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Submissions from 2016

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Transcriptional truncation of the long coding imprinted gene Usp29, Hongzhi He, An Ye, and Joomyeong Kim

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Getting a grip at the edge: recolonization and introgression in eastern Pacific Porites corals, Michael E. Hellberg, Carlos Prada, Maxine H. Tan, Zac H. Forsman, and Iliana B. Baums

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Hepatic autophagy contributes to the metabolic response to dietary protein restriction, Tara M. Henagan, Thomas Laeger, Alexandra M. Navard, Diana Albarado, Robert C. Noland, Krisztian Stadler, Carrie M. Elks, David Burk, and Christopher D. Morrison

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate, Michael W. Henson, V. Celeste Lanclos, Brant C. Faircloth, and J. Cameron Thrash

Adapterama IV: Sequence Capture of Dual-digest RADseq Libraries with Identifiable Duplicates (RADcap), Sandra L. Hoffberg, Troy J. Kieran, Julian M. Catchen, Alison Devault, Brant C. Faircloth, Rodney Mauricio, and Travis C. Glenn

RADcap: sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data, S.L. Hoffberg, T.J. Kieran, J.M. Catchen, A. Devault, B.C. Faircloth, R. Mauricio, and T.C. Glenn

Avoiding missing data biases in phylogenomic inference: An empirical study in the landfowl (Aves: Galliformes), P.A. Hosner, B.C. Faircloth, T.C. Glenn, E.L. Braun, and R.T. Kimball

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TreeScaper: Visualizing and extracting phylogenetic signal from sets of trees, Wen Huang, Guifang Zhou, Melissa Marchand, Jeremy R. Ash, David Morris, Paul Van Dooren, Jeremy M. Brown, Kyle A. Gallivan, and Jim C. Wilgenbusch

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Identification of prohormones and pituitary neuropeptides in the African cichlid, Astatotilapia burtoni, Caroline K. Hu, Bruce R. Southey, Elena V. Romanova, Karen P. Maruska, Jonathan V. Sweedler, and Russell D. Fernald

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Genome content and phylogenomics reveal both ancestral and lateral evolutionary pathways in plant-pathogenic Streptomyces species, Jose C. Huguet-Tapia, Tristan Lefebure, Jonathan H. Badger, Dongli Guan, Gregg S. Pettis, Michael J. Stanhope, and Rosemary Loria

The Two-Pore Potassium Channel Trek-1 Alters Inflammasome Activation In Alveolar Macrophages, C. N. Immanuel, J. A. Kennedy, B. Teng, C. Luellen, S. A. Cormier, E. A. Fitzpatrick, A. Schwingshackl, and C. M. Waters

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Deletion of a predicted β-sheet domain within the amino terminus of herpes simplex virus glycoprotein K conserved among alphaherpesviruses prevents virus entry into neuronal axons, Nithya Jambunathan, Anu Susan Charles, Ramesh Subramanian, Ahmad A. Saied, Misagh Naderi, Paul Rider, Michal Brylinski, Vladimir N. Chouljenko, and Konstantin G. Kousoulas

EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms, Daniel A. Janies, Zach Witter, Gregorio V. Linchangco, David W. Foltz, Allison K. Miller, Alexander M. Kerr, Jeremy Jay, and Robert W. Reid

Syntheses and cellular investigations of di-aspartate and aspartate-lysine chlorin e(6) conjugates, R G. Jinadasa, Zehua Zhou, M Graça Vicente, and Kevin M. Smith

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N-terminal lipid modification is required for the stable accumulation of CyanoQ in Synechocystis sp. PCC 6803, Andrea D. Juneau, Laurie K. Frankel, Terry M. Bricker, and Johnna L. Roose

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Discovery of Novel Nonactive Site Inhibitors of the Prothrombinase Enzyme Complex, Karan Kapoor, Nicole McGill, Cynthia B. Peterson, Harold V. Meyers, Michael N. Blackburn, and Jerome Baudry

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Adaptation to climate change: trade-offs among responses to multiple stressors in an intertidal crustacean, Morgan W. Kelly, Melissa B. DeBiasse, Vidal A. Villela, Hope L. Roberts, and Colleen F. Cecola

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Siah2 protein mediates early events in commitment to an adipogenic pathway, Gail Kilroy, David H. Burk, and Z. Elizabeth Floyd

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Phylogenetic and epigenetic footprinting of the putative enhancers of the peg3 domain, Joomyeong Kim and An Ye

