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Submissions from 2016

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Mechanisms of regulation of invasive processes in phytoplankton on the example of the north-eastern part of the Black Sea, V. A. Silkin, A. I. Abakumov, L. A. Pautova, S. V. Pakhomova, and A. V. Lifanchuk

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Crystal Structure of Carboxyltransferase from Staphylococcus aureus Bound to the Antibacterial Agent Moiramide B, Molly A. Silvers, Svetlana Pakhomova, David B. Neau, William C. Silvers, Nicholas Anzalone, Carol M. Taylor, and Grover L. Waldrop

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Environmental stress in the Gulf of Mexico and its potential impact on public health, B. Singleton, J. Turner, L. Walter, N. Lathan, D. Thorpe, P. Ogbevoen, J. Daye, D. Alcorn, S. Wilson, J. Semien, et al.

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Streptomyces coelicolor XdhR is a direct target of (p)ppGpp that controls expression of genes encoding xanthine dehydrogenase to promote purine salvage, Smitha Sivapragasam and Anne Grove

Methods for Efficient Elimination of Mitochondrial DNA from Cultured Cells, Domenico Spadafora, Nataliya Kozhukhar, Vladimir N. Chouljenko, Konstantin G. Kousoulas, and Mikhail F. Alexeyev

Differences in Mitochondrial Coupling Reveal a Novel Signature of Mitohormesis in Muscle of Healthy Individuals, Lauren M. Sparks, Leanne M. Redman, Kevin E. Conley, Mary-Ellen Harper, Andrew Hodges, Alexey Eroshkin, Sheila R. Costford, and Meghan E. Gabriel

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IGF1 and adipose tissue homeostasis, Jacqueline M. Stephens

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Exposure to environmentally persistent free radicals during gestation lowers energy expenditure and impairs skeletal muscle mitochondrial function in adult mice, Erin J. Stephenson, Alyse Ragauskas, Sridhar Jaligama, Jeanna R. Redd, Jyothi Parvathareddy, Matthew J. Peloquin, Jordy Saravia, Joan C. Han, Stephania A. Cormier, and Dave Bridges

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The macroecology of infectious diseases: a new perspective on global-scale drivers of pathogen distributions and impacts, Patrick R. Stephens, Sonia Altizer, Katherine F. Smith, A. Alonso Aguirre, James H. Brown, Sarah A. Budischak, James E. Byers, Tad A. Dallas, T. Jonathan Davies, John M. Drake, et al.

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Synthesis, Characterization, and Biological Studies of a Piperidinyl Appended Dipicolylamine Ligand and Its Rhenium Tricarbonyl Complex as Potential Therapeutic Agents for Human Breast Cancer, Amali Subasinghe, Inoka C. Perera, Svetlana Pakhomova, and Theshini Perera

No evidence for metabolic adaptation in thermic effect of food by dietary protein, Elizabeth F. Sutton, George A. Bray, Jeffrey H. Burton, Steven R. Smith, and Leanne M. Redman

Smartphone applications to aid weight loss and management: current perspectives, Elizabeth F. Sutton and Leanne M. Redman

Assessment of genetically engineered Trabulsiella odontotermitis as a 'Trojan Horse' for paratransgenesis in termites, Chinmay Vijay Tikhe, Thomas M. Martin, Andréa Howells, Jennifer Delatte, and Claudia Husseneder

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Impaired Mitochondrial Fat Oxidation Induces FGF21 in Muscle, Bolormaa Vandanmagsar, Jaycob D. Warfel, Shawna E. Wicks, Sujoy Ghosh, J. Michael Salbaum, David Burk, Olga S. Dubuisson, Tamra M. Mendoza, Jingying Zhang, Robert C. Noland, et al.

