Open Access is free, unrestricted, online access to scientific and scholarly research. This collection includes Open Access journal articles authored by researchers, faculty, staff, and students of the University of Massachusetts Medical School.

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Publications from 2012

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The DNA glycosylases Ogg1 and Nth1 do not contribute to Ig class switching in activated mouse splenic B cells, Anna J. Ucher, Erin K. Linehan, George W. Teebor, Carol E. Schrader, and Janet Stavnezer

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Host-pathogen interactions of retroviruses, Abdul A. Waheed, Abraham L. Brass, Suryaram Gummuluru, and Gilda Tachedjian

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Plasmacytoid dendritic cell interferon-alpha production to R-848 stimulation is decreased in male infants, Jennifer P. Wang, Lei Zhang, Rachel F. Madera, Marcia Woda, and Daniel H. Libraty

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The Ottawa Statement on the Ethical Design and Conduct of Cluster Randomized Trials, Charles Weijer, Jeremy M. Grimshaw, Martin P. Eccles, Andrew D. McRae, Angela White, Jamie C. Brehaut, Monica Taljaard, Ottawa Ethics of Cluster Randomized Trials Consensus Group, and Catarina I. Kiefe

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Type 1 interferons and antiviral CD8 T-cell responses, Raymond M. Welsh, Kapil Bahl, Heather D. Marshall, and Stina L. Urban

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Functional analysis of transcription factor binding sites in human promoters, Troy W. Whitfield, Jie Wang, Patrick J. Collins, E. Christopher Partridge, Shelley Force Aldred, Nathan D. Trinklein, Richard M. Myers, and Zhiping Weng

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Combining comparative proteomics and molecular genetics uncovers regulators of synaptic and axonal stability and degeneration in vivo, Thomas M. Wishart, Timothy M. Rooney, Douglas J. Lamont, Ann K. Wright, A. Jennifer Morgon, Mandy Jackson, Marc R. Freeman, and Thomas H. Gillingwater

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Mullerian Inhibiting Substance Recruits ALK3 to Regulate Leydig Cell Differentiation, Xiufeng Wu, Ningning Zhang, and Mary M. Lee

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FANCJ/BACH1 Acetylation at Lysine 1249 Regulates the DNA Damage Response, Jenny X. Xie, Min Peng, Shawna Guillemette, Steven Quan, Stephanie Maniatis, Yuliang Wu, Aditya Venkatesh, Scott A. Shaffer, Robert M. Brosh Jr., and Sharon B. Cantor

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A Synthetic Interaction Screen Identifies Factors Selectively Required for Proliferation and TERT Transcription in p53-Deficient Human Cancer Cells, Li Xie, Claude Gazin, Sung Mi Park, Lihua Julie Zhu, Marie-Anne Debily, Ellen L. W. Kittler, Maria L. Zapp, David S. Lapointe, Stephane Gobeil, Ching-Man A. Virbasius, and Michael R. Green

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Genome-wide identification and characterization of replication origins by deep sequencing, Jia Xu, Yoshimi Yanagisawa, Alexander M. Tsankov, Christopher Hart, Keita Aoki, Naveen Kommajosyula, Kathleen E. Steinmann, James Bochicchio, Carsten Russ, Aviv Regev, Oliver J. Rando, Chad Nusbaum, Hironori Niki, Patrice Milos, Zhiping Weng, and Nicholas R. Rhind

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Bleomycin sensitivity in Escherichia coli is medium-dependent, Tao Xu, William Brown, and Martin G. Marinus

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Does a loss of TDP-43 function cause neurodegeneration, Zuoshang Xu

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Modeling formamide denaturation of probe-target hybrids for improved microarray probe design in microbial diagnostics, L. Safak Yilmaz, Alexander Loy, Erik S. Wright, Michael Wagner, and Daniel R. Noguera

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CD14 deficiency impacts glucose homeostasis in mice through altered adrenal tone, James L. Young, Alfonso Mora, Anna M. Cerny, Michael P. Czech, Bruce A. Woda, Evelyn A. Kurt-Jones, Robert W. Finberg, and Silvia Corvera