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Plasma biomarker analysis in pediatric ARDS: Generating future framework from a pilot randomized control trial of methylprednisolone: A framework for identifying plasma biomarkers related to clinical outcomes in pediatric ARDS, Dai Kimura, Jordy Saravia, Cynthia R. Rovnaghi, Gianfranco Umberto Meduri, Andreas Schwingshackl, Stephania A. Cormier, and Kanwaljeet J. Anand

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Urban microbiomes and urban agriculture: What are the connections and why should we care?, Gary M. King

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition), Daniel J. Klionsky, Kotb Abdelmohsen, Akihisa Abe, Md Joynal Abedin, Hagai Abeliovich, Abraham Acevedo Arozena, Hiroaki Adachi, and Christopher M. Adams

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Differential plant invasiveness is not always driven by host promiscuity with bacterial symbionts, Metha M. Klock, Luke G. Barrett, Peter H. Thrall, and Kyle E. Harms

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Discovery of a new repeat family in the Callithrix jacchus genome, Miriam Konkel, Mark Batzer, Brygg Ullmer, Erika L. Arceneaux, Sreeja Sanampudi, Sarah A. Brantley, Robert Hubley, and Arian F.A. Smit

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Discovery of a new repeat family in the Callithrix jacchus genome, Miriam K. Konkel, Brygg Ullmer, Erika L. Arceneaux, Sreeja Sanampudi, Sarah A. Brantley, Robert Hubley, Arian F.A. Smit, and Mark A. Batzer

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Uncoupling Caveolae from Intracellular Signaling in Vivo, Jan R. Kraehling, Zhengrong Hao, Monica Y. Lee, David J. Vinyard, Heino Velazquez, Xinran Liu, Radu V. Stan, Gary W. Brudvig, and William C. Sessa

Carbon Fixation Driven by Molecular Hydrogen Results in Chemolithoautotrophically Enhanced Growth of Helicobacter pylori, Lisa G. Kuhns, Stéphane L. Benoit, Krishnareddy Bayyareddy, Darryl Johnson, Ron Orlando, Alexandra L. Evans, Grover L. Waldrop, and Robert J. Maier

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Identiication of essential arginine residues of Escherichia coli DedA/Tvp38 family membrane proteins YqjA and YghB, Sujeet Kumar, Cersten L. Bradley, Patience Mukashyaka, and William T. Doerrler

Description of Teunomyces gen. nov. for the Candida kruisii clade, Suhomyces gen. nov. for the Candida tanzawaensis clade and Suhomyces kilbournensis sp. nov, Cletus P. Kurtzman, Christie J. Robnett, and Meredith Blackwell

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The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae), Laura P. Lagomarsino, Fabien L. Condamine, Alexandre Antonelli, Andreas Mulch, and Charles C. Davis

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The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae), Laura P. Lagomarsino, Fabien L. Condamine, Alexandre Antonelli, Andreas Mulch, and Charles C. Davis

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Two new species of Siphocampylus (Campanulaceae, Lobelioideae) from the Central Andes, Laura P. Lagomarsino and Daniel Santamaría-Aguilar

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Two new species of Siphocampylus (Campanulaceae, Lobelioideae) from the Central Andes, Laura P. Lagomarsino and Daniel Santamaría-Aguilar

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A novel phase variant of the cholera pathogen shows stress-adaptive cryptic transcriptomic signatures, Bliss Lambert, Maheshi Dassanayake, Dong Ha Oh, Shana B. Garrett, Sang Yeol Lee, and Gregg S. Pettis

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Does corticosterone regulate the onset of breeding in free-living birds?: The CORT-Flexibility Hypothesis and six potential mechanisms for priming corticosteroid function, Christine R. Lattin, Creagh W. Breuner, and L. Michael Romero

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NGS-based deep bisulfite sequencing, Suman Lee and Joomyeong Kim

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Discordant coral–symbiont structuring: factors shaping geographical variation of Symbiodinium communities in a facultative zooxanthellate coral genus, Oculina, Karine Posbic Leydet and Michael E. Hellberg

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Long-term shifts in the patterns and underlying processes of plant associations in Wisconsin forests, Daijiang Li and Donald Waller

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Evolutionary aspects of plant photoreceptors, Fay Wei Li and Sarah Mathews

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Evolutionary innovation and diversification of carotenoid-based pigmentation in finches, Russell A. Ligon, Richard K. Simpson, Nicholas A. Mason, Geoffrey E. Hill, and Kevin J. McGraw

