Cień dnia (1): Fwd: PNAS Table of Contents for 23 July 2013; Vol. 110, No. 30

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Subject: PNAS Table of Contents for 23 July 2013; Vol. 110, No. 30
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Proceedings of the National Academy of Sciences

23 July 2013; Vol. 110, No. 30

This Week in PNAS

In This Issue

Letters (Online Only)

Valuable oil sands environmental research raises several questions: Steve E. Hrudey

Reply to Hrudey: Tracking the extent of oil sands airborne pollution: Joshua Kurek, Jane L. Kirk, Derek C. G. Muir, Xiaowa Wang, Marlene S. Evans, and John P. Smol

Viral underpinning to the Austrian record of type 2 diabetes?: William Klitz and Bo Niklasson

Reply to Klitz and Niklasson: Can viral infections explain the cross-sectional Austrian diabetes data?: Stefan Thurner, Peter Klimek, Michael Szell, Georg Duftschmid, Gottfried Endel, Alexandra Kautzky-Willer, and David C. Kasper

Opinion

Transdisciplinary electric power grid science: Charles D. Brummitt, Paul D. H. Hines, Ian Dobson, Cristopher Moore, and Raissa M. D'Souza

QnAs

QnAs with Arthur Beaudet: Prashant Nair

Commentaries

Hearing the shape of a room: Mark D. Plumbley

Adaptation of fibrous biopolymers to recurring increasing strains: John W. Weisel and Rustem I. Litvinov

Insight into the unknown marine virus majority: Alexander I. Culley

Anciently duplicated genes reduce uncertainty in molecular clock estimates: Olga Zhaxybayeva

PNAS Plus Significance Statements

PNAS Plus Significance Statements

Physical Sciences

Applied Mathematics

Single-photon sampling architecture for solid-state imaging sensors: Ewout van den Berg, Emmanuel Candès, Garry Chinn, Craig Levin, Peter Demetri Olcott, and Carlos Sing-Long

The counterbend phenomenon in flagellar axonemes and cross-linked filament bundles: Hermes Gadêlha, Eamonn A. Gaffney, and Alain Goriely

Acoustic echoes reveal room shape OPEN ACCESS ARTICLE: Ivan Dokmanić, Reza Parhizkar, Andreas Walther, Yue M. Lu, and Martin Vetterli

Applied Physical Sciences

Ultrahigh-resolution imaging reveals formation of neuronal SNARE/Munc18 complexes in situ: Alexandros Pertsinidis, Konark Mukherjee, Manu Sharma, Zhiping P. Pang, Sang Ryul Park, Yunxiang Zhang, Axel T. Brunger, Thomas C. Südhof, and Steven Chu

Molecule-hugging graphene nanopores: Slaven Garaj, Song Liu, Jene A. Golovchenko, and Daniel Branton

Strain history dependence of the nonlinear stress response of fibrin and collagen networks: Stefan Münster, Louise M. Jawerth, Beverly A. Leslie, Jeffrey I. Weitz, Ben Fabry, and David A. Weitz

Graphene microsheets enter cells through spontaneous membrane penetration at edge asperities and corner sites: Yinfeng Li, Hongyan Yuan, Annette von dem Bussche, Megan Creighton, Robert H. Hurt, Agnes B. Kane, and Huajian Gao

Chemistry

Evolutionary diversification of the multimeric states of proteins: Michael Lynch

Spatiotemporal control and superselectivity in supramolecular polymers using multivalency OPEN ACCESS ARTICLE: Lorenzo Albertazzi, Francisco J. Martinez-Veracoechea, Christianus M. A. Leenders, Ilja K. Voets, Daan Frenkel, and E. W. Meijer

Liquid–liquid transition in supercooled water suggested by microsecond simulations: Yaping Li, Jicun Li, and Feng Wang

Earth, Atmospheric, and Planetary Sciences

Comparison of geomechanical deformation induced by megatonne-scale CO₂ storage at Sleipner, Weyburn, and In Salah OPEN ACCESS ARTICLE: James P. Verdon, J.-Michael Kendall, Anna L. Stork, R. Andy Chadwick, Don J. White, and Rob C. Bissell

Universal fractal scaling in stream chemistry and its implications for solute transport and water quality trend detection: James W. Kirchner and Colin Neal