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RNA: methods and protocols - a new series, Phillip D. Zamore

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Scd1 plays a tumor-suppressive role in survival of leukemia stem cells and the development of chronic myeloid leukemia, Haojian Zhang, Huawei Li, Ngoc Ho, Dongguang Li, and Shaoguang Li

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Chondrolectin mediates growth cone interactions of motor axons with an intermediate target, Zhen Zhong, Jochen Ohnmacht, Michell M. Reimer, Ingolf Bach, Thomas C. Becker, and Catherina G. Becker

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Integrative gene regulatory network analysis reveals light-induced regional gene expression phase shift programs in the mouse suprachiasmatic nucleus, Haisun Zhu, Rajanikanth Vadigepalli, Rachel Rafferty, Gregory E. Gonye, David R. Weaver, and James S. Schwaber

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PU.1 Is Essential for CD11c Expression in CD8(+)/CD8(-) Lymphoid and Monocyte-Derived Dendritic Cells during GM-CSF or FLT3L-Induced Differentiation, Xue-Jun Zhu, Zhongfa Yang, Yaoyu Chen, Junling Wang, and Alan G. Rosmarin

Publications from 2011

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Genomics in 2011: challenges and opportunities, David J. Adams, Bonnie Berger, Olivier Harismendy, Curtis Huttenhower, X. Shirley Liu, Chad L. Myers, Alicia Oshlack, John L. Rinn, and Albertha J. M. Walhout

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Progranulin, a glycoprotein deficient in frontotemporal dementia, is a novel substrate of several protein disulfide isomerase family proteins, Sandra Almeida, Lijuan Zhou, and Fen-Biao Gao

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Target RNA-directed tailing and trimming purifies the sorting of endo-siRNAs between the two Drosophila Argonaute proteins, Stefan L. Ameres, Jui-Hung Hung, Jia Xu, Zhiping Weng, and Phillip D. Zamore

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PPARdelta Regulates Satellite Cell Proliferation and Skeletal Muscle Regeneration, Alison R. Angione, Chunhui Jiang, Dongning Pan, Yong-Xu Wang, and Shihuan Kuang

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Loss of p53 Ser18 and Atm results in embryonic lethality without cooperation in tumorigenesis, Heather L. Armata, Punita Shroff, David S. Garlick, Krista L. Penta, Andrew R. Tapper, and Hayla Karen Sluss

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Underscreened and undertreated, Jesse N. Aronowitz

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Metabolic regulation of mycobacterial growth and antibiotic sensitivity, Seung-Hun Baek, Alice H. Li, and Christopher M. Sassetti

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Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence, Eugene Berezikov, Nicolas Robine, Anastasia Samsonova, Jakub Orzechowski Westholm, Ammar Naqvi, Jui-Hung Hung, Katsutomo Okamura, Qi Dai, Diane Bortolamiol-Becet, Raquel Martin, Yongjun Zhao, Phillip D. Zamore, Gregory J. Hannon, Marco A. Marra, Zhiping Weng, Norbert Perrimon, and Eric C. Lai

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Cyclin-dependent kinase 5 regulates PSD-95 ubiquitination in neurons, Michael J. Bianchetta, TuKiet T. Lam, Stephen N. Jones, and Maria A. Morabito

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Host genetic risk factors for West Nile virus infection and disease progression, Abigail W. Bigham, Kati J. Buckingham, Sofia Husain, Mary J. Edmond, Kathryn M. Bofferding, Heidi Gildersleeve, Ann Rutherford, Natalia M. Astakhova, Andrey A. Perelygin, Michael P. Busch, Kristy O. Murray, James J. Sejvar, Sharone Green, John Kriesel, Margo A. Brinton, and Michael Bamshad

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Low Level Bacterial Endotoxin Activates Two Distinct Signaling Pathways in Human peripheral blood mononuclear cells, Andra L. Blomkalns, Lynn L. Stoll, Wassim Shaheen, Sara A. Romig-Martin, Eric W. Dickson, Neal L. Weintraub, and Gerene M. Denning