Response of salt marshes to oiling from the Deepwater Horizon spill: Implications for plant growth, soil surface-erosion, and shoreline stability, Qianxin Lin, Irving A. Mendelssohn, Sean A. Graham, Aixin Hou, John W. Fleeger, and Donald R. Deis

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A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes, Yuchen Liu, David J. Vinyard, Megan E. Reesbeck, Tateki Suzuki, Kasidet Manakongtreecheep, Patrick L. Holland, Gary W. Brudvig, and Dieter Söll

Sen1, the yeast homolog of human senataxin, plays a more direct role than Rad26 in transcription coupled DNA repair, Wentao Li, Kathiresan Selvam, Sheikh A. Rahman, and Shisheng Li

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Is exposure to Macondo oil reflected in the otolith chemistry of marsh-resident fish?, Paola C. López-Duarte, F. Joel Fodrie, Olaf P. Jensen, Andrew Whitehead, Fernando Galvez, Benjamin Dubansky, and Kenneth W. Able

Template-based identification of protein-protein interfaces using eFindSitePPI, Surabhi Maheshwari and Michal Brylinski

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Comparison of electrophysiological auditory measures in fishes, Karen P. Maruska and Joseph A. Sisneros

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The Thr–His Connection on the Distal Heme of Catalase-Related Hemoproteins: A Hallmark of Reaction with Fatty Acid Hydroperoxides, Zahra Mashhadi, Marcia E. Newcomer, and Alan R. Brash

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Membership trends in the American Ornithologists' Union and the evolving role of professional ornithological societies, Nicholas A. Mason, Michael W. Butler, and Jennifer C. Owen

Sequence capture of ultraconserved elements from bird museum specimens, J.E. McCormack, W.L.E. Tsai, and B.C. Faircloth

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Isolation and characterization of extremely halophilic CO-oxidizing Euryarchaeota from hypersaline cinders, sediments and soils and description of a novel CO oxidizer, Haloferax namakaokahaiae Mke2.3T, sp. nov., S. McDuff, G. M. King, S. Neupane, and M. R. Myers

Replicated divergence in cichlid radiations mirrors a major vertebrate innovation, M.D. McGee, B.C. Faircloth, S.R. Borstein, J. Zheng, C.D. Hulsey, P.C. Wainwright, and M.E. Alfaro

Analysis of a rapid evolutionary radiation using ultraconserved elements: Evidence for a bias in some multispecies coalescent methods, K.A. Meiklejohn, B.C. Faircloth, T.C. Glenn, R.T. Kimball, and E.L. Braun

Modularity: Genes, Development, and Evolution, Diogo Melo, Arthur Porto, James M. Cheverud, and Gabriel Marroig

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Do ploidy level and nuclear genome size and latitude of origin modify the expression of Phragmites australis traits and interactions with herbivores?, Laura A. Meyerson, James T. Cronin, Ganesh P. Bhattarai, Hans Brix, Carla Lambertini, Magdalena Lučanová, Shelby Rinehart, Jan Suda, and Petr Pyšek

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Phragmites australis as a model organism for studying plant invasions, Laura A. Meyerson, James T. Cronin, and Petr Pyšek

THE DYNAMICS OF RESPIRATORY SYNCYTIAL VIRUS (RSV) REPLICATION REVEALS AN AGE-RELATED FUNCTIONAL MATURATION OF THE INFANT ANTIVIRAL IMMUNE RESPONSE, C. R. Miller, A. Shah, L. Harrison, E. Meals, C. Hyrne, B. Bagga, Y. Kim-Hoehamer, L. Benhabiles, S. Cormier, and J. DeVincenzo

A test of biological trait analysis with nematodes and an anthropogenic stressor, Hanan M. Mitwally and John W. Fleeger

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Cryopreservation of lipid bilayers by LEA proteins from Artemia franciscana and trehalose, Daniel S. Moore and Steven C. Hand

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Liposomes with diverse compositions are protected during desiccation by LEA proteins from Artemia franciscana and trehalose, Daniel S. Moore, Richard Hansen, and Steven C. Hand

Tectonic collision and uplift of Wallacea triggered the global songbird radiation, R.G. Moyle, C.H. Oliveros, M.J. Andersen, P.A. Hosner, B.W. Benz, J.D. Manthey, S.L. Travers, R.M. Brown, and B.C. Faircloth

INFANT MUCOSAL RSV-SPECIFIC IGA RESPONSE DYNAMICS DURING AND AFTER INFECTION, N. Mulroy, J. DeVincenzo, B. Bagga, E. Meals, L. Harrison, B. Sealy, J. Hurwitz, L. Benhabilies, S. Cormier, and D. R. Hijano

