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2013

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Nitrogen uptake strategies of edaphically specialized Bornean tree species, Sabrina E. Russo, Amy Kochsiek, Jocelyn Olney, Lauren Thompson, Amy E. Miller, and Sylvester Tan

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Heritability and Inter-Population Differences in Lipid Profiles of Drosophila melanogaster, Cornelia J. F. Scheitz, Yu Guo, Angela M. Early, Lawrence G. Harshman, and Andrew G. Clark

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Role of MerH in mercury resistance in the archaeon Sulfolobus solfataricus, James Schelert, Deepak Rudrappa, Tyler Johnson, and Paul H. Blum

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Predicting invasion in grassland ecosystems: is exotic dominance the real embarrassment of richness?, Eric W. Seabloom, Elizabeth T. Borer, Yvonne Buckley, Elsa E. Cleland, Kendi Davies, Jennifer Firn, W. Stanley Harpole, Yann Hautier, Eric Lind, Andrew Macdougall, John L. Orrock, Suzanne M. Prober, Peter Andler, Juan Alberti, T. Michael Anderson, Jonathan D. Bakker, Lori A. Biederman, Dana Blumenthal, Cynthia S. Brown, Lars A. Brudvig, Maria Caldeira, Chengjin Chu, Michael J. Crawley, Pedro Daleo, Ellen I. Damschen, Carla M. D'Antonio, Nicole M. Decrappeo, Chris R. Dickman, Guozhen Du, Philip A. Fay, Paul Frater, Daniel S. Gruner, Nicole Hagenah, Andrew Hector, Aveliina Helm, Helmut Hillebrand, Kirsten S. Hofmockel, Hope C. Humphries, Oscar Iribarne, Virginia L. Jin, Adam Kay, Kevin P. Kirkman, Julia A. Klein, Johannes M. H. Knops, Kimberly J. La Pierre, Laura M. Ladwig, John G. Lambrinos, Andrew D. B. Leakey, Qi Li, Wei Li, Rebecca McCulley, Brett Melbourne, Charles E. Mitchell, Joslin L. Moore, John Morgan, Brent Mortensen, Lydia R. O'Halloran, Meelis Partel, Jesus Pascual, David A. Pyke, Anita C. Risch, Roberto Salguero-Gomez, Mahesh Sankaran, Martin Schuetz, Anna Simonsen, Melinda Smith, Carly Stevens, Lauren L. Sullivan, Glenda M. Wardle, Elizabeth M. Wolkovich, Peter D. Wragg, Justin Wright, and Louie Yang

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Reductive evolution and the loss of PDC/PAS domains from the genus Staphylococcus, Neethu Shah, Rosmarie Gaupp, Hideaki Moriyama, Kent M. Eskridge, Etsuko N. Moriyama, and Greg A. Somerville

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Inge Revsbech wins The Journal of Experimental Biology’s Outstanding Paper Prize 2013, Nicola Stead, Inge G. Revsbech, Hideaki Moriyama, Jay F. Storz, and Angela Fago

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Low Seroprevalent Species D Adenovirus Vectors as Influenza Vaccines, Eric A. Weaver and Michael A. Barry

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Comparison of Systemic and Mucosal Immunization withHelper-Dependent Adenoviruses for Vaccination against Mucosal Challenge with SHIV, Eric A. Weaver, Pramod N. Nehete, Bharti P. Nehete, Guojun Yang, Stephanie J. Buchl, Patrick W. Hanley, Donna Palmer, David C. Montefiori, Guido Ferrari, Philip Ng, K. Jagannadha Sastry, and Michael A. Barry

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CD20 Antibody Primes B Lymphocytes for Type I Interferon Production, Dongsheng Xu, Andrew Staedman, and Luwen Zhang

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Conformational B-Cell Epitope Prediction on Antigen Protein Structures: A Review of Current Algorithms and Comparison with Common Binding Site Prediction Methods, Bo Yao, Dandan Zheng, Shide Liang, and Chi Zhang

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A Whole-Cell Biosensor for the Detection of Gold, Carla M. Zammit, Davide Quaranta, Shane Gibson, Anita J. Zaitouna, Christine Ta, Joel Brugger, Rebecca Y. Lai, Gregor Grass, and Frank Reith