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Ammonia Binding in the Second Coordination Sphere of the Oxygen-Evolving Complex of Photosystem II, David J. Vinyard, Mikhail Askerka, Richard J. Debus, Victor S. Batista, and Gary W. Brudvig

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Natural isoforms of the Photosystem II D1 subunit differ in photoassembly efficiency of the water-oxidizing complex, David J. Vinyard, Jennifer S. Sun, Javier Gimpel, Gennady M. Ananyev, Stephen P. Mayfield, and G. Charles Dismukes

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MSH1 Is a Plant Organellar DNA Binding and Thylakoid Protein under Precise Spatial Regulation to Alter Development, Kamaldeep S S. Virdi, Yashitola Wamboldt, Hardik Kundariya, John D D. Laurie, Ido Keren, K. R. Sunil Kumar, Anna Block, Gilles Basset, Steve Luebker, Christian Elowsky, et al.

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Physiological evidence for plasticity in glycolate/glycerate transport during photorespiration, Berkley J. Walker, Paul F. South, and Donald R. Ort

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A New Genus and Species of Blind Sleeper (Teleostei: Eleotridae) from Oaxaca, Mexico: First Obligate Cave Gobiiform in the Western Hemisphere, Stephen J. Walsh and Prosanta Chakrabarty

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PDID: Database of molecular-level putative protein-drug interactions in the structural human proteome, Chen Wang, Gang Hu, Kui Wang, Michal Brylinski, Lei Xie, and Lukasz Kurgan

Functional Analysis of a Bacterial Antifreeze Protein Indicates a Cooperative Effect between Its Two Ice-Binding Domains, Chen Wang, Erin E. Oliver, Brent C. Christner, and Bing Hao Luo

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Transcription factor Reb1 is required for proper transcriptional start site usage at the divergently transcribed TFC6-ESC2 locus in Saccharomyces cerevisiae, Qing Wang and David Donze

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14th congress of combustion by-products and their health effects—origin, fate, and health effects of combustion-related air pollutants in the coming era of bio-based energy sources, Eva Weidemann, Patrik L. Andersson, Terry Bidleman, Christoffer Boman, Danielle J. Carlin, Elena Collina, Stephania A. Cormier, Sandra C. Gouveia-Figueira, Brian K. Gullett, Christer Johansson, et al.

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The modulation of adiponectin by STAT5-activating hormones, Ursula A. White, Joel Maier, Peng Zhao, Allison J. Richard, and Jacqueline M. Stephens

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Persistence of neighborhood demographic influences over long phylogenetic distances may help drive post-speciation adaptation in tropical forests, Christopher Wills, Kyle E. Harms, Thorsten Wiegand, Ruwan Punchi-Manage, Gregory S. Gilbert, David Erickson, W. John Kress, Stephen P. Hubbell, C. V.Savitri Gunatilleke, and I. A.U.Nimal Gunatilleke

Synthesis and in Vitro Studies of a Series of Carborane-Containing Boron Dipyrromethenes (BODIPYs), Sunting Xuan, Ning Zhao, Zehua Zhou, Frank R. Fronczek, and M Graça Vicente

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PEG3 binds to H19-ICR as a transcriptional repressor, An Ye, Hongzhi He, and Joomyeong Kim

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Crawling with virus: Translational insights from a neonatal mouse model on the pathogenesis of respiratory syncytial virus in infants, Dahui You, Jordy Saravia, David Siefker, Bishwas Shrestha, and Stephania A. Cormier

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Phenotypes in phylogeography: Species' traits, environmental variation, and vertebrate diversification, Kelly R. Zamudio, Rayna C. Bell, and Nicholas A. Mason

Hidden histories of gene flow in highland birds revealed with genomic markers, Eugenia Zarza, Brant C. Faircloth, Whitney L.E. Tsai, Robert W. Bryson Jr., John Klicka, and John E. McCormack

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Dietary Plant Lectins Appear to Be Transported from the Gut to Gain Access to and Alter Dopaminergic Neurons of Caenorhabditis elegans, a Potential Etiology of Parkinson’s Disease, Jolene Zheng, Mingming Wang, Wenqian Wei, Jeffrey N. Keller, Binita Adhikari, Jason F. King, Michael L. King, Nan Peng, and Roger A. Laine

