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Browsing MIT Open Access Articles by Title

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  • Liang, Ling; Zhang, Jingqing; Lin, Zhanglin (BioMed Central Ltd, 2007-11)
    Background: The NAD(P)H-dependent Pichia stipitis xylose reductase (PsXR) is one of the key enzymes for xylose fermentation, and has been cloned into the commonly used ethanol-producing yeast Saccharomyces cerevisiae. In ...
  • Salvucci, Guido D.; Entekhabi, Dara (American Geophysical Union (AGU), 2011-08)
    [1] Atmospheric models include land surface parameterizations of heat and moisture fluxes. Most parameterizations derive from early models of layered soil and vegetation canopy that account for liquid, vapor and heat ...
  • Lewis, Joel Brewster (Electronic Journal of Combinatorics, 2009-02)
    We study the problem of counting alternating permutations avoiding collections of permutation patterns including 132. We construct a bijection between the set S[subscript n](132) of 132-avoiding permutations and the set ...
  • Peraud, Jean-Philippe Michel; Hadjiconstantinou, Nicolas (American Institute of Physics (AIP), 2012-10)
    Starting from the recently proposed energy-based deviational formulation for solving the Boltzmann equation [J.-P. Péraud and N. G. Hadjiconstantinou, Phys. Rev. B 84, 205331 (2011)], which provides significant computational ...
  • Frank, Christopher Lee; Tsai, Li-Huei (Elsevier, 2009-05)
    Recent studies have demonstrated that boundaries separating a cycling cell from a postmitotic neuron are not as concrete as expected. Novel and unique physiological functions in neurons have been ascribed for proteins ...
  • Murphy, Patrick Andries; Hynes, Richard O. (Ovid Technologies (Wolters Kluwer) -American Heart Association, 2014-06)
    Objective—Abnormally low-flow conditions, sensed by the arterial endothelium, promote aneurysm rupture. Fibronectin (FN) is among the most abundant extracellular matrix proteins and is strongly upregulated in human aneurysms, ...
  • Bradley, Robert K.; Merkin, Jason Jay; Lambert, Nicole J.; Burge, Christopher B. (Public Library of Science, 2012-01)
    Thousands of human genes contain introns ending in NAGNAG (N any nucleotide), where both NAGs can function as 3′ splice sites, yielding isoforms that differ by inclusion/exclusion of three bases. However, few models exist ...
  • Giudice, Jimena; Xia, Zheng; Scavuzzo, Marissa A.; Ward, Amanda J.; Kalsotra, Auinash; Wang, Wei; Wehrens, Xander H. T.; Burge, Christopher B.; Li, Wei; Cooper, Thomas A.; Wang, Eric Tzy-shi (2014-04)
    During postnatal development the heart undergoes a rapid and dramatic transition to adult function through transcriptional and post-transcriptional mechanisms, including alternative splicing (AS). Here we perform deep ...
  • Rojas-Duran, Maria F.; Gilbert, Wendy (Cold Spring Harbor Laboratory Press, 2012-10)
    mRNA levels do not accurately predict protein levels in eukaryotic cells. To investigate contributions of 5′ untranslated regions (5′ UTRs) to mRNA-specific differences in translation, we determined the 5′ UTR boundaries ...
  • Gilbert, Wendy (American Society for Biochemistry and Molecular Biology (ASBMB), 2010-09)
    Internal ribosome entry sites (IRESs) are specialized mRNA elements that allow recruitment of eukaryotic ribosomes to naturally uncapped mRNAs or to capped mRNAs under conditions in which cap-dependent translation is ...
  • Truong, Bao H.; Hu, Lin-Wen; Buongiorno, Jacopo; McKrell, Thomas J. (American Society of Mechanical Engineers, 2009-12)
    Nanofluids are engineered colloidal dispersions of nano-sized particle in common base fluids. Previous pool boiling studies have shown that nanofluids can improve critical heat flux (CHF) up to 200% for pool boiling and ...
  • Xu, Zhiping; Paparcone, Raffaella; Buehler, Markus J.; Xu, Shiping (Elsevier, 2010-05)
    Amyloid fibrils are highly ordered protein aggregates that are associated with several pathological processes, including prion propagation and Alzheimer's disease. A key issue in amyloid science is the need to understand ...
