Virtual Journal of Biological Physics Research -- January 15, 2010

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REVIEW ARTICLES

Quantum physics meets biology
Markus Arndt, Thomas Juffmann, and Vlatko Vedral
HFSP Journal   3, 386-400 (2009)   
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Early T-cell activation biophysics
Nelly Henry and Claire Hivroz
HFSP Journal   3, 401-411 (2009)   
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QUANTUM MECHANICAL DYNAMICS

Decoherence dynamics of coherent electronic excited states in the photosynthetic purple bacterium Rhodobacter sphaeroides
Xian-Ting Liang, Wei-Min Zhang, and Yi-Zhong Zhuo
Physical Review E   81, 011906 (2010) (6 pages)   
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Nonequilibrium molecular dynamics simulation of the energy transport through a peptide helix
Phuong H. Nguyen, Sang-Min Park, and Gerhard Stock
The Journal of Chemical Physics   132, 025102 (2010) (9 pages)   
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Specific formation of negative ions from leucine and isoleucine molecules
Peter Papp, Pavel Shchukin, and Štefan Matejčík
The Journal of Chemical Physics   132, 014301 (2010) (9 pages)   
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Absorption and emission UV-Vis spectra of the TRITC fluorophore molecule in solution: a quantum mechanical study
Alfonso Pedone, Julien Bloino, Susanna Monti, Giacomo Prampolini, and Vincenzo Barone
Physical Chemistry Chemical Physics   12, 1000-1006 (2010)   
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Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations
Johannes M. Dieterich, Hans-Joachim Werner, Ricardo A. Mata, Sebastian Metz, and Walter Thiel
The Journal of Chemical Physics   132, 035101 (2010) (10 pages)   
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PHYSICS OF WATER AND HYDROGEN-BONDED SOLVENTS

Surface effects on nanoscale Poiseuille flows under large driving force
Chong Liu and Zhigang Li
The Journal of Chemical Physics   132, 024507 (2010) (5 pages)   
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Communications: On artificial frequency shifts in infrared spectra obtained from centroid molecular dynamics: Quantum liquid water
Sergei D. Ivanov, Alexander Witt, Motoyuki Shiga, and Dominik Marx
The Journal of Chemical Physics   132, 031101 (2010) (4 pages)   
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Strongly contracted canonical transformation theory
Eric Neuscamman, Takeshi Yanai, and Garnet Kin-Lic Chan
The Journal of Chemical Physics   132, 024106 (2010) (13 pages)   
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The surface tension of TIP4P/2005 water model using the Ewald sums for the dispersion interactions
José Alejandre and Gustavo A. Chapela
The Journal of Chemical Physics   132, 014701 (2010) (6 pages)   
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The glass transition and relaxation behavior of bulk water and a possible relation to confined water
Jan Swenson and José Teixeira
The Journal of Chemical Physics   132, 014508 (2010) (5 pages)   
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A second generation distributed point polarizable water model
Revati Kumar, Fang-Fang Wang, Glen R. Jenness, and Kenneth D. Jordan
The Journal of Chemical Physics   132, 014309 (2010) (12 pages)   
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Spectrum and infrared intensities of OH-stretching bands of water dimers
Kirill Kuyanov-Prozument, Myong Yong Choi, and Andrey F. Vilesov
The Journal of Chemical Physics   132, 014304 (2010) (7 pages)   
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Frozen natural orbitals for ionized states within equation-of-motion coupled-cluster formalism
Arie Landau, Kirill Khistyaev, Stanislav Dolgikh, and Anna I. Krylov
The Journal of Chemical Physics   132, 014109 (2010) (13 pages)   
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A quantitative assessment of the accuracy of centroid molecular dynamics for the calculation of the infrared spectrum of liquid water
Francesco Paesani and Gregory A. Voth
The Journal of Chemical Physics   132, 014105 (2010) (6 pages)   
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The role of van der Waals interactions in surface-supported supramolecular networks
Manh-Thuong Nguyen, Carlo A. Pignedoli, Matthias Treier, Roman Fasel, and Daniele Passerone
Physical Chemistry Chemical Physics   12, 992-999 (2010)   
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MEMBRANE BIOPHYSICS

Inelastic neutron scattering study of light-induced dynamics of a photosynthetic membrane system
A. Furrer and A. Stöckli
Physical Review E   81, 011901 (2010) (5 pages)   
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Adhesion of cylindrical colloids to the surface of a membrane
Sergey Mkrtchyan, Christopher Ing, and Jeff Z. Y. Chen
Physical Review E   81, 011904 (2010) (9 pages)   
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Hydrodynamics in curved membranes: The effect of geometry on particulate mobility
Mark L. Henle and Alex J. Levine
Physical Review E   81, 011905 (2010) (17 pages)   
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Influence of nonequilibrium lipid transport, membrane compartmentalization, and membrane proteins on the lateral organization of the plasma membrane
Jun Fan, Maria Sammalkorpi, and Mikko Haataja
Physical Review E   81, 011908 (2010) (15 pages)   
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Simulation of a toy model of cylindrical cells submitted to nonionizing electromagnetic field: Effect of membrane cell disruption
M. Essone Mezeme and C. Brosseau
Journal of Applied Physics   107, 014701 (2010) (10 pages)   
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Phosphorylation of aquaporin-2 regulates its endocytosis and protein–protein interactions
Hanne B. Moeller, Jeppe Praetorius, Michael R. Rützler, and Robert A. Fenton
Proceedings of the National Academy of Sciences of the United States of America   107, 424-429 (2010)   
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DNA damage and mitochondria dysfunction in cell apoptosis induced by nonthermal air plasma
G. J. Kim, W. Kim, K. T. Kim, and J. K. Lee
Applied Physics Letters   96, 021502 (2010) (3 pages)   
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Lipid membranes with transmembrane proteins in shear flow
Atefeh Khoshnood, Hiroshi Noguchi, and Gerhard Gompper
The Journal of Chemical Physics   132, 025101 (2010) (10 pages)   
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Protrusive growth and periodic contractile motion in surface-adhered vesicles induced by Ca²⁺-gradients
Tatsiana Lobovkina, Irep Gözen, Yavuz Erkan, Jessica Olofsson, Stephen G. Weber, and Owe Orwar
Soft Matter   6, 268-272 (2010)   
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Lipid Rafts As a Membrane-Organizing Principle
Daniel Lingwood and Kai Simons
Science   327, 46-50 (2010)   
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Erratum: “Dynamics of vesicle formation from lipid droplet: Mechanism and controllability” [J. Chem. Phys. 130, 094905 (2009)]
Zilu Wang and Xuehao He
The Journal of Chemical Physics   132, 029901 (2010) (1 page)   
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Consensus motif for integrin transmembrane helix association
Bryan W. Berger, Daniel W. Kulp, Lisa M. Span, Jessica L. DeGrado, Paul C. Billings, Alessandro Senes, Joel S. Bennett, and William F. DeGrado
Proceedings of the National Academy of Sciences of the United States of America   107, 703-708 (2010)   
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FUNDAMENTAL POLYMER STATICS/DYNAMICS

