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2016

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Tiger salamanders disappearing in region, Dennis M. Ferraro

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Nested species- rich networks of scavenging vertebrates support high levels of interspecific competition, ESTHER SEBASTIÁN-GONZÁLEZ, MARCOS MOLEÓN, JEAN P. GIBERT, FRANCISCO BOTELLA, PATRICIA MATEO-TOMÁS, PEDRO P. OLEA, PAULO R. GUIMARÃES JR., and JOSÉ A. SÁNCHEZ-ZAPATA

2015

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Complete Genome Sequences of Evolved Arsenate-Resistant Metallosphaera sedula Strains, Chenbing Ai, Samuel McCarthy, Wendy Schackwitz, Joel Martin, Anna Lipzen, and Paul Blum

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Generation of an Attenuated, Cross-Protective Pepino mosaic virus Variant Through Alignment-Guided Mutagenesis of the Viral Capsid Protein, Godwill M. Chewachong, Sally A. Miller, Joshua J. Blakeslee, David M. Francis, T. Jack Morris, and Feng Qu

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Socio-Economic Instability and the Scaling of Energy Use with Population Size, John P. DeLong and Oskar Burger

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Variation in the local population dynamics of the short-lived Opuntia macrorhiza (Cactaceae), C. V. Haridas, Kathleen H. Keeler, and Brigitte Tenhumberg

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What drives masting? The phenological synchrony hypothesis, Walter D. Koenig, Johannes M. N. Knops, William J. Carmen, and Ian S. Pearse

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Interspecific egg rejection as ecological collateral damage from selection driven by conspecific brood parasitism, Bruce E. Lyon, Daizaburo Shizuka, and John M. Eadie

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Revisiting operons: an analysis of the landscape of transcriptional units in E. coli, Xizeng Mao, Qin Ma, Bingqiang Liu, Xin Chen, Hanyuan Zhang, and Ying Xu

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Convergent Evolution of Hemoglobin Function in High-Altitude Andean Waterfowl Involves Limited Parallelism at the Molecular Sequence Level, Chandrasekhar Natarajan, Joana Projecto-Garcia, Hideaki Moriyama, Roy E. Weber, Violeta Muñoz-Fuentes, Andy J. Green, Cecilia Kopuchian, Pablo L. Tubaro, Luis Alza, Mariana Bulgarella, Matthew M. Smith, Robert E. Wilson, Angela Fago, Kevin G. McCracken, and Jay F. Storz

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Pollen limitation and flower abortion in a wind-pollinated, masting tree, Ian S. Pearse, Walter D. Koenig, Kyle A. Funk, and Mario B. Pesendorfer

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Genetic Diversity in Oxytocin Ligands and Receptors in New World Monkeys, Dongren Ren, Guoqing Lu, Hideaki Moriyama, Aaryn C. Mustoe, Emily B. Harrison, and Jeffery A. French

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The network motif architecture of dominance hierarchies, Daizaburo Shizuka and David B. McDonald

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Transgenic Virus Resistance in Crop-Wild Cucurbita pepo Does Not Prevent Vertical Transmission of Zucchini yellow mosaic virus, H. E. Simmons, H. R. Prendeville, J. P. Dunham, M. J. Ferrari, J. D. Earnest, D. Pilson, G. P. Munkvold, E. C. Holmes, and A. G. Stephenson

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Oxygenation properties and isoform diversity of snake hemoglobins, Jay F. Storz, Chandrasekhar Natarajan, Hideaki Moriyama, Federico G. Hoffmann, Tobias Wang, Angela Fago, Hans Malte, Johannes Overgaard, and Roy E. Weber

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Integral projection models show exotic thistle is more limited than native thistle by ambient competition and herbivory, Brigitte Tenhumberg, Tomomi Suwa, Andrew J. Tyre, F. Leland Russell, and Svata M. Louda

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Distinct and Cooperative Activities of HESO1 and URT1 Nucleotidyl Transferases in MicroRNA Turnover in Arabidopsis, Bin Tu, Li Liu, Chi Xu, Jixinan Zhai, Shengben Li, Miguel A. Lopez, Yuanyuan Zhao, Yu Yu, Vanitharani Ramachandran, Guodong Ren, Bin Yu, Shigui Li, Blake C. Meyers, Beixin Mo, and Xuemei Chen

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Synergistic and Independent Actions of Multiple Terminal Nucleotidyl Transferases in the 3’ Tailing of Small RNAs in Arabidopsis, Xiaoyan Wang, Shuxin Zhang, Yongchao Dou, Chi Zhang, Xuemei Chen, Bin Yu, and Guodong Ren

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Terrestrial orchids in a tropical forest: best sites for abundance differ from those for reproduction, Melissa Whitman and James D. Ackerman

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Site-Specific Differences in T Cell Frequencies and Phenotypes in the Blood and Gut of HIVUninfected and ART-Treated HIV+ Adults, Steven A. Yukl, Amandeep K. Shergill, Valerie Girling, Qingsheng Li, Maudi Killian, Lorrie Epling, Peilin Li, Philipp Kaiser, Ashley Haase, Diane V. Havlir, Kenneth McQuaid, Elizabeth Sinclair, and Joseph K. Wong

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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The body-size dependence of mutual interference, John P. DeLong

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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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Temperature alters food web body-size structure, Jean P. Gibert and John P. DeLong

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Spatiotemporal variation in flow-dependent recruitment of long-lived riverine fish: Model development and evaluation, Daisuke Goto, Martin J. Hamel, Jeremy J. Hammen, Mathew L. Rugg, Mark A. Pegg, and Valery E. Forbes

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Variation in the local population dynamics of the short-lived Opuntia macrorhiza (Cactaceae), Chirakkal V. Haridas, Kathleen Keeler, and Brigitte Tenhumberg

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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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Leaky termination at premature stop codons antagonizes nonsense-mediated mRNA decay in S. cerevisiae, Kim M. Keeling, Jessica Lanier, Ming Du, Joe Salas-Marco, Lin Gao, Anisa Kaenjak-Angeletti, and David M. Bedwell

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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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Effects of Nitrogen and Phosphorus Fertilization on Soil Carbon Fractions in Alpine Meadows on the Qinghai-Tibetan Plateau, Jin Hua Li, Yu Jie Yang, Bo Wen Li, Wen Jin Li, Gang Wang, and Johannes M. H. Knops

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De novo assembly of the common marmoset transcriptome from NextGen mRNA sequences, Mnirnal D. Maudhoo, Dongren Ren, Julien S. Gradnigo, Robert M. Gibbs, Austin C. Lubker, Etsuko N. Moriyama, Jeffrey A. French, and Robert B. Norgen Jr.

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The temperature independence of interaction strength in a sit-and-wait predator, Rachel A. Novich, Emma K. Erickson, Ryan M. Kalinoski, and John DeLong

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Loss of Sirt1 Function Improves Intestinal Anti-Bacterial Defense and Protects from Colitis-Induced Colorectal Cancer, Giuseppe Lo Sasso, Dongryeol Ryu, Laurent Mouchiroud, Samodha C. Fernando, Christopher L. Anderson, Elena Katsyuba, Alessandra Piersigilli, Michael O. Hottiger, Kristina Schoonjans, and Johan Auwerx

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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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Large-scale spatial synchrony and cross-synchrony in acorn production by two California oaks, Walter D. Koenig and Johannes M.H. Knops

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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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Population-level scaling of avian migration speed with body size and migration distance for powered fliers, Frank A. La Sorte, Daniel Fink, Wesley M. Hochachka, John DeLong, and Steve Kelling

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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

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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, C. 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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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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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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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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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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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 Blum

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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