Browsing HMS Scholarly Articles by Title

Now showing items 7113-7132 of 17922

    • Genomic Signatures Characterize Leukocyte Infiltration in Myositis Muscles 

      Zhu, Wei; Streicher, Katie; Shen, Nan; Higgs, Brandon W; Morehouse, Chris; Greenlees, Lydia; Amato, Anthony A.; Ranade, Koustubh; Richman, Laura; Fiorentino, David; Jallal, Bahija; Greenberg, Steven A.; Yao, Yihong (BioMed Central, 2012)
      Background: Leukocyte infiltration plays an important role in the pathogenesis and progression of myositis, and is highly associated with disease severity. Currently, there is a lack of: efficacious therapies for myositis; ...

    • A Genomic Storm in Critically Injured Humans 

      Mindrinos, Michael N.; Seok, Junhee; Cuschieri, Joseph; Cuenca, Alex G.; Hayden, Douglas L.; Hennessy, Laura; Moore, Ernest E.; Minei, Joseph P.; Bankey, Paul E.; Sperry, Jason; Nathens, Avery B.; Billiar, Timothy R.; Brownstein, Bernard H.; Mason, Philip H.; Baker, Henry V.; Finnerty, Celeste C.; Jeschke, Marc G.; López, M. Cecilia; Klein, Matthew B.; Gamelli, Richard L.; Gibran, Nicole S.; Arnoldo, Brett; Xu, Weihong; Zhang, Yuping; Calvano, Steven E.; McDonald-Smith, Grace P.; Storey, John D.; Moldawer, Lyle L.; Herndon, David N.; Lowry, Stephen F.; Maier, Ronald V.; Davis, Ronald W.; Xiao, Wenzhong; Gao, Hong; Johnson, Jeffrey L.; West, Michael A.; Schoenfeld, David Alan; Cobb, Joseph Perren; Warren, H. Shaw; Tompkins, Ronald Gary (The Rockefeller University Press, 2011)
      Human survival from injury requires an appropriate inflammatory and immune response. We describe the circulating leukocyte transcriptome after severe trauma and burn injury, as well as in healthy subjects receiving low-dose ...

    • Genomic Studies with Escherichia coli MelR Protein: Applications of Chromatin Immunoprecipitation and Microarrays 

      Grainger, DC; Overton, TW; Reppas, N; Wade, JT; Tamai, E; Hobman, JL; Constantinidou, C; Struhl, Kevin; Church, George; Busby, SJW (American Society for Microbiology, 2004)
      Escherichia coli MelR protein is a transcription activator that is essential for melibiose-dependent expression of the melAB genes. We have used chromatin immunoprecipitation to study the binding of MelR and RNA polymerase ...

    • The genomic substrate for adaptive radiation in African cichlid fish 

      Brawand, David; Wagner, Catherine E.; Li, Yang I.; Malinsky, Milan; Keller, Irene; Fan, Shaohua; Simakov, Oleg; Ng, Alvin Y.; Lim, Zhi Wei; Bezault, Etienne; Turner-Maier, Jason; Johnson, Jeremy; Alcazar, Rosa; Noh, Hyun Ji; Russell, Pamela; Aken, Bronwen; Alföldi, Jessica; Amemiya, Chris; Azzouzi, Naoual; Baroiller, Jean-François; Barloy-Hubler, Frederique; Berlin, Aaron; Bloomquist, Ryan; Carleton, Karen L.; Conte, Matthew A.; D'Cotta, Helena; Eshel, Orly; Gaffney, Leslie; Galibert, Francis; Gante, Hugo F.; Gnerre, Sante; Greuter, Lucie; Guyon, Richard; Haddad, Natalie S.; Haerty, Wilfried; Harris, Rayna M.; Hofmann, Hans A.; Hourlier, Thibaut; Hulata, Gideon; Jaffe, David B.; Lara, Marcia; Lee, Alison P.; MacCallum, Iain; Mwaiko, Salome; Nikaido, Masato; Nishihara, Hidenori; Ozouf-Costaz, Catherine; Penman, David J.; Przybylski, Dariusz; Rakotomanga, Michaelle; Renn, Suzy C. P.; Ribeiro, Filipe J.; Ron, Micha; Salzburger, Walter; Sanchez-Pulido, Luis; Santos, M. Emilia; Searle, Steve; Sharpe, Ted; Swofford, Ross; Tan, Frederick J.; Williams, Louise; Young, Sarah; Yin, Shuangye; Okada, Norihiro; Kocher, Thomas D.; Miska, Eric A.; Lander, Eric S.; Venkatesh, Byrappa; Fernald, Russell D.; Meyer, Axel; Ponting, Chris P.; Streelman, J. Todd; Lindblad-Toh, Kerstin; Seehausen, Ole; Di Palma, Federica (2014)
      Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes ...

    • Genomic testing to determine drug response: measuring preferences of the public and patients using Discrete Choice Experiment (DCE) 

      Najafzadeh, Mehdi; Johnston, Karissa M; Peacock, Stuart J; Connors, Joseph M; Marra, Marco A; Lynd, Larry D; Marra, Carlo A (BioMed Central, 2013)
      Background: The extent to which a genomic test will be used in practice is affected by factors such as ability of the test to correctly predict response to treatment (i.e. sensitivity and specificity of the test), invasiveness ...