Probe molecules in polymer melts near the glass transition: A molecular dynamics study of chain length effects
R. A. L. Vallée, W. Paul, and K. Binder
The Journal of Chemical Physics   132, 034901 (2010) (9 pages)   
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Tension thickening, molecular shape, and flow birefringence of an H-shaped polymer melt in steady shear and planar extension
Chunggi Baig and Vlasis G. Mavrantzas
The Journal of Chemical Physics   132, 014904 (2010) (10 pages)   
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Simulations of two-dimensional unbiased polymer translocation using the bond fluctuation model
Debabrata Panja and Gerard T. Barkema
The Journal of Chemical Physics   132, 014902 (2010) (10 pages)   
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Heterogeneous dynamics during deformation of a polymer glass
Robert A. Riggleman, Hau-Nan Lee, M. D. Ediger, and Juan J. de Pablo
Soft Matter   6, 287-291 (2010)   
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Chain dynamics of poly(ethylene-alt-propylene) melts by means of coarse-grained simulations based on atomistic molecular dynamics
R. Pérez-Aparicio, J. Colmenero, F. Alvarez, J. T. Padding, and W. J. Briels
The Journal of Chemical Physics   132, 024904 (2010) (11 pages)   
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Phase behavior of repulsive polymer-tethered colloids
Behnaz Bozorgui, Maya Sen, William L. Miller, Josep C. Pàmies, and Angelo Cacciuto
The Journal of Chemical Physics   132, 014901 (2010) (6 pages)   
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Effect of shear on nanoparticle dispersion in polymer melts: A coarse-grained molecular dynamics study
Vibha Kalra, Fernando Escobedo, and Yong Lak Joo
The Journal of Chemical Physics   132, 024901 (2010) (11 pages)   
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Nature of steady flow in entangled fluids revealed by superimposed small amplitude oscillatory shear
Pouyan E. Boukany and Shi-Qing Wang
Journal of Rheology   53, 1425-1435 (2009)   
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Effect of chain stiffness on ion distributions around a polyelectrolyte in multivalent salt solutions
Yu-Fu Wei and Pai-Yi Hsiao
The Journal of Chemical Physics   132, 024905 (2010) (12 pages)   
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Exploring stress overshoot phenomenon upon startup deformation of entangled linear polymeric liquids
Yangyang Wang and Shi-Qing Wang
Journal of Rheology   53, 1389-1401 (2009)   
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PROTEIN CONFORMATIONAL DYNAMICS/FOLDING

Gatekeeper residues in the major curlin subunit modulate bacterial amyloid fiber biogenesis
Xuan Wang, Yizhou Zhou, Juan-Jie Ren, Neal D. Hammer, and Matthew R. Chapman
Proceedings of the National Academy of Sciences of the United States of America   107, 163-168 (2010)   
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Elastic energy of proteins and the stages of protein folding
J. Lei and K. Huang
Europhysics Letters   88, 68004- (2009)   
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Ligand-specific regulation of the extracellular surface of a G-protein-coupled receptor
Michael P. Bokoch, Yaozhong Zou, Søren G. F. Rasmussen, Corey W. Liu, Rie Nygaard, Daniel M. Rosenbaum, Juan José Fung, Hee-Jung Choi, Foon Sun Thian, Tong Sun Kobilka, Joseph D. Puglisi, William I. Weis, Leonardo Pardo, R. Scott Prosser, Luciano Mueller, and Brian K. Kobilka
Nature   463, 108-112 (2010)   
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Structural basis for cofactor-independent dioxygenation of N-heteroaromatic compounds at the /-hydrolase fold
Roberto A. Steiner, Helge J. Janssen, Pietro Roversi, Aaron J. Oakley, and Susanne Fetzner
Proceedings of the National Academy of Sciences of the United States of America   107, 657-662 (2010)   
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Optimal modeling of atomic fluctuations in protein crystal structures for weak crystal contact interactions
Jeffrey Hafner and Wenjun Zheng
The Journal of Chemical Physics   132, 014111 (2010) (11 pages)   
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Crystal structure of DNA-PKcs reveals a large open-ring cradle comprised of HEAT repeats
Bancinyane L. Sibanda, Dimitri Y. Chirgadze, and Tom L. Blundell
Nature   463, 118-121 (2010)   
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Structure of an RNA Polymerase II–TFIIB Complex and the Transcription Initiation Mechanism
Xin Liu, David A. Bushnell, Dong Wang, Guillermo Calero, and Roger D. Kornberg
Science   327, 206-209 (2010)   
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How telomeric protein POT1 avoids RNA to achieve specificity for single-stranded DNA
Jayakrishnan Nandakumar, Elaine R. Podell, and Thomas R. Cech
Proceedings of the National Academy of Sciences of the United States of America   107, 651-656 (2010)   
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Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism
Meigang Gu and Charles M. Rice
Proceedings of the National Academy of Sciences of the United States of America   107, 521-528 (2010)   
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Stereoelectronic and steric effects in side chains preorganize a protein main chain
Matthew D. Shoulders, Kenneth A. Satyshur, Katrina T. Forest, and Ronald T. Raines
Proceedings of the National Academy of Sciences of the United States of America   107, 559-564 (2010)   
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DNA CONFORMATIONAL DYNAMICS