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Prevalence and correlates of Kaposi’s sarcoma-associated herpesvirus infection in a sample of men who have sex with men in eastern China, T. Zhang, H. Lin, V. Minhas, W. Zhu, Charles Wood, and N. He

2012

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Evolution of the PWWP-Domain Encoding Genes in the Plant and Animal Lineages, Raul Alvarez-Venegas and Zoya Avramova

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Eavesdropping Parasitoids Do Not Cause the Evolution of Less Conspicuous Signaling Behavior in a Field Cricket, Oliver M. Beckers and William E. Wagner

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Draft Genome Sequence of the Anaerobic, Nitrate-Dependent, Fe(II)-Oxidizing Bacterium Pseudogulbenkiania ferrooxidans Strain 2002, Kathryne G. Byrne-Bailey, Karrie A. Weber, and John D. Coates

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A peptide photoaffinity probe specific for the active conformation of the Abl tyrosine kinase, Yang Deng, Brian A. Couch, Anthony J. Koleske, and Benjamin E. Turk

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Multiple exposures to drought ‘train’ transcriptional responses in Arabidopsis, Yong Ding, Michael Fromm, and Zoya Avramova

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ATX1-Generated H3K4me3 Is Required for Efficient Elongation of Transcription, Not Initiation, at ATX1- Regulated Genes, Yong Ding, Ivan Ndamukong, Zaoshi Xu, Hanna Lapko, Michael E. Fromm, and Zoya Avramova

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Divergent Functions of the Myotubularin (MTM) Homologs AtMTM1 and AtMTM2 in Arabidopsis thaliana: Evolution of the Plant MTM Family, Yong Ding, Ivan Ndamukong, Yang Zhao, Yuannan Xia, Jean-Jack Riethoven, David R. Jones, Nullin Divecha, and Zoya Avramova

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Divergent functions of the myotubularin (MTM) homologs AtMTM1 and AtMTM2 in Arabidopsis thaliana: evolution of the plant MTM family, Yong Ding, Ivan Ndamukong, Yang Zhao, Yuannan Xia, Jean-Jack Riethoven, David R. Jones, Nullin Divecha, and Zoya Avramova

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L1pred: A Sequence-Based Prediction Tool for Catalytic Residues in Enzymes with the L1-logreg Classifier, Yongchao Dou, Jun Wang, Jialiang Yang, and Chi Zhang

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Insect herbivory and propagule pressure influence Cirsium vulgare invasiveness across the landscape, James O. Eckberg, Brigitte Tenhumberg, and Svata M. Louda

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Indirect consequences of hypolimnetic hypoxia on zooplankton growth in a large eutrophic lake, Daisuke Goto, Kara Lindelof, David L. Fanslow, Stuart A. Ludsin, Steven A. Pothoven, James J. Roberts, Henry A. Vanderploeg, Alan E. Wilson, and Tomas O. Höök

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Do Clark’s nutcrackers demonstrate what-where-when memory on a cache-recovery task?, Kristy L. Gould, Amy J. Ort, and Alan C. Kamil

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Viscoelastic Properties of Cell Walls of Single Living Plant Cells Determined by Dynamic Nanoindentation, Céline M. Hayot, Elham Forouzesh, Ashwani Goel, Zoya Avramova, and Joseph A. Turner

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Larval Performance and Kill Rate of Convergent Ladybird Beetles, Hippodamia convergens, on Black Bean Aphids, Aphis fabae, and Pea Aphids, Acyrthosiphon pisum, Travis M. Hinkelman and Brigitte Tenhumberg

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Sex Allocation in California Oaks: Trade-Offs or Resource Tracking?, Johannes Knops and Walter D. Koenig

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Carbohydrate Hydrolysis and Transport in the Extreme Thermoacidophile Sulfolobus solfataricus, Sreedevi Lalithambika, Landon Peterson, Karl Dana, and Paul H. Blum

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The Epigenetics of Emerging and Nonmodel Organisms, Vett K. Lloyd, Jennifer A. Brisson, Kathleen A. Fitzpatrick, Lori A. McEachern, and Eveline C. Verhulst