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Use of Protein Cross-Linking and Radiolytic Labeling to Elucidate the Structure of PsbO within Higher-Plant Photosystem II, Manjula P. Mummadisetti, Laurie K. Frankel, Henry D. Bellamy, Larry Sallans, Jost S. Goettert, Michal Brylinski, and Terry M. Bricker

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Use of Protein Cross-Linking and Radiolytic Labeling to Elucidate the Structure of PsbO within Higher-Plant Photosystem II, Manjula P. Mummadisetti, Laurie K. Frankel, Henry D. Bellamy, Larry Sallans, Jost S. Goettert, Michal Brylinski, and Terry M. Bricker

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Isolation and characterization of Acidobacterium ailaaui sp. Nov., a novel member of Acidobacteria subdivision 1, from a geothermally heated Hawaiian microbial mat, Marisa R. Myers and G. M. King

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A graph-based approach to construct target-focused libraries for virtual screening, Misagh Naderi, Chris Alvin, Yun Ding, Supratik Mukhopadhyay, and Michal Brylinski

E4orf1 Enhances Glucose Uptake Independent of Proximal Insulin Signaling, Ha-Na Na, Vijay Hegde, Olga Dubuisson, and Nikhil V. Dhurandhar

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Modulation of IL-27 in adipocytes during inflammatory stress, Heesun Nam, Bradley S. Ferguson, Jacqueline M. Stephens, and Ron F. Morrison

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Correlates of sociometric status in Russian preschoolers: Aggression, victimization, and sociability, David A. Nelson, Kathryn C. Burner, Sarah M. Coyne, Craig H. Hart, and Clyde C. Robinson

Smoking cessation counseling in vascular surgical practice using the results of interviews and focus groups in the Vascular Surgeon offer and report smoking cessation pilot trial, Karina Newhall, Mary Burnette, Benjamin S. Brooke, Andres Schanzer, TzeWoei Tan, Susan Flocke, Alik Farber, and Philip Goodney

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Sequence capture and next-generation sequencing of ultraconserved elements in a large-genome salamander, Catherine E. Newman and Christopher C. Austin

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An extract of Urtica dioica L. mitigates obesity induced insulin resistance in mice skeletal muscle via protein phosphatase 2A (PP2A), Diana N. Obanda, David Ribnicky, Yongmei Yu, Jacqueline Stephens, and William T. Cefalu

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Stinging nettle (Urtica dioica L.) attenuates FFA induced ceramide accumulation in 3T3- L1 adipocytes in an adiponectin dependent manner, Diana N. Obanda, Peng Zhao, Allison J. Richard, David Ribnicky, William T. Cefalu, and Jacqueline M. Stephens

Effect of Different Fluids on Rectified Motion of Leidenfrost Droplets on Micro/Sub-Micron Ratchets, Jeong Tae Ok, Junseo Choi, Emily Brown, and Sunggook Park

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Willet be one species or two? A genomic view of the evolutionary history of Tringa semipalmata, Jessica A. Oswald, Michael G. Harvey, Rosalind C. Remsen, Depaul U. Foxworth, Steven W. Cardiff, Donna L. Dittmann, Libby C. Megna, Matthew D. Carling, and Robb T. Brumfield

Experimental inoculation of Louisiana red swamp crayfish Procambarus clarkii with white spot syndrome virus (WSSV), Barcley T. Pace, John P. Hawke, Ramesh Subramanian, and Christopher C. Green

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Physiological plasticity and local adaptation to elevated pCO2 in calcareous algae: an ontogenetic and geographic approach, Jacqueline L. Padilla-Gamiño, Juan Diego Gaitán-Espitia, Morgan W. Kelly, and Gretchen E. Hofmann

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The high mobility group protein HMO1 functions as a linker histone in yeast, Arvind Panday and Anne Grove

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Vector species richness increases haemorrhagic disease prevalence through functional diversity modulating the duration of seasonal transmission, Andrew W. Park, Christopher A. Cleveland, Tad A. Dallas, and Joseph L. Corn

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Variation in the whole mitogenome of reef-building Porites corals, David A. Paz-García, Carolina Galván-Tirado, Juan José Alvarado, Jorge Cortés, Francisco J. García-De-León, Michael E. Hellberg, and Eduardo F. Balart

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Alternative promoters of Peg3 with maternal specificity, Bambarendage P.U. Perera and Joomyeong Kim

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Next-generation sequencing-based 5′ rapid amplification of cDNA ends for alternative promoters, Bambarendage P.U. Perera and Joomyeong Kim