Topology Links RNA Secondary Structure with Global Conformation, Dynamics, and Adaptation
Maximillian H. Bailor, Xiaoyan Sun, and Hashim M. Al-Hashimi
Science   327, 202-206 (2010)   
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Anomalous reaction-diffusion as a model of nonexponential DNA escape kinetics
Debarati Chatterjee and Binny J. Cherayil
The Journal of Chemical Physics   132, 025103 (2010) (5 pages)   
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Observation of negative differential resistance in DNA molecular junctions
Ning Kang, Artur Erbe, and Elke Scheer
Applied Physics Letters   96, 023701 (2010) (3 pages)   
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How are nucleosomes disrupted during transcription elongation?
Jordanka Zlatanova and Jean-Marc Victor
HFSP Journal   3, 373-378 (2009)   
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Electric and electrophoretic inversion of the DNA charge in multivalent electrolytes
Binquan Luan and Aleksei Aksimentiev
Soft Matter   6, 243-246 (2010)   
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Saccharomyces cerevisiae Msh2-Msh6 DNA binding kinetics reveal a mechanism of targeting sites for DNA mismatch repair
Jie Zhai and Manju M. Hingorani
Proceedings of the National Academy of Sciences of the United States of America   107, 680-685 (2010)   
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Spontaneous formation of the unlocked state of the ribosome is a multistep process
James B. Munro, Roger B. Altman, Chang-Shung Tung, Jamie H. D. Cate, Kevin Y. Sanbonmatsu, and Scott C. Blanchard
Proceedings of the National Academy of Sciences of the United States of America   107, 709-714 (2010)   
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SINGLE MOLECULE DYNAMICS

Conformational transitions in DNA polymerase I revealed by single-molecule FRET
Yusdi Santoso, Catherine M. Joyce, Olga Potapova, Ludovic Le Reste, Johannes Hohlbein, Joseph P. Torella, Nigel D. F. Grindley, and Achillefs N. Kapanidis
Proceedings of the National Academy of Sciences of the United States of America   107, 715-720 (2010)   
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INTERMOLECULAR INTERACTIONS

Formation of quantum dots in single stranded DNA-wrapped single-walled carbon nanotubes
Y. F. Li, T. Kaneko, and R. Hatakeyama
Applied Physics Letters   96, 023104 (2010) (3 pages)   
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Kinetics of network formation by telechelic polypeptides with trimeric nodes
Paulina J. Skrzeszewska, Frits A. de Wolf, Martien A. Cohen Stuart, and Jasper van der Gucht
Soft Matter   6, 416-422 (2010)   
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Ultrafast energy transfer within pyropheophorbide-a tethered to self-assembling DNA quadruplex
Jianfeng Cai, Dariusz M. Niedzwiedzki, Harry A. Frank, and Andrew D. Hamilton
Chemical Communications   46, 544-546 (2010)   
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Energy transfer in nonlinear network models of proteins
F. Piazza and Y.-H. Sanejouand
Europhysics Letters   88, 68001- (2009)   
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Molecular basis of factor IXa recognition by heparin-activated antithrombin revealed by a 1.7-Å structure of the ternary complex
Daniel J. D. Johnson, Jonathan Langdown, and James A. Huntington
Proceedings of the National Academy of Sciences of the United States of America   107, 645-650 (2010)   
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Coiled-coil helix bundle, a peptide tertiary structural motif toward hybrid functional materials
Ting Xu and Jessica Shu
Soft Matter   6, 212-217 (2010)   
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PHYSICAL STUDIES OF CELL MECHANICS

Propagating waves separate two states of actin organization in living cells
Britta Schroth-Diez, Silke Gerwig, Mary Ecke, Reiner Hegerl, Stefan Diez, and Günther Gerisch
HFSP Journal   3, 412-427 (2009)   
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Drosophila morphogenesis: tissue force laws and the modeling of dorsal closure
Anita T. Layton, Yusuke Toyama, Guo-Qiang Yang, Glenn S. Edwards, Daniel P. Kiehart, and Stephanos Venakides
HFSP Journal   3, 441-460 (2009)   
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Phosphorylation of H2A by Bub1 Prevents Chromosomal Instability Through Localizing Shugoshin
Shigehiro A. Kawashima, Yuya Yamagishi, Takashi Honda, Kei-ichiro Ishiguro, and Yoshinori Watanabe
Science   327, 172-177 (2010)   
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Structure and dynamics of cross-linked actin networks
Oliver Lieleg, Mireille M. A. E. Claessens, and Andreas R. Bausch
Soft Matter   6, 218-225 (2010)   
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Nanoindentation of virus capsids in a molecular model
Marek Cieplak and Mark O. Robbins
The Journal of Chemical Physics   132, 015101 (2010) (12 pages)   
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Relax? Don't do it!—Linking presynaptic vesicle clustering with mechanical tension
Peter Engerer and Stephan J. Sigrist
HFSP Journal   3, 367-372 (2009)   
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Control of myosin-I force sensing by alternative splicing
Joseph M. Laakso, John H. Lewis, Henry Shuman, and E. Michael Ostap
Proceedings of the National Academy of Sciences of the United States of America   107, 698-702 (2010)   
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Using Lagrangian coherent structures to analyze fluid mixing by cilia
Sarah Lukens, Xingzhou Yang, and Lisa Fauci
Chaos   20, 017511 (2010) (8 pages)   
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Laser microdissection of Arabidopsis cells at the powdery mildew infection site reveals site-specific processes and regulators
Divya Chandran, Noriko Inada, Greg Hather, Christiane K. Kleindt, and Mary C. Wildermuth
Proceedings of the National Academy of Sciences of the United States of America   107, 460-465 (2010)   
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Microtubule Elasticity: Connecting All-Atom Simulations with Continuum Mechanics
David Sept and Fred C. MacKintosh
Physical Review Letters   104, 018101 (2010) (4 pages)   
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Effect of osteogenesis imperfecta mutations in tropocollagen molecule on strength of biomimetic tropocollagen-hydroxyapatite nanocomposites
Devendra K. Dubey and Vikas Tomar
Applied Physics Letters   96, 023703 (2010) (3 pages)   
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A protein secretion system linked to bacteroidete gliding motility and pathogenesis
Keiko Sato, Mariko Naito, Hideharu Yukitake, Hideki Hirakawa, Mikio Shoji, Mark J. McBride, Ryan G. Rhodes, and Koji Nakayama
Proceedings of the National Academy of Sciences of the United States of America   107, 276-281 (2010)   
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Structure and Mechanisms of a Protein-Based Organelle in Escherichia coli
Shiho Tanaka, Michael R. Sawaya, and Todd O. Yeates
Science   327, 81-84 (2010)   
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INFORMATION TRANSFER IN BIOLOGICAL SYSTEMS