Downscaling CMIP5 climate models shows increased tropical cyclone activity over the 21st century: Kerry A. Emanuel

Evidence for a water system transition beneath Thwaites Glacier, West Antarctica OPEN ACCESS ARTICLE: Dustin M. Schroeder, Donald D. Blankenship, and Duncan A. Young

Engineering

Recycling rice husks for high-capacity lithium battery anodes: Dae Soo Jung, Myung-Hyun Ryou, Yong Joo Sung, Seung Bin Park, and Jang Wook Choi

A small animal Raman instrument for rapid, wide-area, spectroscopic imaging: Sarah E. Bohndiek, Ashwin Wagadarikar, Cristina L. Zavaleta, Dominique Van de Sompel, Ellis Garai, Jesse V. Jokerst, Siavash Yazdanfar, and Sanjiv S. Gambhir

Physics

Universal sheet resistance and revised phase diagram of the cuprate high-temperature superconductors: Neven Barišić, Mun K. Chan, Yuan Li, Guichuan Yu, Xudong Zhao, Martin Dressel, Ana Smontara, and Martin Greven

Statistics

Evaluation of mixed-source, low-template DNA profiles in forensic science OPEN ACCESS ARTICLE: David J. Balding

Quantitative trait analysis in sequencing studies under trait-dependent sampling OPEN ACCESS ARTICLE: Dan-Yu Lin, Donglin Zeng, and Zheng-Zheng Tang

Biclustering with heterogeneous variance OPEN ACCESS ARTICLE: Guanhua Chen, Patrick F. Sullivan, and Michael R. Kosorok

Social Sciences

Environmental Sciences

Economic repercussions of fisheries-induced evolution OPEN ACCESS ARTICLE: Anne Maria Eikeset, Andries Richter, Erin S. Dunlop, Ulf Dieckmann, and Nils Chr. Stenseth

Social Sciences

Within-mother analysis of seasonal patterns in health at birth: Janet Currie and Hannes Schwandt

Biological Sciences

Biochemistry

Ex-527 inhibits Sirtuins by exploiting their unique NAD⁺-dependent deacetylation mechanism: Melanie Gertz, Frank Fischer, Giang Thi Tuyet Nguyen, Mahadevan Lakshminarasimhan, Mike Schutkowski, Michael Weyand, and Clemens Steegborn

Thermodynamic framework for identifying free energy inventories of enzyme catalytic cycles: Stephen D. Fried and Steven G. Boxer

Extrahelical (CAG)/(CTG) triplet repeat elements support proliferating cell nuclear antigen loading and MutLα endonuclease activation OPEN ACCESS ARTICLE: Anna Pluciennik, Vickers Burdett, Celia Baitinger, Ravi R. Iyer, Kevin Shi, and Paul Modrich

Blasticidin S inhibits translation by trapping deformed tRNA on the ribosome: Egor Svidritskiy, Clarence Ling, Dmitri N. Ermolenko, and Andrei A. Korostelev

tRNA tK^UUU, tQ^UUG, and tE^UUC wobble position modifications fine-tune protein translation by promoting ribosome A-site binding OPEN ACCESS ARTICLE: Vanessa Anissa Nathalie Rezgui, Kshitiz Tyagi, Namit Ranjan, Andrey L. Konevega, Joerg Mittelstaet, Marina V. Rodnina, Matthias Peter, and Patrick G. A. Pedrioli

Biophysics and Computational Biology

Thermodynamic origins of protein folding, allostery, and capsid formation in the human hepatitis B virus core protein OPEN ACCESS ARTICLE: Crispin G. Alexander, Maike C. Jürgens, Dale A. Shepherd, Stefan M. V. Freund, Alison E. Ashcroft, and Neil Ferguson

Deciphering the rules by which 5′-UTR sequences affect protein expression in yeast: Shlomi Dvir, Lars Velten, Eilon Sharon, Danny Zeevi, Lucas B. Carey, Adina Weinberger, and Eran Segal

Isolated pseudo–RNA-recognition motifs of SR proteins can regulate splicing using a noncanonical mode of RNA recognition: Antoine Cléry, Rahul Sinha, Olga Anczuków, Anna Corrionero, Ahmed Moursy, Gerrit M. Daubner, Juan Valcárcel, Adrian R. Krainer, and Frédéric H.-T. Allain