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The Mouse-colored Tyrannulet (Phaeomyias murina) is a species complex that includes the Cocos Flycatcher (Nesotriccus ridgwayi), an island form that underwent a population bottleneck, Marc R. Zucker, Michael G. Harvey, Jessica A. Oswald, Andrés Cuervo, Elizabeth Derryberry, and Robb T. Brumfield

Submissions from 2015

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On exotic and perverse-coherent sheaves, Pramod N. Achar

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Geometric Satake, Springer correspondence, and small representations II, Pramod N. Achar, Anthony Henderson, and Simon Riche

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Sheaves on nilpotent cones, fourier transform, and a geometric ringel duality, Pramod N. Achar and Carl Mautner

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Constructible sheaves on affine Grassmannians and geometry of the dual nilpotent cone, Pramod N. Achar and Simon Riche

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Parity sheaves on the affine Grassmannian and the Mirković–Vilonen conjecture, Pramod N. Achar and Laura Rider

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An extract of Artemisia dracunculus L. stimulates insulin secretion from β cells, activates AMPK and suppresses inflammation, Sita Aggarwal, Giri Shailendra, David M. Ribnicky, David Burk, Namrata Karki, and M. S. Qingxia Wang

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Multitrophic enemy escape of invasive Phragmites australis and its introduced herbivores in North America, Warwick J. Allen, Randee E. Young, Ganesh P. Bhattarai, Jordan R. Croy, Adam M. Lambert, Laura A. Meyerson, and James T. Cronin

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Unusual Example of Chelate Ring Opening upon Coordination of the 9-Ethylguanine Nucleobase to [Pt(di-(6-methyl-2-picolyl)amine)Cl]Cl, Chase Andrepont, Svetlana Pakhomova, Patricia A. Marzilli, and Luigi G. Marzilli

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NH3 Binding to the S2 State of the O2-Evolving Complex of Photosystem II: Analogue to H2O Binding during the S2 → S3 Transition, Mikhail Askerka, David J. Vinyard, Gary W. Brudvig, and Victor S. Batista

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Analysis of the radiation-damage-free x-ray structure of photosystem ii in light of exafs and QM/MM data, Mikhail Askerka, David J. Vinyard, Jimin Wang, Gary W. Brudvig, and Victor S. Batista

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A global reference for human genetic variation, Adam Auton, Gonçalo R. Abecasis, David M. Altshuler, Richard M. Durbin, David R. Bentley, Aravinda Chakravarti, Andrew G. Clark, Peter Donnelly, Evan E. Eichler, Paul Flicek, et al.

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Biological evidence supports an early and complex emergence of the Isthmus of Panama, Christine D. Bacona, Daniele Silvestro, Carlos Jaramillo, Brian Tilston Smith, Prosanta Chakrabarty, and Alexandre Antonelli

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Correction: Biological evidence supports an early and complex emergence of the Isthmus of Panama (Proceedings of National Academy of Sciences United States of America (2015), 112 (6110-6115) DOI: 10.1073/pnas.1423853112), Christine D. Bacon, Daniele Silvestro, Carlos Jaramillo, Brian Tilston Smith, Prosanta Chakrabarty, and Alexandre Antonelli

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Erratum: Biological evidence supports an early and complex emergence of the Isthmus of Panama (Proceedings of the National Academy of Sciences of the United States of America (2015) 112:19 (6110-6115) DOI: 10.1073/pnas.1423853112), Christine D. Bacon, Daniele Silvestro, Carlos Jaramillo, Brian Tilston Smith, Prosanta Chakrabarty, and Alexandre Antonelli

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Reply to Lessios and Marko et al.: Early and progressive migration across the Isthmus of Panama is robust to missing data and biases, Christine D. Bacon, Daniele Silvestro, Carlos Jaramillo, Brian Tilston Smith, Prosanta Chakrabarty, and Alexandre Antonelli