Cytoskeleton-based forecasting of stem cell lineage fates
Matthew D. Treiser, Eric H. Yang, Simon Gordonov, Daniel M. Cohen, Ioannis P. Androulakis, Joachim Kohn, Christopher S. Chen, and Prabhas V. Moghe
Proceedings of the National Academy of Sciences of the United States of America   107, 610-615 (2010)   
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Kicked by Mos and tuned by MPF—the initiation of the MAPK cascade in Xenopus oocytes
C. Russo, R. Beaujois, J.-F. Bodart, and R. Blossey
HFSP Journal   3, 428-440 (2009)   
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WDR5 is essential for assembly of the VISA-associated signaling complex and virus-triggered IRF3 and NF-B activation
Yan-Yi Wang, Li-Juan Liu, Bo Zhong, Tian-Tian Liu, Ying Li, Yan Yang, Yong Ran, Shu Li, Po Tien, and Hong-Bing Shu
Proceedings of the National Academy of Sciences of the United States of America   107, 815-820 (2010)   
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Chronic active B-cell-receptor signalling in diffuse large B-cell lymphoma
R. Eric Davis, Vu N. Ngo, Georg Lenz, Pavel Tolar, Ryan M. Young, Paul B. Romesser, Holger Kohlhammer, Laurence Lamy, Hong Zhao, Yandan Yang, Weihong Xu, Arthur L. Shaffer, George Wright, Wenming Xiao, John Powell, Jian-kang Jiang, Craig J. Thomas, Andreas Rosenwald, German Ott, Hans Konrad Muller-Hermelink, Randy D. Gascoyne, Joseph M. Connors, Nathalie A. Johnson, Lisa M. Rimsza, Elias Campo, Elaine S. Jaffe, Wyndham H. Wilson, Jan Delabie, Erlend B. Smeland, Richard I. Fisher, Rita M. Braziel, Raymond R. Tubbs, J. R. Cook, Dennis D. Weisenburger, Wing C. Chan, Susan K. Pierce, and Louis M. Staudt
Nature   463, 88-92 (2010)   
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The Dbf4Cdc7 kinase promotes S phase by alleviating an inhibitory activity in Mcm4
Yi-Jun Sheu and Bruce Stillman
Nature   463, 113-117 (2010)   
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MULTICELLULAR PHENOMENA

Plasmid copy number noise in monoclonal populations of bacteria
Jérôme Wong Ng, Didier Chatenay, Jérôme Robert, and Michael Guy Poirier
Physical Review E   81, 011909 (2010) (8 pages)   
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Wave-train-induced termination of weakly anchored vortices in excitable media
Alain Pumir, Sitabhra Sinha, S. Sridhar, Médéric Argentina, Marcel Hörning, Simonetta Filippi, Christian Cherubini, Stefan Luther, and Valentin Krinsky
Physical Review E   81, 010901 (2010) (4 pages)   
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A Transient Niche Regulates the Specification of Drosophila Intestinal Stem Cells
Divya Mathur, Alyssa Bost, Ian Driver, and Benjamin Ohlstein
Science   327, 210-213 (2010)   
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Nanoscale cues regulate the structure and function of macroscopic cardiac tissue constructs
Deok-Ho Kim, Elizabeth A. Lipke, Pilnam Kim, Raymond Cheong, Susan Thompson, Michael Delannoy, Kahp-Yang Suh, Leslie Tung, and Andre Levchenko
Proceedings of the National Academy of Sciences of the United States of America   107, 565-570 (2010)   
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BIOLOGICAL NETWORKS

Mean-field theory of a plastic network of integrate-and-fire neurons
Chun-Chung Chen and David Jasnow
Physical Review E   81, 011907 (2010) (12 pages)   
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Building biological memory by linking positive feedback loops
Dong-Eun Chang, Shelly Leung, Mariette R. Atkinson, Aaron Reifler, Daniel Forger, and Alexander J. Ninfa
Proceedings of the National Academy of Sciences of the United States of America   107, 175-180 (2010)   
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Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum
Guangan Hu, Ana Cabrera, Maya Kono, Sachel Mok, Balbir K Chaal, Silvia Haase, Klemens Engelberg, Sabna Cheemadan, Tobias Spielmann, Peter R Preiser, Tim-W Gilberger, and Zbynek Bozdech
Nature Biotechnology   28, 91-98 (2010)   
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QUANTITATIVE GENOMICS