    • Genomic transition of enterococci from gut commensals to leading causes of multidrug-resistant hospital infection in the antibiotic era 

      Gilmore, Michael S.; Lebreton, Francois Herve; van Schaik, Willem (Elsevier BV, 2013)
      The enterococci evolved over eons as highly adapted members of gastrointestinal consortia of a wide variety of hosts, but for reasons that are not entirely clear, emerged in the 1970s as leading causes of multidrug resistant ...

    • Genomic variation landscape of the human gut microbiome 

      Schloissnig, Siegfried; Arumugam, Manimozhiyan; Sunagawa, Shinichi; Mitreva, Makedonka; Tap, Julien; Zhu, Ana; Waller, Alison; Mende, Daniel R.; Kultima, Jens Roat; Martin, John; Kota, Karthik; Sunyaev, Shamil R.; Weinstock, George M.; Bork, Peer (2012)
      While large-scale efforts have rapidly advanced the understanding and practical impact of human genomic variation, the latter is largely unexplored in the human microbiome. We therefore developed a framework for metagenomic ...

    • Genomically Informed Surveillance for Carbapenem-Resistant Enterobacteriaceae in a Health Care System 

      Pecora, Nicole D.; Li, Ning; Allard, Marc; Li, Cong; Albano, Esperanza; Delaney, Mary; Dubois, Andrea; Onderdonk, Andrew B.; Bry, Lynn (American Society of Microbiology, 2015)
      ABSTRACT Carbapenem-resistant Enterobacteriaceae (CRE) are an urgent public health concern. Rapid identification of the resistance genes, their mobilization capacity, and strains carrying them is essential to direct hospital ...

    • Genomically Recoded Organisms Expand Biological Functions 

      Lajoie, Marc J.; Rovner, Alexis J.; Goodman, Daniel B.; Aerni, Hans-Rudolf; Haimovich, Adrian D.; Kuznetsov, Gleb; Mercer, Jaron A.; Wang, Harris H.; Carr, Peter A.; Mosberg, Joshua A.; Rohland, Nadin; Schultz, Peter G.; Jacobson, Joseph M.; Rinehart, Jesse; Church, George; Isaacs, Farren J. (American Association for the Advancement of Science (AAAS), 2013-10-18)
      We describe the construction and characterization of a genomically recoded organism (GRO). We replaced all known UAG stop codons in Escherichia coli MG1655 with synonymous UAA codons, which permitted the deletion of release ...

    • Genomics of Drug Sensitivity in Cancer (GDSC): a Resource for Therapeutic Biomarker Discovery in Cancer Cells 

      Yang, Wanjuan; Soares, Jorge; Greninger, Patricia; Edelman, Elena J.; Lightfoot, Howard; Forbes, Simon; Bindal, Nidhi; Beare, Dave; Smith, James A.; Thompson, I. Richard; Ramaswamy, Sridhar; Futreal, P. Andrew; Haber, Daniel Arie; Stratton, Michael R.; Benes, Cyril Henri; McDermott, Ultan; Garnett, Mathew J. (Oxford University Press, 2012)
      Alterations in cancer genomes strongly influence clinical responses to treatment and in many instances are potent biomarkers for response to drugs. The Genomics of Drug Sensitivity in Cancer (GDSC) database (www.cancerRxgene.org) ...

    • Genomics of Loa loa, a Wolbachia-free filarial parasite of humans 

      Desjardins, Christopher A.; Cerqueira, Gustavo C.; Goldberg, Jonathan M.; Hotopp, Julie C. Dunning; Haas, Brian J.; Zucker, Jeremy; Ribeiro, Jose’ M.C.; Saif, Sakina; Levin, Joshua Z.; Fan, Lin; Zeng, Qiandong; Russ, Carsten; Wortman, Jennifer R.; Fink, Doran L.; Birren, Bruce W.; Nutman, Thomas B. (2014)
      Loa loa, the African eyeworm, is a major filarial pathogen of humans. Unlike most filariae, Loa loa does not contain the obligate intracellular Wolbachia endosymbiont. We describe the 91.4 Mb genome of Loa loa, and the ...

    • Genotator: A Disease-Agnostic Tool for Genetic Annotation of Disease 

      Wall, Dennis Paul Paul; Pivovarov, Rimma; Tong, Mark; Jung, Jae-Yoon; Fusaro, Vincent Alfred; DeLuca, Todd; Tonellato, Peter J (BioMed Central, 2010)
      Background: Disease-specific genetic information has been increasing at rapid rates as a consequence of recent improvements and massive cost reductions in sequencing technologies. Numerous systems designed to capture and ...

