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2012

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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

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The Role of Litter Quality Feedbacks in Terrestrial Nitrogen and Phosphorus Cycling, Johannes M.H. Knops, David A. Wedin, and Shahid Naeem

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Activity and Toxicity of Farnesol towards Candida albicans Are Dependent on Growth Conditions, Melanie L. Langford, Sahar Hasim, Kenneth W. Nickerson, and Audrey L. Atkin

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EPSVR and EPMeta: Prediction of Antigenic Epitopes Using Support Vector Regression and Multiple Server Results, Shide Liang, Dandan Zheng, Daron M. Standley, Bo Yao, Martin Zacharias, and Chi Zhang

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Agmatidine, a modified cytidine in the anticodon of archaeal tRNAIle, base pairs with adenosine but not with guanosine, Debabrata Mandal, Caroline Köhrer, Dan Su, Susan P. Russell, Kady Krivos, Colette M. Castleberry, Paul H. Blum, Patrick A. Limbach, Dieter Söll, and Uttam L. RajBhandary

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Female Field Crickets Incur Increased Parasitism Risk When Near Preferred Song, Cassandra M. Martin and William E. Wagner Jr.

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Genetic conflict and sex chromosome evolution, Colin D. Meiklejohn and Yun Tao

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Contributions of demography and dispersal parameters to the spatial spread of a stage-structured insect invasion, Tom E. X. Miller and Brigitte Tenhumberg

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Mitochondrial-nuclear epistasis affects fitness within species but does not contribute to fixed incompatibilities between species of Drosophila, Kristi L. Montooth, Colin D. Meiklejohn, Dawn N. Abt, and David M. Rand

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Phosphatidylinositol 5-Phosphate Links Dehydration Stress to the Activity of Arabidopsis Trithorax-Like Factor ATX1, Ivan Ndamukong, David R. Jones, Hanna Lapko, Nullin Divecha, and Zoya V. Avramova

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Evolution of the Kdo2-lipid A Biosynthesis in Bacteria, Stephen O. Opiyo, Rosevelt L. Pardy, Hideaki Moriyama, and Etsuko N. Moriyama

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The Abl and Arg non-receptor tyrosine kinases regulate different zones of stress fiber, focal adhesion, and contractile network localization in spreading fibroblasts, Justin G. Peacock, Brian A. Couch, and Anthony J. Koleske

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Synaptic Clustering of PSD-95 Is Regulated by c-Abl through Tyrosine Phosphorylation, Karen Perez de Arce, Lorena Varela-Nallar, Olivia Farias, Alejandra Cifuentes, Paulina Bull, Brian A. Couch, Anthony J. Koleske, Nibaldo C. Inestrosa, and Alejandra R. Alvarez

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Viral trans-Factor Independent Replication of Human Papillomavirus Genomes, Daraporn Pittayakhajonwut and Peter C. Angeletti

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Seed availability and insect herbivory limit recruitment and adult density of native tall thistle, F. Leland Russell, Karen E. Rose, and Svata M. Louda

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Variation in Leaf Stomatal Traits of 28 Tree Species in Relation to Gas Exchange along an Edaphic Gradient in a Bornean Rain Forest, Sabrina E. Russo, Whitney Logan Cannon, Christian Elowsky, Sylvester Tan, and Stuart J. Davies

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Interspecific Relationships among Growth, Mortality and Xylem Traits of Woody Species from New Zealand, Sabrina E. Russo, Kerry L. Jenkins, Susan K. Wiser, Maria Uriarte, Richard P. Duncan, and David A. Coomes

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Positive Carotenoid Balance Correlates with Greater Reproductive Performance in a Wild Bird, Rebecca Safran, Kevin J. McGraw, Matt Wilkins, Joanna K. Hubbard, and Julie Marling

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Isolation and Characterization of Bacteria Resistant to Metallic Copper Surfaces, Christophe Espírito Santo, Paula Vasconcelos Morais, and Gregor Grass

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The Effects of Flower Color Transitions on Diversification Rates in Morning Glories (Ipomoea subg. Quamoclit, Convolvulaceae), Stacey DeWitt Smith, Richard E. Miller, Sarah P. Otto, Richard G. FitzJohn, and Mark D. Rausher

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Ignoring Population Structure Can Lead to Erroneous Predictions of Future Population Size, Brigitte Tenhumberg

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COMPOSITIONS AND METHODS FOR CONTROLLING PLANT PARASITIC NEMATODES, Harold N. Trick, Judith L. Roe, Timothy C. Todd, and Michael A. Herman

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Dynamic Changes in Genome-Wide Histone H3 Changes Lysine 4 Methylation Patterns in Response to Dehydration Stress in Arabidopsis thaliana, Karin V. van Dijk, Yong Ding, Sridar Achary Malkaram, Jean-Jack Riethoven, Rong Liu, Jingyi Yang, Peter Laczko, Han Chen, Yuannan Xia, Istvan Ladunga, Zoya V. Avramova, and Michael E. Fromm

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A Detailed Phylogenetic Analysis of FIV in the United States, Eric A. Weaver

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Integrating spatial and temporal approaches to understanding species richness, Ethan P. White, S. K. Morgan Ernest, Peter B. Adler, Allen H. Hurlbert, and S. Kathleen Lyons

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Structural Insight into Dynamic Bypass of the Major Cisplatin-DNA Adduct by Y-family Polymerase Dpo4, Jimson HY Wong, Jessica A. Brown, Zucai Suo, Paul H. Blum, Takehiko Nohmi, and Hong Ling

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Analysis of miRNA Modifications, Bin Yu and Xuemei Chen

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Differences in HIV Burden and Immune Activation within the Gut of HIV-Positive Patients Receiving Suppressive Antiretroviral Therapy, Steven A. Yukl, Sara Gianella, Elizabeth Sinclair, Lorrie Epling, Qingsheng Li, Lijie Duan, Alex L.M. Choi, Valerie Girling, Terence Ho, Peilin Li, Katsuya Fujimoto, Harry Lampiris, C. Bradley Hare, Mark Pandori, Ashley T. Haase, Huldrych F. Günthard, Marek Fischer, Amandeep K. Shergill, Kenneth McQuaid, Diane V. Havlir, and Joseph K. Wong

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Microevolution of intermediary metabolism: evolutionary genetics meets metabolic biochemistry, Anthony J. Zera

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Purification and characterization of cytoplasmic NADP+- isocitrate dehydrogenase, and amplification of the Nadp+-Idh gene from the wing-dimorphic sand field cricket, Gryllus firmus, Anthony J. Zera, Susan Newman, David Berkheim, Christine Black, Lindsay Klug, and Erica Crone

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Molecular Determinants of HIV-1 Subtype C Coreceptor Transition from R5 to R5X4, Hong Zhang, Damien C. Tully, Tiejun Zhang, Hideaki Moriyama, Jesse Thompson, and Charles Wood

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Dual Functions of Interferon Regulatory Factors 7C in Epstein-Barr Virus–Mediated Transformation of Human B Lymphocytes, Yong Zhao, Dongsheng Xu, Yanjun Jiang, and Luwen Zhang

2009

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Interactive Effects of Time, CO2, N, and Diversity on Total Belowground Carbon Allocation and Ecosystem Carbon Storage in a Grassland Community, E. Carol Adair, Peter B. Reich, Sarah E. Hobbie, and Johannes M.H. Knops

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Evolution and pleiotropy of TRITHORAX function in Arabidopsis, Zoya Avramova