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Template-Based Structure Prediction and Classification of Transcription Factors in Arabidopsis thaliana, Tao Lu, Yuedong Yang, Bo Yao, Song Liu, Yaoqi Zhou, and Chi Zhang

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DFVF: database of fungal virulence factors, Tao Lu, Bo Yao, and Chi Zhang

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Survival of the Fittest: Overcoming Oxidative Stress at the Extremes of Acid, Heat and Metal, Yukari Maezato and Paul H. Blum

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Metal Resistance and Lithoautotrophy in the Extreme Thermoacidophile Metallosphaera sedula, Yukari Maezato, Tyler Johnson, Samuel McCarthy, Karl Dana, and Paul H. Blum

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Comparative Transitive and Temporal Orderliness in Dominance Networks, David McDonald and Daizaburo Shizuka

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Urea Amidolyase (DUR1,2) Contributes to Virulence and Kidney Pathogenesis of Candida albicans, Dhammika H. M. L. P Navarathna, Michail S. Lionakis, Martin J. Lizak, Jeeva Munasinghe, Kenneth W. Nickerson, and David D. Roberts

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Thoughts on Quorum Sensing and Fungal Dimorphism, Kenneth W. Nickerson, Audrey L. Atkin, Jessica C. Hargarten, Ruvini U. Pathirana, and Sahar Hasim

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Reducing odorous VOC emissions from swine manure using soybean peroxidase and peroxides, David B. Parker, Lingshuang Cai, Ki-Hyun Kim, Kristin E. Hales, Mindy J. Spiehs, Bryan L. Woodbury, Audrey L. Atkin, Kenneth Nickerson, and Krista D. Patefield

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Influence of aphid honeydew on the foraging behavior of Hippodamia convergens larvae, Swapna R. Purandare and Brigitte Tenhumberg

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Bacterial community structure of contrasting soils underlying Bornean rain forests: Inferences from microarray and next-generation sequencing methods, Sabrina E. Russo, Ryan Legge, Karrie A. Weber, Eoin L. Brodie, Katherine C. Goldfarb, Andrew K. Benson, and Sylvester Tan

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Covariation between understorey light environments and soil resources in Bornean mixed dipterocarp rain forest, Sabrina E. Russo, Lin Zhang, and Sylvester Tan

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Antimicrobial metallic copper surfaces kill Staphylococcus haemolyticus via membrane damage, Christophe Espirito Santo, Davide Quaranta, and Gregor Grass

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Evolution of a Large, Conserved, and Syntenic Gene Family in Insects, Neethu Shah, Douglas R. Dorer, Etsuko N. Moriyama, and Alan C. Christensen

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Family Dynamics Through Time: Brood Reduction Followed by Parental Compensation with Aggression and Favoritism, Daizaburo Shizuka and Bruce E. Lyon

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A Social Network Perspective on Measurements of Dominance Hierarchies, Daizaburo Shizuka and David B. McDonald

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Tradeoffs limit the evolution of male traits that are attractive to females, William E. Wagner, Oliver M. Beckers, Amanda E. Tolle, and Alexandra Basolo

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Concatenation and Concordance in the Reconstruction of Mouse Lemur Phylogeny: An Empirical Demonstration of the Effect of Allele Sampling in Phylogenetics, David W. Weisrock, Stacey DeWitt Smith, Lauren M. Chan, Karla Biebouw, Peter M. Kappeler, and Anne D. Yoder

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SVMTriP: A Method to Predict Antigenic Epitopes Using Support Vector Machine to Integrate Tri-Peptide Similarity and Propensity, Bo Yao, Lin Zhang, Shide Liang, and Chi Zhang

2011

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SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation, Catherine L. Anderson, Cory L. Strope, and Etsuko N. Moriyama

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Use of Nape Tags for Marking Offspring of Precocial Waterbirds, Todd W. Arnold, Daizaburo Shizuka, Bruce E. Lyon, Jeffrey T. Pelayo, Katherine R. Mehl, Joshua J. Traylor, Wendy L. Reed, and Courtney L. Amundson

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Epigenetic Regulatory Mechanisms in Plants, Zoya Avramova

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Crystallization of Chlorella deoxyuridine triphosphatase, Laura Badalucco, Ishwari Poudel, Mamoru Yamanishi, Chandrasekhar Natarajan, and Hideaki Moriyama

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Survival Rates of Planidial Larvae of the Parasitoid Fly Ormia ochracea (Diptera: Tachinidae), Oliver M. Beckers, Cassandra M. Martin, and William E. Wagner Jr.