  • Srivastava, Gyan; Lunnon, Katie; Burgess, Jeremy; Yu, Lei; Ernst, Jason; McCabe, Cristin; Tang, Anna; Raj, Towfique; Replogle, Joseph; Brodeur, Wendy; Gabriel, Stacey; Younkin, Curtis; Zou, Fanggeng; Szyf, Moshe; Meissner, Alexander; Ertekin-Taner, Nilufer; Kellis, Manolis; Mill, Jonathan; De Jager, Philip L.; Schalkwyk, Leonard C.; Eaton, Matthew Lucas; Eaton, Matthew L.; Keenan, Brendan T.; Ernst, Jason; Chai, High S.; Younkin, Steven G.; Epstein, Charles B.; Schneider, Julie A.; Bernstein, Bradley E.; Chibnik, Lori B.; Bennett, David A. (Nature Publishing Group, 2014-08)
    We used a collection of 708 prospectively collected autopsied brains to assess the methylation state of the brain's DNA in relation to Alzheimer's disease (AD). We found that the level of methylation at 71 of the 415,848 ...
  • Chibnik, Lori B.; Yu, Lei; Srivastava, Gyan; Schneider, Julie A.; Kellis, Manolis; Bennett, David A.; De Jager, Philip L.; Eaton, Matthew Lucas (American Neurological Association, 2015-04)
    Objective We explore the role of DNA methylation in Alzheimer's disease (AD). To elucidate where DNA methylation falls along the causal pathway linking risk factors to disease, we examine causal models to assess its role ...
  • Christian, Theresa M.; Beaton, Daniel A.; Mukherjee, Kunal; Alberi, Kirstin; Fitzgerald, Eugene A.; Mascarenhas, Angelo (American Institute of Physics (AIP), 2013-08)
    We demonstrate amber-green emission from Al[subscript x]In[subscript 1– x]P light-emitting diodes (LEDs) with luminescence peaked at 566 nm and 600 nm. The LEDs are metamorphically grown on GaAs substrates via a graded ...
  • Foley, Megan A.; Jamison, Timothy F. (American Chemical Society (ACS), 2010-08)
    A rapid carboxylic acid-promoted lactone aminolysis is reported. A number of carboxylic acids were found to promote this amide bond-forming transformation, with aliphatic acids being the most efficient. This reaction is ...
  • DeFlores, Lauren P.; Ganim, Ziad; Nicodemus, Rebecca A.; Tokmakoff, Andrei (American Chemical Society, 2009-02)
    We demonstrate how multimode 2D IR spectroscopy of the protein amide I′ and II′ vibrations can be used to distinguish protein secondary structure. Polarization-dependent amide I′−II′ 2D IR experiments on poly-l-lysine in ...
  • Brander, Christian; Walker, Bruce D.; Goulder, Philip J. R.; Rolland, Morgane; Carlson, Jonathan M.; Manocheewa, Siriphan; Rousseau, Christine M.; Raugi, Dana N.; Learn, Gerald H.; Maust, Brandon S.; Coovadia, Hoosen M.; Ndung'u, Thumbi; Heckerman, David; Mullins, James I.; Swain, J. Victor; Lanxon-Cookson, Erinn; Deng, Wenjie (Public Library of Science, 2010-09)
    Background Despite high potential for HIV-1 genetic variation, the emergence of some mutations is constrained by fitness costs, and may be associated with compensatory amino acid (AA) co-variation. To characterize the ...
  • Petsche Connell, Jennifer; Camci-Unal, Gulden; Khademhosseini, Ali; Jacot, Jeffrey G. (Mary Ann Liebert, Inc., 2013-03)
    Recent research has demonstrated that a population of stem cells can be isolated from amniotic fluid removed by amniocentesis that are broadly multipotent and nontumorogenic. These amniotic fluid-derived stem cells (AFSC) ...
  • Ritvo, Harriet (White Horse Press, 2014-11)
    The tendency to see humans as special and separate influences even practices like scientific taxonomy which explicitly place them among other animals. The animal-related scholarship that has emerged throughout the humanities ...
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