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Locus-specific DNA methylation analysis of retrotransposons in ES, somatic and cancer cells using High-Throughput Targeted Repeat Element Bisulfite Sequencing, Arundhati Bakshi, Muhammad B. Ekram, and Joomyeong Kim

Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest, A. Barberán, K.L. Mcguire, J.A. Wolf, F.A. Jones, S.J. Wright, B.L. Turner, A. Essene, S.P. Hubbell, B.C. Faircloth, and N. Fierer

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Interspecific competition affects evolutionary links between cavity nesting, migration and clutch size in Old World flycatchers (Muscicapdae), Sahas Barve and Nicholas A. Mason

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High yield non-detergent isolation of photosystem I-light-harvesting chlorophyll II membranes from spinach thylakoids: Implications for the organization of the PS I antennae in higher plants, Adam J. Bell, Laurie K. Frankel, and Terry M. Bricker

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Positive priming of terrestrially derived dissolved organic matter in a freshwater microcosm system, Thomas S. Bianchi, Daniel C.O. Thornton, Shari A. Yvon-Lewis, Gary M. King, Timothy I. Eglinton, Michael R. Shields, Nicholas D. Ward, and Jason Curtis

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Experimental Support for a Single Electron-Transfer Oxidation Mechanism in Firefly Bioluminescence, Bruce R. Branchini, Curran E. Behney, Tara L. Southworth, Danielle M. Fontaine, Andrew M. Gulick, David J. Vinyard, and Gary W. Brudvig

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Reciprocal osmotic challenges reveal mechanisms of divergence in phenotypic plasticity in the killifish Fundulus heteroclitus, Reid S. Brennan, Fernando Galvez, and Andrew Whitehead

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Epigenetic instability at imprinting control regions in a KrasG12D-induced T-cell neoplasm, Corey L. Bretz, Ingeborg M. Langohr, Suman Lee, and Joomyeong Kim

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Recent advances in the use of mass spectrometry to examine structure/function relationships in photosystem II, Terry M. Bricker, Manjula P. Mummadisetti, and Laurie K. Frankel

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Structural Analysis of Substrate, Reaction Intermediate, and Product Binding in Haemophilus influenzae Biotin Carboxylase, Tyler C. Broussard, Svetlana Pakhomova, David B. Neau, Ross Bonnot, and Grover L. Waldrop

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Correction: Functional characterization of the Chlamydomonas reinhardtii ERG3 ortholog, a gene involved in the biosynthesis of ergosterol, Kristy M. Brumfield, James V. Moroney, Thomas S. Moore, Tiffany A. Simms, and David Donze

Is the growth rate of Protein Data Bank sufficient to solve the protein structure prediction problem using template-based modeling?, Michal Brylinski

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CCL20 is elevated during obesity and differentially regulated by NF-κB subunits in pancreatic β-cells, Susan J. Burke, Michael D. Karlstad, Kellie M. Regal, Tim E. Sparer, Danhong Lu, Carrie M. Elks, Ryan W. Grant, Jacqueline M. Stephens, David H. Burk, and J. Jason Collier

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Thiobenzothiazole-modified hydrocortisones display anti-inflammatory activity with reduced impact on islet β-cell function, Susan J. Burke, Amanda L. May, Robert C. Noland, Danhong Lu, Marcela Brissova, Alvin C. Powers, Elizabeth M. Sherrill, Michael D. Karlstad, Shawn R. Campagna, Jacqueline M. Stephens, et al.