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Male Field Crickets Infested by Parasitoid Flies Express Phenotypes that May Benefit the Parasitoids, Oliver M. Beckers and William E. Wagner

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Composite Effects of Polymorphisms near Multiple Regulatory Elements Create a Major-Effect QTL, Ryan D. Bickel, Artyom Kopp, and Sergey V. Nuzhdin

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EFFECTS OF POSTMORTEM INTERVAL AND PRESERVATION METHOD ON RNA ISOLATED FROM FIELD-PRESERVED AVIAN TISSUES Efectos del Intervalo Post-Mortem y del Método de Preservación en el ARN Aislado de Tejidos de Aves Preservados en el Campo, Zachary A. Cheviron, Matthew D. Carling, and Robb T. Brumfield

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Normalization and centering of array-based heterologous genome hybridization based on divergent control probes, Brian J. Darby, Kenneth L. Jones, David Wheeler, and Michael A. Herman

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Copper Tolerance of Saccharomyces cerevisiae Nonsense-Mediated mRNA Decay Mutants, Rafael Deliz-Aguirre, Audrey L. Atkin, and Bessie W. Kebaara

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Variations on a theme: diversification of cuticular hydrocarbons in a clade of cactophilic Drosophila, Cássia C. de Oliveira, Maura H. Manfrin, Fábio de M Sene, Larry L. Jackson, and William J. Etges

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The Arabidopsis Trithorax-like Factor ATX1 Functions in Dehydration Stress Responses via ABA-Dependent and ABA-Independent Pathways, Yong Ding, Zoya Avramova, and Michael Fromm

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Environmental and genetic perturbations reveal different networks of metabolic regulation, Anthony J. Greenberg, Sean R. Hacket, Lawrence G. Harshman, and Andrew G. Clark

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The Effects of Belowground Resources on Aboveground Allometric Growth in Bornean Tree Species, Katherine D. Heineman, Ethan Jensen, Autumn Shapland, Brett Bogenrief, Sylvester Tan, Richard Rebarber, and Sabrina E. Russo

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Real-Time Dynamic Imaging of Virus Distribution In Vivo, Sean E. Hofherr, Kristen E. Adams, Christopher Y. Chen, Shannon May, Eric A. Weaver, and Michael A. Barry

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Increased transsulfuration mediates longevity and dietary restriction in Drosophila, Hadise Kabil, Omer Kabil, Ruma Banerjee, Lawrence G. Harshman, and Scott D. Pletcher

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Population Dynamics of the Western Prickly Pear, Opuntia macrorhiza (Cactaceae), Kathleen H. Keeler and Brigitte Tenhumberg

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Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis, Karsten Klopffleisch, Nguyen Phan, Kelsey Augustin, Robert S. Bayne, Katherine S. Booker, Jose R. Botella, Nicholas C. Carpita, Tyrell Carr, Jin-Gui Chen, Thomas Ryan Cooke, Arwen Frick-Cheng, Erin J. Friedman, Brandon Fulk, Michael G. Hahn, Kun Jiang, Lucia Jorda, Lydia Kruppe, Chenggang Liu, Justine Lorek, Maureen C. McCann, Antonio Molina, Etsuko N. Moriyama, M. Shahid Mukhtar, Yashwanti Mudgil, Sivakumar Pattathil, John Schwarz, Steven Seta, Matthew Tan, Ulrike Temp, Yuri Trusov, Daisuke Urano, Bastian Welter, Jing Yang, Ralph Panstruga, Joachim F. Uhrig, and Alan M. Jones

