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2014

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Using an Ecosystem Approach to complement protection schemes based on organism-level endpoints, Clare Bradshaw, Lawrence Kapustka, Lawrence Barenthouse, Justin Brown, Philippe Ciffroy, Valery E. Forbes, Stanislav Geras'kin, Ulrik Kautsky, and Francois Brechignac

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Genes and Junk in Plant Mitochondria—Repair Mechanisms and Selection, Alan C. Christensen

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Dehydration stress memory genes of Zea mays; comparison with Arabidopsis thaliana, Yong Ding, Laetitia Virlouvet, Ning Liu, Jean-Jack Riethoven, Michael Fromm, and Zoya Avramova

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Molecular Evolution of Glycoside Hydrolase Genes in the Western Corn Rootworm (Diabrotica virgifera virgifera), Seong-il Eyun, Haichuan Wang, Yannick Pauchet, Richard H. ffrench-Constant, Andrew K. Benson, Arnubio Valencia-Jimenez, Etsuko Moriyama, and Blair Siegfried

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Eutrophication weakens stabilizing effects of diversity in natural grasslands, Yann Hautier, Eric W. Seabloom, Elizabeth T. Borer, Peter B. Adler, W. Stanley Harpole, Helmut Hillebrand, Eric M. Lind, Andrew S. MacDougall, Carly J. Stevens, Jonathan D. Bakker, Yvonne M. Buckley, Chengjin Chu, Scott L. Collins, Pedro Daleo, Ellen I. Damschen, Kendi F. Davies, Philip A. Fay, Jennifer Firn, Daniel S. Gruner, Virginia L. Jin, Julia A. Klein, Johannes M. N. Knops, Kimberly J. La Pierre, Wei Li, Rebecca L. McCulley, Brett A. Melbourne, Joslin L. Moore, Lydia R. O’Halloran, Suzanne M. Prober, Anita C. Risch, Mahesh Sankaran, Martin Schuetz, and Andy Hector

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Effect of the Internet Commerce on Dispersal Modes of Invasive Alien Species, Magdalena Lenda, Piotr Skorka, Johannes M.H. Knops, Dawid Moron, William J. Sutherland, Karolina Kuszewska, and Michal Woyciechowski

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Early song discrimination by nestling sparrows in the wild, Daizaburo Shizuka

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Across-year social stability shapes network structure in wintering migrant sparrows, Daizaburo Shizuka, Alexis S. Chaine, Jennifer Anderson, Oscar Johnson, Inger Marie Laursen, and Bruce E. Lyon

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Estimating the Frequency of Cry1F Resistance in Field Populations of the European Corn Borer (Lepidoptera: Crambidae), Blair D. Siegfried, Murugesan Rangasamy, Haichuan Wang, Terence A. Spencer, Chirakkal V. Haridas, Brigitte Tenhumberg, Douglas V. Sumerford, and Nicholas P. Storer

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De Novo Transcriptome Assembly from Fat Body and Flight Muscles Transcripts to Identify Morph-Specific Gene Expression Profiles in Gryllus firmus, Neetha Nanoth Vellichirammal, Anthony J. Zera, Rudolf J. Schilder, Cody Wehrkamp, Jean-Jack M. Riethoven, and Jennifer A. Brisson

2013

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Parasitoid Infestation Changes Female Mating Preferences, Oliver M. Beckers and William E. Wagner

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Experimental confirmation that avian plumage traits function as multiple status signals in winter contests, Alexis S. Chaine, Allison M. Roth, Daizaburo Shizuka, and Bruce E. Lyon

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DNA SEQUENCING REVEALS PATTERNS OF PREY SELECTION IN MIGRATING SHARP-SHINNED HAWKS Las Secuencias de ADN Revelan Patrones de Selección de Presas por Individuos Migratorios de Accipiter striatus, John DeLong, Nancy Cox, Steve Cox, Zachary Hurst, and Jeff Smith

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Four distinct types of dehydration stress memory genes in Arabidopsis thaliana, Yong Ding, Ning Liu, Laetitia Virlouvet, Jean-Jack Riethoven, Michael Fromm, and Zoya Avramova