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library
Hugo Y K Lam, Xinmeng Jasmine Mu, Adrian M Stütz, Andrea Tanzer, Philip D Cayting, Michael Snyder, Philip M Kim, Jan O Korbel, and Mark B Gerstein
Nature Biotechnology   28, 47-55 (2010)   
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Identification of sister chromatids by DNA template strand sequences
Ester Falconer, Elizabeth A. Chavez, Alexander Henderson, Steven S. S. Poon, Steven McKinney, Lindsay Brown, David G. Huntsman, and Peter M. Lansdorp
Nature   463, 93-97 (2010)   
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Sequencing newly replicated DNA reveals widespread plasticity in human replication timing
R. Scott Hansen, Sean Thomas, Richard Sandstrom, Theresa K. Canfield, Robert E. Thurman, Molly Weaver, Michael O. Dorschner, Stanley M. Gartler, and John A. Stamatoyannopoulos
Proceedings of the National Academy of Sciences of the United States of America   107, 139-144 (2010)   
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Diversity and evolution of 11 innate immune genes in Bos taurus taurus and Bos taurus indicus cattle
Christopher M. Seabury, Paul M. Seabury, Jared E. Decker, Robert D. Schnabel, Jeremy F. Taylor, and James E. Womack
Proceedings of the National Academy of Sciences of the United States of America   107, 151-156 (2010)   
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R loops stimulate genetic instability of CTG·CAG repeats
Yunfu Lin, Sharon Y. R. Dent, John H. Wilson, Robert D. Wells, and Marek Napierala
Proceedings of the National Academy of Sciences of the United States of America   107, 692-697 (2010)   
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Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3
Anja Ragvin, Enrico Moro, David Fredman, Pavla Navratilova, Øyvind Drivenes, Pär G. Engström, M. Eva Alonso, Elisa de la Calle Mustienes, José Luis Gómez Skarmeta, Maria J. Tavares, Fernando Casares, Miguel Manzanares, Veronica van Heyningen, Anders Molven, Pål R. Njølstad, Francesco Argenton, Boris Lenhard, and Thomas S. Becker
Proceedings of the National Academy of Sciences of the United States of America   107, 775-780 (2010)   
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Genome-wide patterns of population structure and admixture in West Africans and African Americans
Katarzyna Bryc, Adam Auton, Matthew R. Nelson, Jorge R. Oksenberg, Stephen L. Hauser, Scott Williams, Alain Froment, Jean-Marie Bodo, Charles Wambebe, Sarah A. Tishkoff, and Carlos D. Bustamante
Proceedings of the National Academy of Sciences of the United States of America   107, 786-791 (2010)   
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Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays
Radoje Drmanac, Andrew B. Sparks, Matthew J. Callow, Aaron L. Halpern, Norman L. Burns, Bahram G. Kermani, Paolo Carnevali, Igor Nazarenko, Geoffrey B. Nilsen, George Yeung, Fredrik Dahl, Andres Fernandez, Bryan Staker, Krishna P. Pant, Jonathan Baccash, Adam P. Borcherding, Anushka Brownley, Ryan Cedeno, Linsu Chen, Dan Chernikoff, Alex Cheung, Razvan Chirita, Benjamin Curson, Jessica C. Ebert, Coleen R. Hacker, Robert Hartlage, Brian Hauser, Steve Huang, Yuan Jiang, Vitali Karpinchyk, Mark Koenig, Calvin Kong, Tom Landers, Catherine Le, Jia Liu, Celeste E. McBride, Matt Morenzoni, Robert E. Morey, Karl Mutch, Helena Perazich, Kimberly Perry, Brock A. Peters, Joe Peterson, Charit L. Pethiyagoda, Kaliprasad Pothuraju, Claudia Richter, Abraham M. Rosenbaum, Shaunak Roy, Jay Shafto, Uladzislau Sharanhovich, Karen W. Shannon, Conrad G. Sheppy, Michel Sun, Joseph V. Thakuria, Anne Tran, Dylan Vu, Alexander Wait Zaranek, Xiaodi Wu, Snezana Drmanac, Arnold R. Oliphant, William C. Banyai, Bruce Martin, Dennis G. Ballinger, George M. Church, and Clifford A. Reid
Science   327, 78-81 (2010)   
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Building the sequence map of the human pan-genome
Ruiqiang Li, Yingrui Li, Hancheng Zheng, Ruibang Luo, Hongmei Zhu, Qibin Li, Wubin Qian, Yuanyuan Ren, Geng Tian, Jinxiang Li, Guangyu Zhou, Xuan Zhu, Honglong Wu, Junjie Qin, Xin Jin, Dongfang Li, Hongzhi Cao, Xueda Hu, Hélène Blanche, Howard Cann, Xiuqing Zhang, Songgang Li, Lars Bolund, Karsten Kristiansen, Huanming Yang, Jun Wang, and Jian Wang
Nature Biotechnology   28, 57-63 (2010)   
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Endogenous non-retroviral RNA virus elements in mammalian genomes
Masayuki Horie, Tomoyuki Honda, Yoshiyuki Suzuki, Yuki Kobayashi, Takuji Daito, Tatsuo Oshida, Kazuyoshi Ikuta, Patric Jern, Takashi Gojobori, John M. Coffin, and Keizo Tomonaga
Nature   463, 84-87 (2010)   
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Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing
Josh T. Cuperus, Taiowa A. Montgomery, Noah Fahlgren, Russell T. Burke, Tiffany Townsend, Christopher M. Sullivan, and James C. Carrington
Proceedings of the National Academy of Sciences of the United States of America   107, 466-471 (2010)   
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AP-1 homolog BZLF1 of Epstein–Barr virus has two essential functions dependent on the epigenetic state of the viral genome
Markus Kalla, Anne Schmeinck, Martin Bergbauer, Dagmar Pich, and Wolfgang Hammerschmidt
Proceedings of the National Academy of Sciences of the United States of America   107, 850-855 (2010)   
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CANCER PHYSICS