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Characterization of a Dipartite Iron Uptake System from Uropathogenic Escherichia coli Strain, Doreen Koch, Anson C. K. Chan, Michael E.P. Murphy, Hauke Lilie, Gregor Grass, and Dietrich H. Nies

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Maize cellulosic biofuels: soil carbon loss can be a hidden cost of residue removal, Amy Kochsiek and Johannes Knops

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Phylogenetic diversity of Fe(III)-reducing microorganisms in rice paddy soil: Enrichment cultures with different short-chain fatty acids as electron donors, Huijuan Li, Jingjing Peng, Karrie A. Weber, and Yongguan Zhu

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Morphologic Clues to the Origins of Iron Oxide–Cemented Spheroids, Boxworks, and Pipelike Concretions, Navajo Sandstone of South-Central Utah, U.S.A., David B. Loope, Richard M. Kettler, and Karrie A. Weber

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Priority resource access mediates competitive intensity between an invasive weevil and native floral herbivores, Svata M. Louda, Tatyana A. Rand, A. A. R. Kula, A. E. Arnett, N. M. West, and Brigitte Tenhumberg

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VapC6, a ribonucleolytic toxin regulates thermophilicity in the crenarchaeote Sulfolobus solfataricus, Yukari Maezato, Amanda Daugherty, Karl Dana, Edith Soo, Charlotte Cooper, Sabrina Tachdjian, Robert M. Kelly, and Paul H. Blum

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Sex Chromosome-Specific Regulation in the Drosophila Male Germline But Little Evidence for Chromosomal Dosage Compensation or Meiotic Inactivation, Colin D. Meiklejohn, Emily L. Landeen, Jodi M. Cook, Sarah B. Kingan, and Daven C. Presgraves

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A cytoplasm-specific activity encoded by the Trithorax-like ATX1 gene, Ivan Ndamukong, Hanna Lapko, Ronald L. Cerny, and Zoya Avramova

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Integral projection model of insect herbivore effects on Cirsium altissimum populations along productivity gradients, Karen E. Rose, F. Leland Russell, and Svata M. Louda

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Genomic and Resistance Gene Homolog Diversity of the Dominant Tallgrass Prairie Species across the U.S. Great Plains Precipitation Gradient, Matthew N. Rouse, Amgad A. Saleh, Amadou Seck, Kathleen H. Keeler, Steven E. Travers, Scot H. Hulbert, and Karen A. Garrett

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Evidence for Air Movement Signals in the Agonistic Behaviour of a Nocturnal Arachnid (Order Amblypygi), Roger D. Santer and Eileen A. Hebets

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Comparative genomics of proteins involved in RNA nucleocytoplasmic export, Mariana Serpeloni, Newton M. Vidal, Samuel Goldenberg, Andréa R. Ávila, and Federico G. Hoffmann

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Analyses of Fruit Flies That Do Not Express Selenoproteins or Express the Mouse Selenoprotein, Methionine Sulfoxide Reductase B1, Reveal a Role of Selenoproteins in Stress Resistance, Valentina A. Shchedrina, Hadise Kabil, Gerd Vorbruggen, Byung Cheon Lee, Anton A. Turanov, Mitsuko Hirosawa- Takamori, Hwa- Young Kim, Lawrence G. Harshman, Dolph L. Hatfield, and Vadim N. Gladyshev

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Hosts Improve the Reliability of Chick Recognition by Delaying the Hatching of Brood Parasitic Eggs, Daizaburo Shizuka and Bruce E. Lyon

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Aphids: A Model for Polyphenism and Epigenetics, Dayalan G. Srinivasan and Jennifer A. Brisson

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Molecular evolution of urea amidolyase and urea carboxylase in fungi, Pooja K. Strope, Kenneth W. Nickerson, Steven D. Harris, and Etsuko N. Moriyama

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Humic Acid-Oxidizing, Nitrate-Reducing Bacteria in Agricultural Soils, J. Ian Van Trump, Kelly C. Wrighton, J. Cameron Thrash, Karrie A. Weber, Gary L. Andersen, and John D. Coates