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Sex and tissue specificity of Peg3 promoters, Bambarendage P.U. Perera and Joomyeong Kim

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Insights from the pollination drop proteome and the ovule transcriptome of Cephalotaxus at the time of pollination drop production, Cary Pirone-Davies, Natalie Prior, Patrick Von Aderkas, Derek Smith, Darryl Hardie, William E. Friedman, and Sarah Mathews

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Pyrogenic fuels produced by savanna trees can engineer humid savannas, William J. Platt, Darin P. Ellair, Jean M. Huffman, Stephen E. Potts, and Brian Beckage

Biomass resilience of Neotropical secondary forests, Lourens Poorter, Frans Bongers, T Mitchell Aide, Angélica M. Almeyda Zambrano, Patricia Balvanera, Justin M. Becknell, Vanessa Boukili, and Pedro H. Brancalion

Evolution of the Genotype-to-Phenotype Map and the Cost of Pleiotropy in Mammals, Arthur Porto, Ryan Schmelter, John L. VandeBerg, Gabriel Marroig, and James M. Cheverud

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Distinct encounter complexes of PAI-1 with plasminogen activators and vitronectin revealed by changes in the conformation and dynamics of the reactive center loop, Tihami Qureshi, Sumit Goswami, Carlee S. McClintock, Matthew T. Ramsey, and Cynthia B. Peterson

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Single fluorescence probes along the reactive center loop reveal site-specific changes during the latency transition of PAI-1, Tihami Qureshi and Cynthia B. Peterson

A Meta-analysis of Multiple Myeloma Risk Regions in African and European Ancestry Populations Identifies Putatively Functional Loci, Kristin A. Rand, Chi Song, Eric Dean, Daniel J. Serie, Karen Curtin, Xin Sheng, Donglei Hu, and Carol Ann Huff

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A conceptual framework for graduate teaching assistant professional development evaluation and research, Todd D. Reeves, Gili Marbach-Ad, Kristen R. Miller, Judith Ridgway, Grant E. Gardner, Elisabeth E. Schussler, and E. William Wischusen

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Astrocytes regulate GLP-1 receptor-mediated effects on energy balance, David J. Reiner, Elizabeth G. Mietlicki-Baase, Lauren E. McGrath, Derek J. Zimmer, Kendra K. Bence, Gregory L. Sousa, Vaibhav R. Konanur, Joanna Krawczyk, David H. Burk, Scott E. Kanoski, et al.

Comparative genomics of biotechnologically important yeasts, Robert Riley, Sajeet Haridas, Kenneth H. Wolfe, Mariana R. Lopes, Chris Todd Hittinger, Markus Göker, Asaf A. Salamov, and Jennifer H. Wisecaver

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Editorial: Ethylene’s role in plant mineral nutrition, Francisco J. Romera, Aaron P. Smith, and Rafael Pérez-Vicente

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The extrinsic proteins of photosystem II: update, Johnna L. Roose, Laurie K. Frankel, Manjula P. Mummadisetti, and Terry M. Bricker

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Characterization of the drosophila BEAF-32A and BEAF-32B insulator proteins, S. V. Satya Prakash Avva and Craig M. Hart

Status of the Archaeal and Bacterial Census: an Update, Patrick D. Schloss, Rene A. Girard, Thomas Martin, Joshua Edwards, and J Cameron Thrash

The effects of high fat diet and estradiol on hypothalamic prepro-QRFP mRNA expression in female rats, Allyson L. Schreiber, Kenneth P. Arceneaux, Raphael A. Malbrue, Alan J. Mouton, Christina S. Chen, Elias M. Bench, H Douglas Braymer, and Stefany D. Primeaux

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Regulation of inflammatory biomarkers by intravenous methylprednisolone in pediatric ARDS patients: Results from a double-blind, placebo-controlled randomized pilot trial, Andreas Schwingshackl, Dai Kimura, Cynthia R. Rovnaghi, Jordy S. Saravia, Stephania A. Cormier, Bin Teng, Alina N. West, Umberto G. Meduri, and Kanwaljeet J.S. Anand

New compartment model analysis of lean-mass and fat-mass growth with overfeeding, Dmytro Shumilov, Steven B. Heymsfield, Leanne M. Redman, Steven R. Smith, George A. Bray, Kesava Kalluri, and Joyoni Dey

The influence of genetic diversity on neonatal respiratory syncytial virus disease, D. Siefker, R. W. Williams, L. Lu, D. H. You, and S. Cormier