Now showing items 220-239 of 298

    • Quantifying Interhospital Patient Sharing as a Mechanism for Infectious Disease Spread 

      Huang, Susan S.; Avery, Takuser R.; Song, Yeohan H.; Elkins, Kristen R.; Nguyen, Christopher C.; Nutter, Sandra K.; Nafday, Alaka. A.; Condon, Curtis J.; Chang, Michael T.; Chrest, David; Boos, John; Bobashev, Georgiy; Wheaton, William; Frank, Steven A.; Platt, Richard; Lipsitch, Marc; Bush, Robin M.; Eubank, Stephen; Burke, Donald S.; Lee, Bruce Y. (University of Chicago Press, 2010-11)
      BACKGROUND. Assessments of infectious disease spread in hospitals seldom account for interfacility patient sharing. This is particularly important for pathogens with prolonged incubation periods or carrier states. METHODS. ...
    • Quantifying spatio-temporal variation of invasion spread 

      Goldstein, J.; Park, J.; Haran, M.; Liebhold, A.; Bjørnstad, O.N. (Royal Society Publishing, 2019-01-09)
      The spread of invasive species can have far-reaching environmental and ecological consequences. Understanding invasion spread patterns and the underlying process driving invasions are key to predicting and managing invasions. ...
    • Quantitative Genetic Background of the Host Influences Gut Microbiomes in Chickens 

      Zhao, L. L.; Wang, G.; Siegel, P.; He, C.; Wang, H. Z.; Zhao, W. J.; Zhai, Z. X.; Tian, F. W.; Zhao, J. X.; Zhang, H.; Sun, Z. K.; Chen, W.; Zhang, Y.; Meng, H. (Nature Publishing Group, 2013-01)
      Host genotype and gender are among the factors that influence the composition of gut microbiota. We studied the population structure of gut microbiota in two lines of chickens maintained under the same husbandry and dietary ...
    • A quantitative study of the division cycle of Caulobacter crescentus stalked cells. 

      Li, S.; Brazhnik, P.; Sobral, B.; Tyson, John J. (2008-01)
      Progression of a cell through the division cycle is tightly controlled at different steps to ensure the integrity of genome replication and partitioning to daughter cells. From published experimental evidence, we propose ...
    • A rapid conditional enumeration haplotyping method in pedigrees 

      Gao, Guimin; Hoeschele, Ina (2008-01-15)
      Haplotyping in pedigrees provides valuable information for genetic studies (e.g., linkage analysis and association study). In order to identify a set of haplotype configurations with the highest likelihoods for a large ...
    • Rapid genomic changes in Drosophila melanogaster adapting to desiccation stress in an experimental evolution system 

      Kang, Lin; Aggarwal, Dau Dayal; Rashkovetsky, Eugenia; Korol, Abraham B.; Michalak, Pawel (BMC, 2016-03-15)
      Background Experimental evolution studies, coupled with whole genome resequencing and advances in bioinformatics, have become a powerful tool for exploring how populations respond to selection at the genome-wide level, ...
    • RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes 

      Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Thomason, James A., III; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang (Springer Nature, 2015-02-10)
      The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features ...
    • RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response 

      Krishnan, Arjun; Gupta, Chirag; Ambavaram, Madana M. R.; Pereira, Andy (2017-09-20)
      Transcriptional profiling is a prevalent and powerful approach for capturing the response of crop plants to environmental stresses, e.g., response of rice to drought. However, functionally interpreting the resulting ...
    • Reconstruction of endosomal organization and function by a combination of ODE and agent-based modeling strategies 

      Mayorga, Luis S; Cebrian, Ignacio; Verma, Meghna; Hoops, Stefan; Bassaganya-Riera, Josep (2018-11-23)
      Abstract Background Reproducing cell processes using an in silico system is an essential tool for understanding the underlying mechanisms and emergent properties of this ...
    • Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates 

      Yablonovitch, Arielle L.; Fu, Jeremy; Li, Kexin; Mahato, Simpla; Kang, Lin; Rashkovetsky, Eugenia; Korol, Abraham B.; Tang, Hua; Michalak, Pawel; Zelhof, Andrew C.; Nevo, Eviatar; Li, Jin Billy (Springer Nature, 2017-11-17)
      Determining the mechanisms by which a species adapts to its environment is a key endeavor in the study of evolution. In particular, relatively little is known about how transcriptional processes are fine-tuned to adjust ...
    • Reproducibility, bioinformatic analysis and power of the SAGE method to evaluate changes in transcriptome 

      Dinel, S; Bolduc, C; Belleau, P; Boivin, A; Yoshioka, M; Calvo, E; Piedboeuf, B; Snyder, EE; Labrie, F; St-Amand, J (2005-01-01)
      The serial analysis of gene expression (SAGE) method is used to study global gene expression in cells or tissues in various experimental conditions. However, its reproducibility has not yet been definitively assessed. In ...
    • Research and Education at the Virginia Bioinformatics Institute at Virginia Tech 