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A stele-enriched gene regulatory network in the Arabidopsis root, Siobhan M. Brady, Lifang Zhang, Molly Megraw, Natalia Julia Martinez, Eric Jiang, Charles S. Yi, Weilin Liu, Anna Zeng, Mallorie Taylor-Teeples, Dahae Kim, Sebastian Ahnert, Uwe Ohler, Doreen Ware, Albertha J. M. Walhout, and Philip N. Benfey

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Adherence with tobramycin inhaled solution and health care utilization, Becky A. Briesacher, Alexandra L. Quittner, Lisa Saiman, Patricia Sacco, Hassan Fouayzi, and Lynne M. Quittell

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Mechanism and regulation of nucleocytoplasmic trafficking of smad, Xiaochu Chen and Lan Xu

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Pelvic inflammatory disease, Thomas L. Cherpes, Peter A. Rice, and Richard L. Sweet

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RIP1-dependent and independent effects of necrostatin-1 in necrosis and T cell activation, YoungSik Cho, Thomas McQuade, Haibing Zhang, Jianke Zhang, and Francis Ka-Ming Chan

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A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity, Ryan G. Christensen, Ankit Gupta, Zheng Zuo, Lawrence A. Schriefer, Scot A. Wolfe, and Gary D. Stormo

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Design and methods for a randomized clinical trial comparing three outreach efforts to improve screening mammography adherence, Mary E. Costanza, Roger S. Luckmann, Mary Jo White, Milagros C. Rosal, Caroline Cranos, George W. Reed, Robin E. Clark, Susan Sama, and Robert A. Yood

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Assessment of health sciences and science and technology librarian e-science educational needs to develop an e-science web portal for librarians, Andrew Creamer, Myrna E. Morales, Javier Crespo, Donna Kafel, and Elaine Russo Martin

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Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants, Federico De Masi, Christian A. Grove, Anastasia Vedenko, Andreu Alibés, Stephen S. Gisselbrecht, Luis Serrano, Martha L. Bulyk, and Albertha J. M. Walhout

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TRAIL and DcR1 expressions are differentially regulated in the pancreatic islets of STZ- versus CY-applied NOD mice, Ercument Dirice, Sevin Kahraman, Gulsum Ozlem Elpek, Cigdem Aydin, Mustafa Kemal Balci, Abdulkadir Omer, Salih Sanlioglue, and Ahter Dilsad Sanlioglue

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Determinants of inapparent and symptomatic dengue infection in a prospective study of primary school children in Kamphaeng Phet, Thailand, Timothy P. Endy, Kathryn B. Anderson, Ananda Nisalak, In-Kyu Yoon, Sharone Green, Alan L. Rothman, Stephen J. Thomas, Richard G. Jarman, Daniel H. Libraty, and Robert V. Gibbons

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Does Global Health Funding Respond to Recipients’ Needs? Comparing Public and Private Donors’ Allocations in 2005–2007, Daniel E. Esser and Kara Keating Bench

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An E2F1-mediated DNA damage response contributes to the replication of human cytomegalovirus, Xiaofei E., Mary Theresa Pickering, Michelle E. Debatis, Jonathan Patrick Castillo, Alexander Lagadinos, Shixia Wang, Shan Lu, and Timothy F. Kowalik

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From synapse to nucleus and back again--communication over distance within neurons, Mike Fainzilber, Vivian Budnik, Rosalind A. Segal, and Michael R. Kreutz

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Making enhancers from spare parts of the genome, David Fedman, Xianjun Dong, and Boris Lenhard

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Scalable Functional Bone Substitutes: Strategic Integration of Key Structural Elements of Bone in Synthetic Biomaterials, Tera M. Filion and Jie Song

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Dosing strategies for lithium monotherapy in children and adolescents with bipolar I disorder, Robert L. Findling, Vivian Kafantaris, Mani Pavuluri, Nora K. McNamara, Jon McClellan, Jean A. Frazier, Linmarie Sikich, Robert Kowatch, Jacqui Lingler, Jon Faber, Brieana M. Rowles, Traci E. Clemons, and Perdita Taylor-Zapata

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Improved Responsiveness and Reduced Sample Size Requirements of PROMIS Physical Function Scales with Item Response Theory, James F. Fries, Eswar Krishnan, Matthias S. F. Rose, Bharathi Lingala, and Bonnie Bruce