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IL-1β reciprocally regulates chemokine and insulin secretion in pancreatic β-cells via NF-κB, Susan J. Burke, Krisztian Stadler, Danhong Lu, Evanna Gleason, Anna Han, Dallas R. Donohoe, Richard C. Rogers, Gerlinda E. Hermann, Michael D. Karlstad, and J. Jason Collier

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The mechanosensory lateral line is used to assess opponents and mediate aggressive behaviors during territorial interactions in an African cichlid fish, Julie M. Butler and Karen P. Maruska

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Developmental changes in hypoxic exposure and responses to anoxia in Drosophila melanogaster, Viviane Callier, Steven C. Hand, Jacob B. Campbell, Taylor Biddulph, and Jon F. Harrison

Non-ionic water-soluble "clickable" α-helical polypeptides: Synthesis, characterization and side chain modification, Jinbao Cao, Ping Hu, Lu Lu, Brandon A. Chan, Bing Hao Luo, and Donghui Zhang

Amino acid specificity of fibers of the facial/trigeminal complex innervating the maxillary barbel in the Japanese sea catfish, Plotosus japonicus, John Caprio, Mami Shimohara, Takayuki Marui, Jun Kohbara, Shuitsu Harada, and Sadao Kiyohara

Formalizing the names of subfamilies and tribes of ponyfishes (Leiognathidae Gill 1893), Prosanta Chakrabarty and John S. Sparks

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Externally and Internally Functionalized Copper(II) β-Diketonate Molecular Squares, Jackson K. Cherutoi, Jace D. Sandifer, Uttam R. Pokharel, Frank R. Fronczek, Svetlana Pakhomova, and Andrew W. Maverick

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Binding of dinitrogen to an iron-sulfur-carbon site, Ilija Čorić, Brandon Q. Mercado, Eckhard Bill, David J. Vinyard, and Patrick L. Holland

Exposure to combustion-derived particulate matter: an unrecognized risk factor in severity of respiratory viral infection in infants, S. Cormier, G. Lee, J. Saravia, D. H. You, B. Shrestha, S. Jaligama, V. Hebert, and T. Dugas

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Human adipose tissue as a reservoir for memory CD4+ T cells and HIV, Jacob Couturier, James W. Suliburk, Jeremy M. Brown, David J. Luke, Neeti Agarwal, Xiaoying Yu, Chi Nguyen, Dinakar Iyer, Claudia A. Kozinetz, Paul A. Overbeek, et al.

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Human Adipose Tissue As A Reservoir For Memory Cd4(+) T Cells And Hiv, J Couturier, J W. Suliburk, J M. Brown, D J. Luke, J Couturier, X Y. Yu, C Nguyen, D Iyer, C A. Kozinetz, P A. Overbeek, et al.

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Human Adipose Tissue As A Reservoir For Memory Cd4(+) T Cells And Hiv, J Couturier, J W. Suliburk, J M. Brown, D J. Luke, J Couturier, X Y. Yu, C Nguyen, D Iyer, C A. Kozinetz, P A. Overbeek, et al.

A phylogenomic analysis of turtles, N.G. Crawford, J.F. Parham, A.B. Sellas, B.C. Faircloth, T.C. Glenn, T.J. Papenfuss, J.B. Henderson, M.H. Hansen, and W.B. Simison

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Biogeography of a plant invasion: Plant-herbivore interactions, James T. Cronin, Ganesh P. Bhattarai, Warwick J. Allen, and Laura A. Meyerson

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Co-extinction in a host-parasite network: Identifying key hosts for network stability, Tad Dallas and Emily Cornelius

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Toll-like receptor 4 inhibition within the paraventricular nucleus attenuates blood pressure and inflammatory response in a genetic model of hypertension, Rahul B. Dange, Deepmala Agarwal, Ryoichi Teruyama, and Joseph Francis

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Effect of 12 weeks of periodized resistance training upon total plasma adiponectin concentration in healthy young men, Greggory R. Davis, Jacqueline M. Stephens, and Arnold G. Nelson

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Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia, Melissa B. Debiasse and Michael E. Hellberg

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Examining evolutionary relationships and shifts in depth preferences in batfishes (Lophiiformes: Ogcocephalidae), Valerie Derouen, William B. Ludt, Hsuan Ching Ho, and Prosanta Chakrabarty