The counterbend phenomenon in flagellar axonemes and cross-linked filament bundles: Hermes Gadêlha, Eamonn A. Gaffney, and Alain Goriely

Molecule-hugging graphene nanopores: Slaven Garaj, Song Liu, Jene A. Golovchenko, and Daniel Branton

Graphene microsheets enter cells through spontaneous membrane penetration at edge asperities and corner sites: Yinfeng Li, Hongyan Yuan, Annette von dem Bussche, Megan Creighton, Robert H. Hurt, Agnes B. Kane, and Huajian Gao

Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling: Matthew L. Baker, Corey F. Hryc, Qinfen Zhang, Weimin Wu, Joanita Jakana, Cameron Haase-Pettingell, Pavel V. Afonine, Paul D. Adams, Jonathan A. King, Wen Jiang, and Wah Chiu

Fast spatiotemporal correlation spectroscopy to determine protein lateral diffusion laws in live cell membranes: Carmine Di Rienzo, Enrico Gratton, Fabio Beltram, and Francesco Cardarelli

Cell Biology

Ultrahigh-resolution imaging reveals formation of neuronal SNARE/Munc18 complexes in situ: Alexandros Pertsinidis, Konark Mukherjee, Manu Sharma, Zhiping P. Pang, Sang Ryul Park, Yunxiang Zhang, Axel T. Brunger, Thomas C. Südhof, and Steven Chu

Maturation, not initiation, is the major roadblock during reprogramming toward pluripotency from human fibroblasts: Koji Tanabe, Michiko Nakamura, Megumi Narita, Kazutoshi Takahashi, and Shinya Yamanaka

Phage ϕ29 protein p1 promotes replication by associating with the FtsZ ring of the divisome in Bacillus subtilis OPEN ACCESS ARTICLE: David Ballesteros-Plaza, Isabel Holguera, Dirk-Jan Scheffers, Margarita Salas, and Daniel Muñoz-Espín

Genetic loss or pharmacological blockade of testes-expressed taste genes causes male sterility: Bedrich Mosinger, Kevin M. Redding, M. Rockwell Parker, Valeriya Yevshayeva, Karen K. Yee, Katerina Dyomina, Yan Li, and Robert F. Margolskee

CTGF antagonism with mAb FG-3019 enhances chemotherapy response without increasing drug delivery in murine ductal pancreas cancer OPEN ACCESS ARTICLE: Albrecht Neesse, Kristopher K. Frese, Tashinga E. Bapiro, Tomoaki Nakagawa, Mark D. Sternlicht, Todd W. Seeley, Christian Pilarsky, Duncan I. Jodrell, Suzanne M. Spong, and David A. Tuveson

Loss of corepressor PER2 under hypoxia up-regulates OCT1-mediated EMT gene expression and enhances tumor malignancy: Wendy W. Hwang-Verslues, Po-Hao Chang, Yung-Ming Jeng, Wen-Hung Kuo, Pei-Hsun Chiang, Yi-Cheng Chang, Tsung-Han Hsieh, Fang-Yi Su, Liu-Chen Lin, Serena Abbondante, Cheng-Yuan Yang, Huan-Ming Hsu, Jyh-Cherng Yu, King-Jen Chang, Jin-Yuh Shew, Eva Y.-H. P. Lee, and Wen-Hwa Lee

Activation loop phosphorylation of a protein kinase is a molecular marker of organelle size that dynamically reports flagellar length: Muqing Cao, Dan Meng, Liang Wang, Shuqing Bei, William J. Snell, and Junmin Pan

Ecology

Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans: Ilnam Kang, Hyun-Myung Oh, Dongmin Kang, and Jang-Cheon Cho

Environmental Sciences

Universal fractal scaling in stream chemistry and its implications for solute transport and water quality trend detection: James W. Kirchner and Colin Neal

Evolution

Evolutionary diversification of the multimeric states of proteins: Michael Lynch

Economic repercussions of fisheries-induced evolution OPEN ACCESS ARTICLE: Anne Maria Eikeset, Andries Richter, Erin S. Dunlop, Ulf Dieckmann, and Nils Chr. Stenseth