      Smith, EJ; Ohara, K (2014-04-13)
      Virginia Tech, the largest research university in the Commonwealth of Virginia, has developed over the last 15 years resources essential for high throughput biological and computational research. Using these resources, VT ...
    • Response of the Hepatic Transcriptome to Aflatoxin B-1 in Domestic Turkey (Meleagris gallopavo) 

      Monson, Melissa S.; Settlage, Robert E.; McMahon, Kevin W.; Mendoza, Kristelle M.; Rawal, Sumit; El-Nezami, Hani S.; Coulombe, Roger A.; Reed, Kent M. (PLOS, 2014-06-30)
      Dietary exposure to aflatoxin B1 (AFB1) is detrimental to avian health and leads to major economic losses for the poultry industry. AFB1 is especially hepatotoxic in domestic turkeys (Meleagris gallopavo), since these birds ...
    • Resveratrol Enhances Antitumor Activity of TRAIL in Prostate Cancer Xenografts through Activation of FOXO Transcription Factor 

      Ganapathy, Suthakar; Chen, Qinghe; Singh, Karan P.; Shankar, Sharmila; Srivastava, Rakesh K. (PLOS, 2010-12-28)
      Background Resveratrol (3, 4′, 5 tri-hydroxystilbene), a naturally occurring polyphenol, exhibits anti-inflammatory, antioxidant, cardioprotective and antitumor activities. We have recently shown that resveratrol can ...
    • Resveratrol Induces Growth Arrest and Apoptosis through Activation of FOXO Transcription Factors in Prostate Cancer Cells 

      Chen, Qinghe; Ganapathy, Suthakar; Singh, Karan P.; Shankar, Sharmila; Srivastava, Rakesh K. (PLOS, 2010-12-14)
      Background Resveratrol, a naturally occurring phytopolyphenol compound, has attracted extensive interest in recent years because of its diverse pharmacological characteristics. Although resveratrol possesses chemopreventive ...
    • Rickettsia Phylogenomics: Unwinding the Intricacies of Obligate Intracellular Life 

      Gillespie, Joseph J.; Williams, Kelly; Shukla, Maulik; Snyder, Eric E.; Nordberg, Eric K.; Ceraul, Shane M.; Dharmanolla, Chitti; Rainey, Daphne; Soneja, Jeetendra; Shallom, Joshua M.; Vishnubhat, Nataraj Dongre; Wattam, Rebecca; Purkayastha, Anjan; Czar, Michael; Crasta, Oswald; Setubal, João C.; Azad, Abdu F.; Sobral, Bruno S. (Public Library of Science, 2008-04-16)
      Background: Completed genome sequences are rapidly increasing for Rickettsia, obligate intracellular α-proteobacteria responsible for various human diseases, including epidemic typhus and Rocky Mountain spotted fever. In ...
    • Rickettsia typhi Possesses Phospholipase A(2) Enzymes that Are Involved in Infection of Host Cells 

      Rahman, M. Sayeedu; Gillespie, Joseph J.; Kaur, Simran Jeet; Sears, Khandra T.; Ceraul, Shane M.; Beier-Sexton, Magda; Azad, Abdu F. (Public Library of Science, 2013-06-20)
      The long-standing proposal that phospholipase A2 (PLA2) enzymes are involved in rickettsial infection of host cells has been given support by the recent characterization of a patatin phospholipase (Pat2) with PLA2 activity ...
    • Risk Map of Cholera Infection for Vaccine Deployment: The Eastern Kolkata Case 

      You, Young Ae; Ali, Mohammad; Kanungo, Suman; Sah, Binod; Manna, Byomkesh; Puri, Mahesh; Nair, G. Balakrish; Bhattacharya, Sujit Kumar; Convertino, Matteo; Deen, Jacqueline L.; Lopez, Anna Lena; Wierzba, Thomas F.; Clemens, John; Sur, Dipika (PLOS, 2013-08-02)
      Background Despite advancement of our knowledge, cholera remains a public health concern. During March-April 2010, a large cholera outbreak afflicted the eastern part of Kolkata, India. The quantification of importance ...
    • Role of information and communication networks in malaria survival 

      Mozumder, Pallab; Marathe, Achla (2007-10-10)
      Background Quite often symptoms of malaria go unrecognized or untreated. According to the Multilateral Initiative on Malaria, 70% of the malaria cases that are treated at home are mismanaged. Up to 82% of all malaria ...
    • The Role of Peroxisome Proliferator-Activated Receptor γ in Immune Responses to Enteroaggregative Escherichia coli Infection 

      Philipson, Casandra W.; Bassaganya-Riera, Josep; Viladomiu, Monica; Pedragosa, Mireia; Guerrant, Richard L.; Roche, James K.; Hontecillas, Raquel (Public Library of Science, 2013-02-28)
      Background: Enteroaggregative Escherichia coli (EAEC) is recognized as an emerging cause of persistent diarrhea and enteric disease worldwide. Mucosal immunity towards EAEC infections is incompletely understood due in part ...