    • Genotype Directed Therapy in Murine Mismatch Repair Deficient Tumors 

      Kucherlapati, Melanie H.; Esfahani, Shadi; Habibollahi, Peiman; Wang, Junning; Still, Eric R.; Bronson, Roderick T.; Mahmood, Umar; Kucherlapati, Raju S. (Public Library of Science, 2013)
      The PI3K/AKT/mTOR pathway has frequently been found activated in human tumors. We show that in addition to Wnt signaling dysfunction, the PI3K/AKT/mTOR pathway is often upregulated in mouse Msh2−/− initiated intestinal ...

    • Genotypic and Functional Impact of HIV-1 Adaptation to Its Host Population during the North American Epidemic 

      Cotton, Laura A.; Kuang, Xiaomei T.; Le, Anh Q.; Carlson, Jonathan M.; Chan, Benjamin; Chopera, Denis R.; Brumme, Chanson J.; Markle, Tristan J.; Martin, Eric; Shahid, Aniqa; Anmole, Gursev; Mwimanzi, Philip; Nassab, Pauline; Penney, Kali A.; Rahman, Manal A.; Milloy, M.-J.; Schechter, Martin T.; Markowitz, Martin; Carrington, Mary; Walker, Bruce D.; Wagner, Theresa; Buchbinder, Susan; Fuchs, Jonathan; Koblin, Beryl; Mayer, Kenneth H.; Harrigan, P. Richard; Brockman, Mark A.; Poon, Art F. Y.; Brumme, Zabrina L. (Public Library of Science, 2014)
      HLA-restricted immune escape mutations that persist following HIV transmission could gradually spread through the viral population, thereby compromising host antiviral immunity as the epidemic progresses. To assess the ...

    • Genotyping Analyses of Tuberculosis Cases in U.S.- and Foreign-Born Massachusetts Residents 

      Sharnprapai, Sharon; Miller, Ann C.; Suruki, Robert; Corkren, Edward; Etkind, Sue; Driscoll, Jeffrey; McGarry, Michael; Nardell, Edward Anthony (Centers for Disease Control and Prevention, 2002)
      We used molecular genotyping to further understand the epidemiology and transmission patterns of tuberculosis (TB) in Massachusetts. The study population included 983 TB patients whose cases were verified by the Massachusetts ...

    • Genotyping Cancer-Associated Genes in Chordoma Identifies Mutations in Oncogenes and Areas of Chromosomal Loss Involving CDKN2A, PTEN, and SMARCB1 

      Choy, Edwin; MacConaill, Laura E.; Cote, Gregory M.; Le, Long P.; Shen, Jacson K.; Nielsen, Gunnlaugur P.; Iafrate, Anthony J.; Garraway, Levi A.; Hornicek, Francis J.; Duan, Zhenfeng (Public Library of Science, 2014)
      The molecular mechanisms underlying chordoma pathogenesis are unknown. We therefore sought to identify novel mutations to better understand chordoma biology and to potentially identify therapeutic targets. Given the ...

    • Geographic Access to Breast Imaging for US Women 

      Onega, Tracy; Hubbard, Rebecca; Hill, Deirdre; Lee, Christoph I.; Haas, Jennifer S.; Carlos, Heather A.; Alford-Teaster, Jennifer; Bogart, Andy; DeMartini, Wendy B.; Kerlikowske, Karla; Virnig, Beth A.; Buist, Diana S.M.; Henderson, Louise; Tosteson, Anna N.A. (Elsevier BV, 2014)
      The breast imaging modalities of mammography, ultrasound, and MRI are widely used for screening, diagnosis, treatment, and surveillance of breast cancer. Geographic access to breast imaging services in various modalities ...

    • Geographic and Temporal Variation in Cardiac Implanted Electric Devices to Treat Heart Failure 

      Hatfield, Laura A.; Kramer, Daniel B.; Volya, Rita; Reynolds, Matthew R.; Normand, Sharon‐Lise T. (John Wiley and Sons Inc., 2016)
      Background: Cardiac implantable electric devices are commonly used to treat heart failure. Little is known about temporal and geographic variation in use of cardiac resynchronization therapy (CRT) devices in usual care ...

    • The Geographic Distribution of Breast Cancer Incidence in Massachusetts 1988 to 1997, Adjusted for Covariates 

      Joseph Sheehan, T; DeChello, Laurie M; Gregorio, David I; Gershman, Susan; Mroszczyk, Mary; Kulldorff, Martin (BioMed Central, 2004)
      Background: The aims of this study were to determine whether observed geographic variations in breast cancer incidence are random or statistically significant, whether statistically significant excesses are temporary or ...

    • Geographic patterns in patient demographics and insulin use in 18 countries, a global perspective from the multinational observational study assessing insulin use: understanding the challenges associated with progression of therapy (MOSAIc) 

      Polinski, Jennifer M.; Kim, Seoyoung C.; Jiang, Dingfeng; Hassoun, Ahmed; Shrank, William H.; Cos, Xavier; Rodríguez-Vigil, Efraín; Suzuki, Shuichi; Matsuba, Ikuro; Seeger, John D.; Eddings, Wesley; Brill, Gregory; Curtis, Bradley H. (BioMed Central, 2015)
      Background: Among patients with type 2 diabetes, insulin intensification to achieve glycemic targets occurs less often than clinically indicated. Barriers to intensification are not well understood. We present patients’ ...