Decreased necrotizing fasciitis capacity caused by a single nucleotide mutation that alters a multiple gene virulence axis
Randall J. Olsen, Izabela Sitkiewicz, Ara A. Ayeras, Vedia E. Gonulal, Concepcion Cantu, Stephen B. Beres, Nicole M. Green, Benfang Lei, Tammy Humbird, Jamieson Greaver, Ellen Chang, Willie P. Ragasa, Charles A. Montgomery, Joiner Cartwright, Allison McGeer, Donald E. Low, Adeline R. Whitney, Philip T. Cagle, Terry L. Blasdel, Frank R. DeLeo, and James M. Musser
Proceedings of the National Academy of Sciences of the United States of America   107, 888-893 (2010)   
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The Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer
Elizabeth P. Murchison, Cesar Tovar, Arthur Hsu, Hannah S. Bender, Pouya Kheradpour, Clare A. Rebbeck, David Obendorf, Carly Conlan, Melanie Bahlo, Catherine A. Blizzard, Stephen Pyecroft, Alexandre Kreiss, Manolis Kellis, Alexander Stark, Timothy T. Harkins, Jennifer A. Marshall Graves, Gregory M. Woods, Gregory J. Hannon, and Anthony T. Papenfuss
Science   327, 84-87 (2010)   
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A cancer-associated DNA polymerase variant modeled in yeast causes a catastrophic increase in genomic instability
Danielle L. Daee, Tony M. Mertz, and Polina V. Shcherbakova
Proceedings of the National Academy of Sciences of the United States of America   107, 157-162 (2010)   
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JNK-mediated turnover and stabilization of the transcription factor p45/NF-E2 during differentiation of murine erythroleukemia cells
Tung-Liang Lee, Yu-Chiau Shyu, Pang-Hung Hsu, Chiung-Wen Chang, Shau-Ching Wen, Wei-Yuan Hsiao, Ming-Daw Tsai, and Che-Kun James Shen
Proceedings of the National Academy of Sciences of the United States of America   107, 52-57 (2010)   
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Longitudinal optical imaging of tumor metabolism and hemodynamics
Melissa C. Skala, Andrew Fontanella, Lan Lan, Joseph A. Izatt, and Mark W. Dewhirst
Journal of Biomedical Optics   15, 011112 (2010) (8 pages)   
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Deubiquitinase USP9X stabilizes MCL1 and promotes tumour cell survival
Martin Schwickart, XiaoDong Huang, Jennie R. Lill, Jinfeng Liu, Ronald Ferrando, Dorothy M. French, Heather Maecker, Karen ORourke, Fernando Bazan, Jeffrey Eastham-Anderson, Peng Yue, David Dornan, David C. S. Huang, and Vishva M. Dixit
Nature   463, 103-107 (2010)   
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DNA aptamer–micelle as an efficient detection/delivery vehicle toward cancer cells
Yanrong Wu, Kwame Sefah, Haipeng Liu, Ruowen Wang, and Weihong Tan
Proceedings of the National Academy of Sciences of the United States of America   107, 5-10 (2010)   
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Photothermal therapy in a murine colon cancer model using near-infrared absorbing gold nanorods
Glenn P. Goodrich, LiLi Bao, Kelly Gill-Sharp, Krystina L. Sang, James Wang, and J. Donald Payne
Journal of Biomedical Optics   15, 018001 (2010) (8 pages)   
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Dielectrophoretic separation of colorectal cancer cells
Fang Yang, Xiaoming Yang, Hong Jiang, Phillip Bulkhaults, Patricia Wood, William Hrushesky, and Guiren Wang
Biomicrofluidics   4, 013204 (2010) (13 pages)   
Abstract    Full Text: [ PDF (771 kB)  ]

Optical spectroscopy of the breast in premenopausal women reveals tissue variation with changes in age and parity
Julia A. Knight, Kristina M. Blackmore, Jody Wong, Sukirtha Tharmalingam, and Lothar Lilge
Medical Physics   37, 419-426 (2010)   
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DNA methylation of developmental genes in pediatric medulloblastomas identified by denaturation analysis of methylation differences
Scott J. Diede, Jamie Guenthoer, Linda N. Geng, Sarah E. Mahoney, Michael Marotta, James M. Olson, Hisashi Tanaka, and Stephen J. Tapscott
Proceedings of the National Academy of Sciences of the United States of America   107, 234-239 (2010)   
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Mutant p53 drives metastasis and overcomes growth arrest/senescence in pancreatic cancer
Jennifer P. Morton, Paul Timpson, Saadia A. Karim, Rachel A. Ridgway, Dimitris Athineos, Brendan Doyle, Nigel B. Jamieson, Karin A. Oien, Andrew M. Lowy, Valerie G. Brunton, Margaret C. Frame, T. R. Jeffry Evans, and Owen J. Sansom
Proceedings of the National Academy of Sciences of the United States of America   107, 246-251 (2010)   
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Functional screening identifies CRLF2 in precursor B-cell acute lymphoblastic leukemia
Akinori Yoda, Yuka Yoda, Sabina Chiaretti, Michal Bar-Natan, Kartik Mani, Scott J. Rodig, Nathan West, Yun Xiao, Jennifer R. Brown, Constantine Mitsiades, Martin Sattler, Jeffrey L. Kutok, Daniel J. DeAngelo, Martha Wadleigh, Alfonso Piciocchi, Paola Dal Cin, James E. Bradner, James D. Griffin, Kenneth C. Anderson, Richard M. Stone, Jerome Ritz, Robin Foà, Jon C. Aster, David A. Frank, and David M. Weinstock
Proceedings of the National Academy of Sciences of the United States of America   107, 252-257 (2010)   
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miR-221 overexpression contributes to liver tumorigenesis
Pascal Pineau, Stefano Volinia, Katherine McJunkin, Agnès Marchio, Carlo Battiston, Benoît Terris, Vincenzo Mazzaferro, Scott W. Lowe, Carlo M. Croce, and Anne Dejean
Proceedings of the National Academy of Sciences of the United States of America   107, 264-269 (2010)   
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Defined factors induce reprogramming of gastrointestinal cancer cells
Norikatsu Miyoshi, Hideshi Ishii, Ken-ichi Nagai, Hiromitsu Hoshino, Koshi Mimori, Fumiaki Tanaka, Hiroaki Nagano, Mitsugu Sekimoto, Yuichiro Doki, and Masaki Mori
Proceedings of the National Academy of Sciences of the United States of America   107, 40-45 (2010)   
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E3 ubiquitin ligase APC/C-Cdh1 accounts for the Warburg effect by linking glycolysis to cell proliferation
Angeles Almeida, Juan P. Bolaños, and Salvador Moncada
Proceedings of the National Academy of Sciences of the United States of America   107, 738-741 (2010)   
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EVOLUTION PHYSICS

Quasispecies theory for finite populations
Jeong-Man Park, Enrique Muñoz, and Michael W. Deem
Physical Review E   81, 011902 (2010) (12 pages)   
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Network analyses structure genetic diversity in independent genetic worlds
Sébastien Halary, Jessica W. Leigh, Bachar Cheaib, Philippe Lopez, and Eric Bapteste
Proceedings of the National Academy of Sciences of the United States of America   107, 127-132 (2010)   
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SERS aptasensor from nanorod–nanoparticle junction for protein detection
Yuling Wang, Kyuwan Lee, and Joseph Irudayaraj
Chemical Communications   46, 613-615 (2010)   
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STATISTICAL AND NONLINEAR PHYSICS