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Disturbance Frequency and Vertical Distribution of Seeds Affect Long-Term Population Dynamics: A Mechanistic Seed Bank Model, Eric A. Eager, Chirakkal V. Haridas, Diana Pilson, Richard Rebarber, and Brigitte Tenhumberg

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Global Attracting Equilibria for Coupled Systems with Ceiling Density Dependence, Eric A. Eager, Mary Hebert, Elise Hellwig, Francisco Hernandez, Richard Rebarber, Brigitte Tenhumberg, and Bryan Wigianto

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A virus-induced gene silencing method to study soybean cyst nematode parasitism in Glycine max, Pramod K. Kandoth, Robert Heinz, Greg Yeckel, Nathan W. Gross, Parijat S. Juvale, John Hill, Steven A. Whitham, Thomas J. Baum, and Melissa G. Mitchum

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Candida albicans Czf1 and Efg1 Coordinate the Response to Farnesol during Quorum Sensing, White-Opaque Thermal Dimorphism, and Cell Death, Melanie L. Langford, Jessica C. Hargarten, Krista D. Patefield, Elizabeth Marta, Jill R. Blankenship, Saranna Fanning, Kenneth W. Nickerson, and Audrey L. Atkin

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Creating an Interdisciplinary Research Course in Mathematical Ecology, Glenn Ledder and Brigitte Tenhumberg

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An Interdisciplinary Research Course in Theoretical Ecology for Young Undergraduates, Glenn Ledder, Brigitte Tenhumberg, and G. Travis Adams

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Regional Contingencies in the Relationship between Aboveground Biomass and Litter in the World’s Grasslands, Lydia R. O’Halloran, Elizabeth T. Borer, Eric W. Seabloom, Andrew S. MacDougall, Elsa E. Cleland, Rebecca L. McCulley, Sarah Hobbie, W. Stanley Harpole, Nicole M. DeCrappeo, Chengjin Chu, Jonathan D. Bakker, Kendi F. Davies, Guozhen Du, Jennifer Firn, Nicole Hagenah, Kirsten S. Hofmockel, Johannes Knops, Wei Li, Brett A. Melbourne, John W. Morgan, John L. Orrock, Suzanne M. Prober, and Carly J. Stevens

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Repeated elevational transitions in hemoglobin function during the evolution of Andean hummingbirds, Joana Projecto-Garcia, Chandrasekhar Natarajan, Hideaki Moriyama, Roy E. Weber, Angela Fago, Zachary A. Cheviron, Robert Dudley, Jimmy A. McGuire, Christopher C. Witt, and Jay F. Storz

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Repeated elevational transitions in hemoglobin function during the evolution of Andean hummingbirds, Joana Projecto-Garcia, Chandrasekhar Natarajan, Hideaki Moriyama, Roy E. Weber, Angela Fago, Zachary A. Cheviron, Robert Dudley, Jimmy A. McGuire, Christopher C. Witt, and Jay F. Storz

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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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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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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

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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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 Fromm, 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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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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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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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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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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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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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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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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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 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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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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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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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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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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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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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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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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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

2010

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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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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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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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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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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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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 Moriyama

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

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

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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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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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Similar Patterns of Linkage Disequilibrium and Nucleotide Diversity in Native and Introduced Populations of the Pea Aphid, Acyrthosiphon pisum, Jennifer A. Brisson, Sergey V. Nuzhdin, and David L. Stern

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BLOOD SAMPLING REDUCES ANNUAL SURVIVAL IN CLIFF SWALLOWS (PETROCHELIDON PYRRHONOTA) -- La Toma de Muestras de Sangre Reduce la Supervivencia Anual en Petrochelidon pyrrhonota, Charles R. Brown and Mary Bomberger Brown

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Arginine-Induced Germ Tube Formation in Candida albicans Is Essential for Escape from Murine Macrophage Line RAW 264.7, Suman Ghosh, Dhammika H. M. L. P. Navarathna, David D. Roberts, Jake T. Cooper, Audrey L. Atkin, Thomas M. Petro, and Kenneth Nickerson

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Plant Sex and the Evolution of Plant Defenses against Herbivores, Marc T.J. Johnson, Stacey DeWitt Smith, Marc D. Rausher, and Douglas J. Futuyma

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Species-driven changes in nitrogen cycling can provide a mechanism for plant invasions, Johannes M. H. Knops and Ramesh Laungani