hippo pathway in soft-tissue sarcoma promotes FOXM1 expression and tumorigenesis T. S. Karin Eisinger-Mathason, Vera Mucaj, Kevin M. Biju, Michael S. Nakazawa, Mercy Gohil, Timothy P. Cash, Sam S. Yoon, Nicolas Skuli, Kyung Min Park, Sharon Gerecht, and M. Celeste Simon PRUNE2 is a human prostate cancer suppressor regulated by the intronic long noncoding RNA PCA3  Ahmad Salameh, Alessandro K. Lee, Marina Cardó-Vila, Diana N. Nunes, Eleni Efstathiou, Fernanda I. Staquicini, Andrey S. Dobroff, Serena Marchiò, Nora M. Navone, Hitomi Hosoya, Richard C. Lauer, Sijin Wen, Carolina C. Salmeron, Anh Hoang, Irene Newsham, Leandro A. Lima, Dirce M. Carraro, Salvatore Oliviero, Mikhail G. Kolonin, Richard L. Sidman, Kim-Anh Do, Patricia Troncoso, Christopher J. Logothetis, Ricardo R. Brentani, George A. Calin, Webster K. Cavenee, Emmanuel Dias-Neto, Renata Pasqualini, and Wadih Arap Inherited chromosomally integrated human herpesvirus 6 as a predisposing risk factor for the development of angina pectoris Annie Gravel, Isabelle Dubuc, Guillaume Morissette, Ruth H. Sedlak, Keith R. Jerome, and Louis Flamand Microbiology Streptococcus pneumoniae secretes hydrogen peroxide leading to DNA damage and apoptosis in lung cells  Prashant Rai, Marcus Parrish, Ian Jun Jie Tay, Na Li, Shelley Ackerman, Fang He, Jimmy Kwang, Vincent T. Chow, and Bevin P. Engelward Rationally designed chemokine-based toxin targeting the viral G protein-coupled receptor US28 potently inhibits cytomegalovirus infection in vivo  Katja Spiess, Mads G. Jeppesen, Mikkel Malmgaard-Clausen, Karen Krzywkowski, Kalpana Dulal, Tong Cheng, Gertrud M. Hjortø, Olav Larsen, John S. Burg, Michael A. Jarvis, K. Christopher Garcia, Hua Zhu, Thomas N. Kledal, and Mette M. Rosenkilde Three cyanobacteriochromes work together to form a light color-sensitive input system for c-di-GMP signaling of cell aggregation Gen Enomoto, Ni-Ni-Win, Rei Narikawa, and Masahiko Ikeuchi Hemocyte differentiation mediates the mosquito late-phase immune response against Plasmodium in Anopheles gambiae Ryan C. Smith, Carolina Barillas-Mury, and Marcelo Jacobs-Lorena CRISPR-based screening of genomic island excision events in bacteria  Kurt Selle, Todd R. Klaenhammer, and Rodolphe Barrangou Neuroscience Dynamic reorganization of human resting-state networks during visuospatial attention Sara Spadone, Stefania Della Penna, Carlo Sestieri, Viviana Betti, Annalisa Tosoni, Mauro Gianni Perrucci, Gian Luca Romani, and Maurizio Corbetta Dynamics of the echolocation beam during prey pursuit in aerial hawking bats  Lasse Jakobsen, Mads Nedergaard Olsen, and Annemarie Surlykke Cells transplanted onto the surface of the glial scar reveal hidden potential for functional neural regeneration  Tetsuji Sekiya, Matthew C. Holley, Kento Hashido, Kazuya Ono, Koichiro Shimomura, Rie T. Horie, Kiyomi Hamaguchi, Atsuhiro Yoshida, Tatsunori Sakamoto, and Juichi Ito Activation of peroxisome proliferator-activated receptor α stimulates ADAM10-mediated proteolysis of APP Grant T. Corbett, Frank J. Gonzalez, and Kalipada Pahan Transcriptomics of critical period of visual cortical plasticity in mice Jamie Benoit, Albert E. Ayoub, and Pasko Rakic Muscarinic regulation of dopamine and glutamate transmission in the nucleus accumbens  Jung Hoon Shin, Martín F. Adrover, Jürgen Wess, and Veronica A. Alvarez Plant Biology The bHLH transcription factor BIS1 controls the iridoid branch of the monoterpenoid indole alkaloid pathway in Catharanthus roseus Alex Van Moerkercke, Priscille Steensma, Fabian Schweizer, Jacob Pollier, Ivo Gariboldi, Richard Payne, Robin Vanden Bossche, Karel Miettinen, Javiera Espoz, Purin Candra Purnama, Franziska Kellner, Tuulikki Seppänen-Laakso, Sarah E. O'Connor, Heiko Rischer, Johan Memelink, and Alain Goossens Population Biology Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese Tao Luo, Iñaki Comas, Dan Luo, Bing Lu, Jie Wu, Lanhai Wei, Chongguang Yang, Qingyun Liu, Mingyu Gan, Gang Sun, Xin Shen, Feiying Liu, Sebastien Gagneux, Jian Mei, Rushu Lan, Kanglin Wan, and Qian Gao Posterior predictive checks to quantify lack-of-fit in admixture models of latent population structure  David Mimno, David M. Blei, and Barbara E. Engelhardt Psychological and Cognitive Sciences Melodic sound enhances visual awareness of congruent musical notes, but only if you can read music  Minyoung Lee, Randolph Blake, Sujin Kim, and Chai-Youn Kim Unifying account of visual motion and position perception  Oh-Sang Kwon, Duje Tadin, and David C. Knill Systems Biology Iterative experiment design guides the characterization of a light-inducible gene expression circuit Jakob Ruess, Francesca Parise, Andreas Milias-Argeitis, Mustafa Khammash, and John Lygeros Corrections Correction for Kozakov et al., Ligand deconstruction: Why some fragment binding positions are conserved and others are not Correction for Talantova et al., Aβ induces astrocytic glutamate release, extrasynaptic NMDA receptor activation, and synaptic loss Correction for Dance, News Feature: Building benchtop human models SI Correction Correction to Supporting Information for Bacon et al., Biological evidence supports an early and complex emergence of the Isthmus of Panama Correction to Supporting Information for Pérez-Mendoza et al., Novel mixed-linkage β-glucan activated by c-di-GMP in Sinorhizobium meliloti Open Access From the Cover Inaugural Article Classic Cozzarelli Prize Winner Front Matter This message was sent to pascal.alter@gmail.com. (...) 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