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Conversion of tumors into autologous vaccines by intratumoral injection of alpha-Gal glycolipids that induce anti-Gal/alpha-Gal epitope interaction, Uri Galili

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Neuropilin-2 promotes branching morphogenesis in the mouse mammary gland, Hira Lal Goel, Donggoo Bae, Bryan M. Pursell, Lindsey M. Gouvin, Shaolei Lu, and Arthur M. Mercurio

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High-resolution phenotypic profiling defines genes essential for mycobacterial growth and cholesterol catabolism, Jennifer E. Griffin, Jeffrey D. Gawronski, Michael A. Dejesus, Thomas R. Ioerger, Brian J. Akerley, and Christopher M. Sassetti

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Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases, Ankit Gupta, Xiangdong Meng, Lihua Julie Zhu, Nathan D. Lawson, and Scot A. Wolfe

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Crosstalk between NDR kinase pathways coordinates cell cycle dependent actin rearrangements, Sneha Gupta and Dannel McCollum

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NSAIDs and atrial fibrillation, Jerry H. Gurwitz

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Interactions between naive and infected macrophages reduce Mycobacterium tuberculosis viability, Michelle L. Hartman and Hardy Kornfeld

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TIEG1/KLF10 Modulates Runx2 Expression and Activity in Osteoblasts, John R. Hawse, Muzaffer Cicek, Sarah B. Grygo, Elizabeth S. Bruinsma, Nalini M. Rajamannan, Andre J. Van Wijnen, Jane B. Lian, Gary S. Stein, Merry Jo Oursler, Malayannan Subramaniam, and Thomas C. Spelsberg

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Acetaminophen-cysteine adducts during therapeutic dosing and following overdose, Kennon J. Heard, Jody L. Green, Laura P. James, Bryan S. Judge, Liza Zolot, Sean Hyun Rhyee, and Richard C. Dart

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{beta}3GnT2 Maintains Adenylyl Cyclase-3 Signaling and Axon Guidance Molecule Expression in the Olfactory Epithelium, Timothy R. Henion, Ashley A. Faden, Thomas K. Knott, and Gerald A. Schwarting

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Colonization with antibiotic-susceptible strains protects against methicillin-resistant Staphylococcus aureus but not vancomycin-resistant enterococci acquisition: a nested case-control study, Susan S. Huang, Rupak Datta, Sheryl L. Rifas-Shiman, Ken P. Kleinman, Hilary Placzek, Julie Lankiewicz, and Richard Platt

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Temporal trends in serum concentrations of polychlorinated dioxins, furans, and PCBs among adult women living in Chapaevsk, Russia: a longitudinal study from 2000 to 2009, Olivier Humblet, Oleg Sergeyev, Larisa Altshul, Susan A. Korrick, Paige L. Williams, Claude Emond, Linda S. Birnbaum, Jane S. Burns, Mary M. Lee, Boris Revich, Andrey Shelepchikov, Denis Feshin, and Russ Hauser

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Bioluminescence-based high-throughput screen identifies pharmacological agents that target neurotransmitter signaling in small cell lung carcinoma, Ma. Reina D. Improgo, Christopher W. Johnson, Andrew R. Tapper, and Paul D. Gardner

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Scaling behavior of human locomotor activity amplitude: association with bipolar disorder, Premananda Indic, Paola Salvatore, Carlo Maggini, Stefano Ghidini, Gabriella Ferraro, Ross J. Baldessarini, and Greg Murray

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Pathogenic forms of tau inhibit kinesin-dependent axonal transport through a mechanism involving activation of axonal phosphotransferases, Nicholas M. Kanaan, Gerardo A. Morfini, Nichole E. Lapointe, Gustavo F. Pigino, Kristina R. Patterson, Yuyu Song, Athena Andreadis, Yifan Fu, Scott T. Brady, and Lester I. Binder

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MicroRNA biogenesis and regulation of bone remodeling, Kristina Kapinas and Anne M. Delany

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Genome surveyor 2.0: cis-regulatory analysis in Drosophila, Majid Kazemian, Michael H. Brodsky, and Saurabh Sinha