Efficient computation of parameter sensitivities of discrete stochastic chemical reaction networks
Muruhan Rathinam, Patrick W. Sheppard, and Mustafa Khammash
The Journal of Chemical Physics   132, 034103 (2010) (13 pages)   
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Stochastic variation: from single cells to superorganisms
Maria L. Kilfoil, Paul Lasko, and Ehab Abouheif
HFSP Journal   3, 379-385 (2009)   
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Nonlinear diffusion and exclusion processes with contact interactions
Anthony E. Fernando, Kerry A. Landman, and Matthew J. Simpson
Physical Review E   81, 011903 (2010) (11 pages)   
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Detecting dynamical boundaries from kinematic data in biomechanics
Shane D. Ross, Martin L. Tanaka, and Carmine Senatore
Chaos   20, 017507 (2010) (13 pages)   
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Computational analysis of an aortic valve jet with Lagrangian coherent structures
Shawn C. Shadden, Matteo Astorino, and Jean-Frédéric Gerbeau
Chaos   20, 017512 (2010) (10 pages)   
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Using hyperbolic Lagrangian coherent structures to investigate vortices in bioinspired fluid flows
Melissa A. Green, Clarence W. Rowley, and Alexander J. Smits
Chaos   20, 017510 (2010) (11 pages)   
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INSTRUMENTATION DEVELOPMENT

Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis
Noelle M Griffin, Jingyi Yu, Fred Long, Phil Oh, Sabrina Shore, Yan Li, Jim A Koziol, and Jan E Schnitzer
Nature Biotechnology   28, 83-89 (2010)   
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Diffusive reflectance for the free-space light propagation theory
Yuanzheng Si, Heng Mao, Bin Zhang, and Ming Jiang
Applied Physics Letters   96, 013702 (2010) (3 pages)   
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Sense toxins/sewage gases by chemically and biologically functionalized single-walled carbon nanotube sensor based microwave resonator
S. B. Tooski
Journal of Applied Physics   107, 014702 (2010) (8 pages)   
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Fabrication and characterization of a porous silicon based microarray for label-free optical monitoring of biomolecular interactions
Ilaria Rea, Annalisa Lamberti, Ivo Rendina, Giuseppe Coppola, Mariano Gioffrè, Mario Iodice, Maurizio Casalino, Edoardo De Tommasi, and Luca De Stefano
Journal of Applied Physics   107, 014513 (2010) (4 pages)   
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Functional optical imaging at the microscopic level
Beatriz Y. Salazar Vázquez, Ciel Makena Hightower, Francesca Sapuppo, Daniel M. Tartakovsky, and Marcos Intaglietta
Journal of Biomedical Optics   15, 011102 (2010) (9 pages)   
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Bio-electrospraying and aerodynamically assisted bio-jetting whole human blood: Interrogating cell surface marker integrity
Pascal Joly, Naina Chavda, Ayad Eddaoudi, and Suwan N. Jayasinghe
Biomicrofluidics   4, 011101 (2010) (6 pages)   
Abstract    Full Text: [ PDF (395 kB)  ]

Real-time, closed-loop dual-wavelength optical polarimetry for glucose monitoring
Bilal H. Malik and Gerard L. Coté
Journal of Biomedical Optics   15, 017002 (2010) (6 pages)   
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The use of PET images for radiotherapy treatment planning: An error analysis using radiobiological endpoints
R. Perrin, P. M. Evans, S. Webb, and M. Partridge
Medical Physics   37, 516-531 (2010)   
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Detection of an endocrine disrupter biomarker, vitellogenin, in largemouth bass serum using AlGaN/GaN high electron mobility transistors
Byung Hwan Chu, C. Y. Chang, Kevin Kroll, Nancy Denslow, Yu-Lin Wang, S. J. Pearton, A. M. Dabiran, A. M. Wowchak, B. Cui, P. P. Chow, and Fan Ren
Applied Physics Letters   96, 013701 (2010) (3 pages)   
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Imaging morphogenesis of Candida albicans during infection in a live animal
Soumya Mitra, Kristy Dolan, Thomas H. Foster, and Melanie Wellington
Journal of Biomedical Optics   15, 010504 (2010) (3 pages)   
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Active-passive calibration of optical tweezers in viscoelastic media
Mario Fischer, Andrew C. Richardson, S. Nader S. Reihani, Lene B. Oddershede, and Kirstine Berg-Sørensen
Review of Scientific Instruments   81, 015103 (2010) (10 pages)   
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Dielectrophoretic spectra of translational velocity and critical frequency for a spheroid in traveling electric field
Sakshin Bunthawin, Pikul Wanichapichart, Adisorn Tuantranont, and Hans G. L. Coster
Biomicrofluidics   4, 014102 (2010) (13 pages)   
Abstract    Full Text: [ PDF (668 kB)  ]

Onset of channeling during DNA electrophoresis in a sparse ordered post array
Jia Ou, Samuel J. Carpenter, and Kevin D. Dorfman
Biomicrofluidics   4, 013203 (2010) (10 pages)   
Abstract    Full Text: [ PDF (450 kB)  ]

Atomic Layer Deposited Hafnium Oxide Gate Dielectrics for Charge-Based Biosensors
Yi Wei Chen, Maozi Liu, Tetsuya Kaneko, and Paul C. McIntyre
Electrochemical and Solid-State Letters   13, G29-G32 (2010)   
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Integrated nanoplasmonic-nanofluidic biosensors with targeted delivery of analytes
Ahmet Ali Yanik, Min Huang, Alp Artar, Tsung-Yao Chang, and Hatice Altug
Applied Physics Letters   96, 021101 (2010) (3 pages)   
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Dielectrophoretic choking phenomenon in a converging-diverging microchannel
Ye Ai, Shizhi Qian, Sheng Liu, and Sang W. Joo
Biomicrofluidics   4, 013201 (2010) (6 pages)   
Abstract    Full Text: [ PDF (215 kB)  ]

Frequency-dependent behaviors of individual microscopic particles in an optically induced dielectrophoresis device
Xiaolu Zhu, Hong Yi, and Zhonghua Ni
Biomicrofluidics   4, 013202 (2010) (14 pages)   
Abstract    Full Text: [ PDF (1083 kB)  ]