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GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field, Yun Ding, Ye Fang, Wei P. Feinstein, Jagannathan Ramanujam, David M. Koppelman, Juana Moreno, Michal Brylinski, and Mark Jarrell

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Can we identify genes with increased phylogenetic reliability?, Vinson P. Doyle, Randee E. Young, Gavin J.P. Naylor, and Jeremy M. Brown

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Can We Identify Genes With Increased Phylogenetic Reliability?, V P. Doyle, R E. Young, G J. Naylor, J M. Brown, and V P. Doyle

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Can We Identify Genes With Increased Phylogenetic Reliability?, V P. Doyle, R E. Young, G J. Naylor, J M. Brown, and V P. Doyle

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Phylogeography of the military macaw (Ara militaris) and the Great Green Macaw (A. Ambiguus) based on MTDNA sequence data, Jessica R. Eberhard, Eduardo E. Iñigo-Elias, Ernesto Enkerlin-Hoeflich, and E. Paùl Cun

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Oncostatin M modulation of lipid storage, Carrie M. Elks, Jacqueline M. Stephens, and Jacqueline M. Stephens

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Blueberries improve glucose tolerance without altering body composition in obese postmenopausal mice, Carrie M. Elks, Jennifer D. Terrebonne, Donald K. Ingram, and Jacqueline M. Stephens

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Mechanistic species distribution modelling as a link between physiology and conservation, Tyler G. Evans, Sarah E. Diamond, and Morgan W. Kelly

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Ocean acidification research in the 'post-genomic' era: Roadmaps from the purple sea urchin Strongylocentrotus purpuratus, Tyler G. Evans, Jacqueline L. Padilla-Gamiño, Morgan W. Kelly, Melissa H. Pespeni, Francis Chan, Bruce A. Menge, Brian Gaylord, Tessa M. Hill, Ann D. Russell, Stephen R. Palumbi, et al.

PHYLUCE is a software package for the analysis of conserved genomic loci, B.C. Faircloth

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among hymenoptera, B.C. Faircloth, M.G. Branstetter, N.D. White, and S.G. Brady

Accelerated Structural Bioinformatics for Drug Discovery, Wei P. Feinstein and Michal Brylinski

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Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets, Wei P. Feinstein and Michal Brylinski

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Accelerating the pace of protein functional annotation with intel xeon phi coprocessors, Wei P. Feinstein, Juana Moreno, Mark Jarrell, and Michal Brylinski

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Updating models for restoration and management of fiery ecosystems, Jennifer M. Fill, William J. Platt, Shane M. Welch, Jayme L. Waldron, and Timothy A. Mousseau

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Increased phosphate transport of Arabidopsis thalianaPht1;1 by site-directed mutagenesis of tyrosine 312 may be attributed to the disruption of homomeric interactions, Elena B. Fontenot, Sandra Feuer DiTusa, Naohiro Kato, Danielle M. Olivier, Renee Dale, Wei Yi Lin, Tzyy Jen Chiou, Megan A. Macnaughtan, and Aaron P. Smith

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The geographic distribution of a tropical montane bird is limited by a tree: Acorn Woodpeckers (Melanerpes formicivorus) and Colombian oaks (Quercus humboldtii) in the Northern Andes, Benjamin G. Freeman and Nicholas A. Mason

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Tissue-specific contributions of paternally expressed gene 3 in lactation and maternal care of mus musculus, Wesley D. Frey and Joomyeong Kim

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Diosgenin, 4-hydroxyisoleucine, and fiber from fenugreek: Mechanisms of actions and potential effects on metabolic syndrome, Scott Fuller and Jacqueline M. Stephens

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Fuels and fires influence vegetation via above- and belowground pathways in a high-diversity plant community, Paul R. Gagnon, Heather A. Passmore, Matthew Slocum, Jonathan A. Myers, Kyle E. Harms, William J. Platt, and C. E.Timothy Paine