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The rat intervertebral disk degeneration pain model: relationships between biological and structural alterations and pain, Jae-Sung Kim, Jeffrey S. Kroin, Xin Li, Howard S. An, Asokumar Buvanendran, Dongyao Yan, Kenneth J. Tuman, Andre J. Van Wijnen, Di Chen, and Hee-Jeong Im

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Genotypic and functional properties of early infant HIV-1 envelopes, Michael G. Kishko, Mohan Somasundaran, Frank E. Brewster, John L. Sullivan, Paul R. Clapham, and Katherine Luzuriaga

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Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1, Alexei V. Korennykh, Pascal F. Egea, Andrei A. Korostelev, Janet Finer-Moore, Robert M. Stroud, Chao Zhang, Kevan M. Shokat, and Peter Walter

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Structural and functional basis for RNA cleavage by Ire1, Alexei V. Korennykh, Andrei A. Korostelev, Pascal F. Egea, Janet Finer-Moore, Robert M. Stroud, Chao Zhang, Kevan M. Shokat, and Peter Walter

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Dioxin Exposure and Age of Pubertal Onset Among Russian Boys, Susan A. Korrick, Mary M. Lee, Paige L. Williams, Oleg Sergeyev, Jane S. Burns, Donald G. Patterson, Wayman E. Turner, Larry L. Needham, Larisa Altshul, Boris Revich, and Russ Hauser

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Negative autoregulation by Fas stabilizes adult erythropoiesis and accelerates its stress response, Miroslav Koulnis, Ying Liu, Kelly N. Hallstrom, and Merav Socolovsky

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Repeated cleavage failure does not establish centrosome amplification in untransformed human cells, Anna Krzywicka-Racka and Greenfield Sluder

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Functional characterization of the Saccharomyces cerevisiae protein Chl1 reveals the role of sister chromatid cohesion in the maintenance of spindle length during S-phase arrest, Suparna Laha, Shankar Das, Sujata Hajra, Kaustuv Sanyal, and Pratima Sinha

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ESCRT-III subunits Snf7-1 and Snf7-2 differentially regulate transmembrane cargos in hESC-derived human neurons, Jin-A Lee, Lei Liu, Robyn Javier, Anatol C. Kreitzer, Celine Delaloy, and Fen-Biao Gao

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Mycobacterium tuberculosis induces an atypical cell death mode to escape from infected macrophages, Jinhee Lee, Teresa Repasy, Kadamba Papavinasasundaram, Christopher M. Sassetti, and Hardy Kornfeld

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An Expressed Sequence Tag collection from the male antennae of the Noctuid moth Spodoptera littoralis: a resource for olfactory and pheromone detection research, Fabrice Legeai, Sebastien Malpel, Nicolas Montagne, Christelle Monsempes, Francois Cousserans, Christine Merlin, Marie-Christine Francois, Martine Maibeche-Coisne, Frederick Gavory, Julie Poulain, and Emmanuelle Jacquin-Joly

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Uncovering intrinsic connectional architecture of functional networks in awake rat brain, Zhifeng Liang, Jean A. King, and Nanyin Zhang

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Maternal exposure to angiotensin converting enzyme inhibitors in the first trimester and risk of malformations in offspring: a retrospective cohort study, De-Kun Li, Chunmei Yang, Susan E. Andrade, Venessa Tavares, and Jeannette R. Ferber

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Dynamic changes of cytotoxic T lymphocytes (CTLs), natural killer (NK) cells, and natural killer T (NKT) cells in patients with acute hepatitis B infection, Jun Li, Yaping Han, Ke Jin, Yufeng Wan, Shixia Wang, Bo Liu, Yuan Liu, Shan Lu, and Zuhu Huang

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The combination of early and rapid type I IFN, IL-1alpha, and IL-1beta production are essential mediators of RNA-like adjuvant driven CD4+ Th1 responses, Rachel F. Madera, Jennifer P. Wang, and Daniel H. Libraty

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A new approach to monitoring dengue activity, Lawrence C. Madoff, David N. Fisman, and Taha Kass-Hout