High-speed spectral domain polarization- sensitive optical coherence tomography using a single camera and an optical switch at 1.3  µm
Sang-Won Lee, Hyun-Woo Jeong, and Beop-Min Kim
Journal of Biomedical Optics   15, 010501 (2010) (3 pages)   
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Single sensor that outputs narrowband multispectral images
Linghua Kong, Dingrong Yi, Stephen Sprigle, Fengtao Wang, Chao Wang, Fuhan Liu, Ali Adibi, and Rao Tummala
Journal of Biomedical Optics   15, 010502 (2010) (3 pages)   
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Comparison of cobinamide to hydroxocobalamin in reversing cyanide physiologic effects in rabbits using diffuse optical spectroscopy monitoring
Matthew Brenner, Sari B. Mahon, Jangwoen Lee, Jae Kim, David Mukai, Seth Goodman, Kelly A. Kreuter, Rebecca Ahdout, Othman Mohammad, Vijay S. Sharma, William Blackledge, and Gerry R. Boss
Journal of Biomedical Optics   15, 017001 (2010) (8 pages)   
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Utilizing dual frequency band transmit pulse complexes in medical ultrasound imaging
Rune Hansen, Svein-Erik Måsøy, Tonni F. Johansen, and Bjørn A. Angelsen
The Journal of the Acoustical Society of America   127, 579-587 (2010)   
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Intravital imaging of amyloid plaques in a transgenic mouse model using optical-resolution photoacoustic microscopy
Song Hu, Ping Yan, Konstantin Maslov, Jin-Moo Lee, and Lihong V. Wang
Optics Letters   34, 3899-3901 (2009)   
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Construction, figures of merit, and testing of a single-cell fluorescence excitation spectroscopy system
Laura S. Hill, Tammi L. Richardson, Luisa T. M. Profeta, Timothy J. Shaw, Christopher J. Hintz, Benjamin S. Twining, Evelyn Lawrenz, and Michael L. Myrick
Review of Scientific Instruments   81, 013103 (2010) (13 pages)   
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Development of a catheter for combined intravascular ultrasound and photoacoustic imaging
Andrei B. Karpiouk, Bo Wang, and Stanislav Y. Emelianov
Review of Scientific Instruments   81, 014901 (2010) (7 pages)   
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Finite amplitude method for measuring the nonlinearity parameter B/A in small-volume samples using focused ultrasound
Shigemi Saito
The Journal of the Acoustical Society of America   127, 51-61 (2010)   
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A Nanocomposite Modified Electrode: Electrocatalytic Properties and Its Sensing Applications to Hydrogen Peroxide and Glucose
Feng Gao, Jun Yin, Zhen Yao, Maoguo Li, and Lun Wang
Journal of The Electrochemical Society   157, F35-F39 (2010)   
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Magnetomotive laser speckle imaging
Jeehyun Kim, Junghwan Oh, and Bernard Choi
Journal of Biomedical Optics   15, 011110 (2010) (5 pages)   
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Spatiotemporal laser speckle contrast analysis for blood flow imaging with maximized speckle contrast
Jianjun Qiu, Pengcheng Li, Weihua Luo, Jia Wang, Hongyan Zhang, and Qingming Luo
Journal of Biomedical Optics   15, 016003 (2010) (5 pages)   
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The design of a simulated in-line side-coupled 6 MV linear accelerator waveguide
Joel St. Aubin, Stephen Steciw, and B. G. Fallone
Medical Physics   37, 466-476 (2010)   
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Computed tomographic x-ray velocimetry
S. Dubsky, R. A. Jamison, S. C. Irvine, K. K. W. Siu, K. Hourigan, and A. Fouras
Applied Physics Letters   96, 023702 (2010) (3 pages)   
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Segmentation of DNA microarray images using an adaptive graph-based method
N. Karimi, S. Samavi, S. Shirani, and P. Behnamfar
IET Image Processing   4, 19-27 (2010)   
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Atherosclerotic tissue characterization in vivo by optical coherence tomography attenuation imaging
Gijs van Soest, Thadé Goderie, Evelyn Regar, Senada Koljenović, Geert L. J. H. van Leenders, Nieves Gonzalo, Sander van Noorden, Takayuki Okamura, Brett E. Bouma, Guillermo J. Tearney, J. Wolter Oosterhuis, Patrick W. Serruys, and Anton F. W. van der Steen
Journal of Biomedical Optics   15, 011105 (2010) (9 pages)   
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Intravascular near-infrared fluorescence molecular imaging of atherosclerosis: toward coronary arterial visualization of biologically high-risk plaques
Marcella A. Calfon, Claudio Vinegoni, Vasilis Ntziachristos, and Farouc A. Jaffer
Journal of Biomedical Optics   15, 011107 (2010) (6 pages)   
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Laser speckle contrast imaging in biomedical optics
David A. Boas and Andrew K. Dunn
Journal of Biomedical Optics   15, 011109 (2010) (12 pages)   
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Fibroblast encapsulation in hybrid silica–collagen hydrogels
Martín F. Desimone, Christophe Hélary, Gervaise Mosser, Marie-Madeleine Giraud-Guille, Jacques Livage, and Thibaud Coradin
Journal of Materials Chemistry   20, 666-668 (2010)   
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Facile preparation of Langmuir–Blodgett films of water-soluble proteins and hybrid protein–clay films
Shiding Miao, Hugo Leeman, Steven De Feyter, and Robert A. Schoonheydt
Journal of Materials Chemistry   20, 698-705 (2010)   
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Peptide- and polymer-based delivery of therapeutic RNA
Thomas Fröhlich and Ernst Wagner
Soft Matter   6, 226-234 (2010)   
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Protein trapping of silica nanoparticles
Joo Chuan Ang, Jhih-Min Lin, Peter N. Yaron, and John W. White
Soft Matter   6, 383-390 (2010)   
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A direct technique for preparation of magnetically functionalised living yeast cells
Rawil F. Fakhrullin, Javier García-Alonso, and Vesselin N. Paunov
Soft Matter   6, 391-397 (2010)   
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Translocation of Single-Stranded DNA Through Single-Walled Carbon Nanotubes
Haitao Liu, Jin He, Jinyao Tang, Hao Liu, Pei Pang, Di Cao, Predrag Krstic, Sony Joseph, Stuart Lindsay, and Colin Nuckolls
Science   327, 64-67 (2010)   
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MISCELLANEOUS

High-performance genetically targetable optical neural silencing by light-driven proton pumps
Brian Y. Chow, Xue Han, Allison S. Dobry, Xiaofeng Qian, Amy S. Chuong, Mingjie Li, Michael A. Henninger, Gabriel M. Belfort, Yingxi Lin, Patrick E. Monahan, and Edward S. Boyden
Nature   463, 98-102 (2010)   
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