DNA-binding specificity changes in the evolution of forkhead transcription factors OPEN ACCESS ARTICLE: So Nakagawa, Stephen S. Gisselbrecht, Julia M. Rogers, Daniel L. Hartl, and Martha L. Bulyk

Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins: Patrick M. Shih and Nicholas J. Matzke

Genetics

Evaluation of mixed-source, low-template DNA profiles in forensic science OPEN ACCESS ARTICLE: David J. Balding

Quantitative trait analysis in sequencing studies under trait-dependent sampling OPEN ACCESS ARTICLE: Dan-Yu Lin, Donglin Zeng, and Zheng-Zheng Tang

Biclustering with heterogeneous variance OPEN ACCESS ARTICLE: Guanhua Chen, Patrick F. Sullivan, and Michael R. Kosorok

Functional genomic screen of human stem cell differentiation reveals pathways involved in neurodevelopment and neurodegeneration: Ying Zhang, Vincent P. Schulz, Brian D. Reed, Zheng Wang, Xinghua Pan, Jessica Mariani, Ghia Euskirchen, Michael P. Snyder, Flora M. Vaccarino, Natalia Ivanova, Sherman M. Weissman, and Anna M. Szekely

Aneuploidy underlies a multicellular phenotypic switch OPEN ACCESS ARTICLE: Zhihao Tan, Michelle Hays, Gareth A. Cromie, Eric W. Jeffery, Adrian C. Scott, Vida Ahyong, Amy Sirr, Alexander Skupin, and Aimée M. Dudley

Male-specific region of the bovine Y chromosome is gene rich with a high transcriptomic activity in testis development: Ti-Cheng Chang, Yang Yang, Ernest F. Retzel, and Wan-Sheng Liu

Immunology

Zinc-finger antiviral protein mediates retinoic acid inducible gene I–like receptor-independent antiviral response to murine leukemia virus: Hanna Lee, Jun Komano, Yasunori Saitoh, Shoji Yamaoka, Tatsuya Kozaki, Takuma Misawa, Michihiro Takahama, Takashi Satoh, Osamu Takeuchi, Naoki Yamamoto, Yoshiharu Matsuura, Tatsuya Saitoh, and Shizuo Akira

Osteoclast precursors in murine bone marrow express CD27 and are impeded in osteoclast development by CD70 on activated immune cells OPEN ACCESS ARTICLE: Yanling Xiao, Ji-Ying Song, Teun J. de Vries, Christien Fatmawati, Diana B. Parreira, Geerling E. J. Langenbach, Nikolina Bąbała, Martijn A. Nolte, Vincent Everts, and Jannie Borst

Modulation of natural killer cell antitumor activity by the aryl hydrocarbon receptor: June Ho Shin, Luhua Zhang, Oihana Murillo-Sauca, Junmo Kim, Holbrook E. K. Kohrt, Jack D. Bui, and John B. Sunwoo

Intracellular antibody receptor TRIM21 prevents fatal viral infection: Marina Vaysburd, Ruth E. Watkinson, Helen Cooper, Martin Reed, Kevin O'Connell, Jackie Smith, James Cruickshanks, and Leo C. James

CD22 ligand-binding and signaling domains reciprocally regulate B-cell Ca²⁺ signaling: Jennifer Müller, Ingrid Obermeier, Miriam Wöhner, Carolin Brandl, Sarah Mrotzek, Sieglinde Angermüller, Palash C. Maity, Michael Reth, and Lars Nitschke

Medical Sciences

A small animal Raman instrument for rapid, wide-area, spectroscopic imaging: Sarah E. Bohndiek, Ashwin Wagadarikar, Cristina L. Zavaleta, Dominique Van de Sompel, Ellis Garai, Jesse V. Jokerst, Siavash Yazdanfar, and Sanjiv S. Gambhir

Dissection of TBK1 signaling via phosphoproteomics in lung cancer cells: Jae-Young Kim, Eric A. Welsh, Umut Oguz, Bin Fang, Yun Bai, Fumi Kinose, Crystina Bronk, Lily L. Remsing Rix, Amer A. Beg, Uwe Rix, Steven A. Eschrich, John M. Koomen, and Eric B. Haura