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The expression of myogenic microRNAs indirectly requires protein arginine methyltransferase (Prmt)5 but directly requires Prmt4, Chandrashekara Mallappa, Yu-Jie Hu, Priscilla Shamulailatpam, Sookil Tae, Said Sif, and Anthony N. Imbalzano

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No immune responses by the expression of the yeast Ndi1 protein in rats, Mathieu Marella, Byoung Boo Seo, Terence R. Flotte, Akemi Matsuno-Yagi, and Takao Yagi

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Cytotoxic CD4 T cells in antiviral immunity, Nikki B. Marshall and Susan L. Swain

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A User's Guide to the Encyclopedia of DNA Elements (ENCODE), Richard M. Meyers, ENCODE Project Consortium, Job Dekker, Bryan R. Lajoie, Amartya Sanyal, Zhiping Weng, Troy W. Whitfield, and Jie Wang

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Quiescent, slow-cycling stem cell populations in cancer: a review of the evidence and discussion of significance, Nathan Moore and Stephen Lyle

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The human nucleolar protein FTSJ3 associates with NIP7 and functions in pre-rRNA processing, Luis G. Morello, Patricia P. Coltri, Alexandre J.C. Quaresma, Fernando M. Simabuco, Tereza C.L. Sila, Guramrit Singh, Jeffrey A. Nickerson, Carla C. Oliveira, Melissa J. Moore, and Nilson I. T. Zanchin

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PDP-1 Links the TGF-β and IIS Pathways to Regulate Longevity, Development, and Metabolism, Sri Devi Narasimhan, Kelvin Yen, Ankita Bansal, Eun-Soo Kwon, Srivatsan Padmanabhan, and Heidi A. Tissenbaum

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The Plasma Membrane-Associated GTPase Rin Interacts with the Dopamine Transporter and Is Required for Protein Kinase C-Regulated Dopamine Transporter Trafficking, Deanna M. Navaroli, Zachary H. Stevens, Zeljko Uzelac, Luke Gabriel, Michael J. King, Lawrence M. Lifshitz, Harald H. Sitte, and Haley E. Melikian

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Pseudohypoparathyroidism in Children, Benjamin U. Nwosu

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Extended interferon-alpha therapy accelerates telomere length loss in human peripheral blood T lymphocytes, Joel M. O'Bryan, James A. Potts, Herbert L. Bonkovsky, Anuja Mathew, and Alan L. Rothman

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Inhibition of TLR8- and TLR4-induced Type I IFN Induction by Alcohol is Different from its effects on inflammatory cytokine production in monocytes, Maoyin Pang, Shashi Bala, Karen Kodys, Donna Catalano, and Gyongyi Szabo

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Recent trends in the characteristics and prognosis of patients hospitalized with acute heart failure, David Park, David D. McManus, Chad E. Darling, Jordan H. Goldberg, Joel M. Gore, Darleen M. Lessard, and Robert J. Goldberg

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Streptococcus pneumoniae DNA Initiates Type I Interferon Signaling in the Respiratory Tract, Dane Parker, Francis J. Martin, Grace Soong, Bryan S. Harfenist, Jorge L. Aguilar, Adam J. Ratner, Katherine A. Fitzgerald, Christian Schindler, and Alice Prince

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Functional analysis of retinitis pigmentosa 2 (RP2) protein reveals variable pathogenic potential of disease-associated missense variants, Suresh B. Patil, Toby W. Hurd, Amiya K. Gosh, Carlos A. Murga-Zamalloa, and Hemant Khanna

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Accelerating protein docking in ZDOCK using an advanced 3D convolution library, Brian G. Pierce, Yichiro Hourai, and Zhiping Weng

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Identification of Influenza Cases During the H1N1 Pandemic in Massachusetts Using Population-Based Hospital Discharge Data, Hilary Placzek and Lawrence C. Madoff

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Recombination Phenotypes of Escherichia Coli greA Mutants, Anthony R. Poteete

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A Non-Specific Effect Associated with Conditional Transgene Expression Based on Cre-loxP Strategy in Mice, Linghua Qiu, Jaime A. Rivera-Perez, and Zuoshang Xu