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dtorsin, the Drosophila Ortholog of the Early-Onset Dystonia TOR1A (DYT1), Plays a Novel Role in Dopamine Metabolism, Noriko Wakabayashi-Ito, Olugbenga M. Doherty, Hideaki Moriyama, Xandra O. Breakefield, James F. Gusella, Janis M. O’Donnell, and Naoto Ito

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Protection against Divergent Influenza H1N1 Virus by a Centralized Influenza Hemagglutinin, Eric A. Weaver, Adam M. Rubrum, Richard J. Webby, and Michael A. Barry

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Environmental and Taxonomic Bacterial Diversity of Anaerobic Uranium(IV) Bio-Oxidation, Karrie A. Weber, J. Cameron Thrash, J. Ian Van Trump, Laurie A. Achenbach, and John D. Coates

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Interferon Regulatory Factor 4 (IRF-4) Targets IRF-5 to Regulate Epstein-Barr Virus Transformation, Dongsheng Xu, Florencia Meyer, Erica Ehlers, Laura Blasnitz, and Luwen Zhang

2010

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Association of rs780094 in GCKR with Metabolic Traits and Incident Diabetes and Cardiovascular Disease: The ARIC Study, Mark Bi, Wen Hong Linda Kao, Eric Boerwinkle, Ron C. Hoogeveen, Laura J. Rasmussen-Torvik, Brad C. Astor, Kari E. North, Joseph Coresh, and Anna Kottgen

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The spatial influence of aboveground diversity on belowground communities, T. Bliss, Tom Powers, and Chad Brassil

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Cognitive Representation in Transitive Inference: A Comparison of Four Corvid Species, Alan B. Bond, Cynthia A. Wei, and Alan C. Kamil

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Structured Population Dynamics: An Introduction to Integral Modeling, Joseph Briggs, Kathryn Dabbs, Michael Holm, Joan Lubben, Richard Rebarber, Brigitte Tenhumberg, and Daniel Riser-Espinoza

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Genome Sequence of the Pea Aphid Acyrthosiphon pisum, Jennifer A. Brisson, Stephen Richards, and International Aphid Genomics Consortium

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Completed Genome Sequence of the Anaerobic Iron-Oxidizing Bacterium Acidovorax ebreus Strain TPSY, Kathryne G. Byrne-Bailey, Karrie A. Weber, Antinea H. Chair, Saumyaditya Bose, Traci Knox, Trisha L. Spanbauer, Olga Chertkov, and John D. Coates

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The Capsid Protein of Turnip Crinkle Virus Overcomes Two Separate Defense Barriers to Facilitate Systemic Movement of the Virus in Arabidopsis, Mingxia Cao, Xiaohong Yi, Kristen Willie, Junyan Lin, Xiuchun Zhang, Margaret G. Redinbaugh, Anne E. Simon, Thomas Jack Morris, and Feng Qu

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Nm23-H1 can induce cell cycle arrest and apoptosis in B cells, Tathagata Choudhuri, Masanao Murakami, Rajeev Kaul, Sushil K. Sahu, Suchitra Mohanty, Subhash C. Verma, Pankaj Kumar, and Erle S. Robertson

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Increased Dendrite Branching in AβPP/PS1 Mice and Elongation of Dendrite Arbors by Fasudil Administration, Brian A. Couch, George J. DeMarco, Shannon L. Gourley, and Anthony J. Koleske

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Glycopeptidome of a Heavily N-Glycosylated Cell Surface Glycoprotein of Dictyostelium Implicated in Cell Adhesion, Christa L. Feasley, Jennifer M. Johnson, Christopher M. West, and Catherine P. Chia

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Locomotion in Response to Shifting Climate Zones: Not So Fast, Martin E. Feder, Theodore Garland Jr., James H. Marden, and Anthony J. Zera

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What scatter-hoarding animals have taught us about small-scale navigation, Kristy L. Gould, Debbie M. Kelly, and Alan Kamil

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The polypeptide Syn67 interacts physically with human holocarboxylase synthetase, but is not a target for biotinylation, Yousef I. Hassan, Hideaki Moriyama, and Janos Zempleni

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Effects of Plant Sex on Range Distributions and Allocation to Reproduction, Marc T.J. Johnson, Stacey DeWitt Smith, and Mark D. Rausher