PTEN loss defines a PI3K/AKT pathway-dependent germinal center subtype of diffuse large B-cell lymphoma: Matthias Pfeifer, Michael Grau, Dido Lenze, Sören-Sebastian Wenzel, Annette Wolf, Brigitte Wollert-Wulf, Kerstin Dietze, Hendrik Nogai, Benjamin Storek, Hannelore Madle, Bernd Dörken, Martin Janz, Stephan Dirnhofer, Peter Lenz, Michael Hummel, Alexandar Tzankov, and Georg Lenz

Targeted genetic dependency screen facilitates identification of actionable mutations in FGFR4, MAP3K9, and PAK5 in lung cancer OPEN ACCESS ARTICLE: Shameem Fawdar, Eleanor W. Trotter, Yaoyong Li, Natalie L. Stephenson, Franziska Hanke, Anna A. Marusiak, Zoe C. Edwards, Sara Ientile, Bohdan Waszkowycz, Crispin J. Miller, and John Brognard

Abl kinases are required for vascular function, Tie2 expression, and angiopoietin-1–mediated survival: Elizabeth M. Chislock, Colleen Ring, and Ann Marie Pendergast

Microbiology

Structural insights into the regulation of sialic acid catabolism by the Vibrio vulnificus transcriptional repressor NanR OPEN ACCESS ARTICLE: Jungwon Hwang, Byoung Sik Kim, Song Yee Jang, Jong Gyu Lim, Dong-Ju You, Hyun Suk Jung, Tae-Kwang Oh, Jie-Oh Lee, Sang Ho Choi, and Myung Hee Kim

Torins are potent antimalarials that block replenishment of Plasmodium liver stage parasitophorous vacuole membrane proteins OPEN ACCESS ARTICLE: Kirsten K. Hanson, Ana S. Ressurreição, Kathrin Buchholz, Miguel Prudêncio, Jonathan D. Herman-Ornelas, Maria Rebelo, Wandy L. Beatty, Dyann F. Wirth, Thomas Hänscheid, Rui Moreira, Matthias Marti, and Maria M. Mota

Molecular architecture of the uncleaved HIV-1 envelope glycoprotein trimer OPEN ACCESS ARTICLE: Youdong Mao, Liping Wang, Christopher Gu, Alon Herschhorn, Anik Désormeaux, Andrés Finzi, Shi-Hua Xiang, and Joseph G. Sodroski

A mechanism for induction of a hypoxic response by vaccinia virus OPEN ACCESS ARTICLE: Michela Mazzon, Nicholas E. Peters, Christoph Loenarz, Ewelina M. Krysztofinska, Stuart W. J. Ember, Brian J. Ferguson, and Geoffrey L. Smith

Rapid evolution of the human gut virome: Samuel Minot, Alexandra Bryson, Christel Chehoud, Gary D. Wu, James D. Lewis, and Frederic D. Bushman

Neuroscience

Very long-term memories may be stored in the pattern of holes in the perineuronal net OPEN ACCESS ARTICLE: Roger Y. Tsien

Cognitive and motivational deficits together with prefrontal oxidative stress in a mouse model for neuropsychiatric illness: Alexander W. Johnson, Hanna Jaaro-Peled, Neelam Shahani, Thomas W. Sedlak, Sandra Zoubovsky, Daniel Burruss, Francesco Emiliani, Akira Sawa, and Michela Gallagher

Transducin translocation contributes to rod survival and enhances synaptic transmission from rods to rod bipolar cells: Anurima Majumder, Johan Pahlberg, Kimberly K. Boyd, Vasily Kerov, Saravanan Kolandaivelu, Visvanathan Ramamurthy, Alapakkam P. Sampath, and Nikolai O. Artemyev

Pharmacology

Tumor-derived hydrogen sulfide, produced by cystathionine-β-synthase, stimulates bioenergetics, cell proliferation, and angiogenesis in colon cancer: Csaba Szabo, Ciro Coletta, Celia Chao, Katalin Módis, Bartosz Szczesny, Andreas Papapetropoulos, and Mark R. Hellmich

Physiology

Fat cells directly sense temperature to activate thermogenesis: Li Ye, Jun Wu, Paul Cohen, Lawrence Kazak, Melin J. Khandekar, Mark P. Jedrychowski, Xing Zeng, Steven P. Gygi, and Bruce M. Spiegelman