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  • 1
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    Rates of evolution in ancient DNA from Adelie penguins (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-03-23
    Description: Well-preserved subfossil bones of Adelie penguins, Pygoscelis adeliae, underlie existing and abandoned nesting colonies in Antarctica. These bones, dating back to more than 7000 years before the present, harbor some of the best-preserved ancient DNA yet discovered. From 96 radiocarbon-aged bones, we report large numbers of mitochondrial haplotypes, some of which appear to be extinct, given the 380 living birds sampled. We demonstrate DNA sequence evolution through time and estimate the rate of evolution of the hypervariable region I using a Markov chain Monte Carlo integration and a least-squares regression analysis. Our calculated rates of evolution are approximately two to seven times higher than previous indirect phylogenetic estimates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lambert, D M -- Ritchie, P A -- Millar, C D -- Holland, B -- Drummond, A J -- Baroni, C -- New York, N.Y. -- Science. 2002 Mar 22;295(5563):2270-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular BioSciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand. D.M.Lambert@massey.ac.nz〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11910113" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antarctic Regions ; Birds/*genetics ; Bone and Bones/metabolism ; Calibration ; Carbon Radioisotopes ; DNA, Mitochondrial/*genetics/isolation & purification ; Ecosystem ; *Evolution, Molecular ; Fossils ; Haplotypes/genetics ; Least-Squares Analysis ; Markov Chains ; Monte Carlo Method ; Phylogeny ; Polymerase Chain Reaction ; Time Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Rise and fall of the Beringian steppe bison (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-11-30
    Description: The widespread extinctions of large mammals at the end of the Pleistocene epoch have often been attributed to the depredations of humans; here we present genetic evidence that questions this assumption. We used ancient DNA and Bayesian techniques to reconstruct a detailed genetic history of bison throughout the late Pleistocene and Holocene epochs. Our analyses depict a large diverse population living throughout Beringia until around 37,000 years before the present, when the population's genetic diversity began to decline dramatically. The timing of this decline correlates with environmental changes associated with the onset of the last glacial cycle, whereas archaeological evidence does not support the presence of large populations of humans in Eastern Beringia until more than 15,000 years later.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shapiro, Beth -- Drummond, Alexei J -- Rambaut, Andrew -- Wilson, Michael C -- Matheus, Paul E -- Sher, Andrei V -- Pybus, Oliver G -- Gilbert, M Thomas P -- Barnes, Ian -- Binladen, Jonas -- Willerslev, Eske -- Hansen, Anders J -- Baryshnikov, Gennady F -- Burns, James A -- Davydov, Sergei -- Driver, Jonathan C -- Froese, Duane G -- Harington, C Richard -- Keddie, Grant -- Kosintsev, Pavel -- Kunz, Michael L -- Martin, Larry D -- Stephenson, Robert O -- Storer, John -- Tedford, Richard -- Zimov, Sergei -- Cooper, Alan -- New York, N.Y. -- Science. 2004 Nov 26;306(5701):1561-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Henry Wellcome Ancient Biomolecules Centre, Oxford University, South Parks Road, Oxford OX13PS, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15567864" target="_blank"〉PubMed〈/a〉
    Keywords: Alaska ; Animals ; Bayes Theorem ; *Bison/classification/genetics ; Canada ; China ; *Climate ; DNA, Mitochondrial/genetics ; Environment ; *Fossils ; Genetic Variation ; Genetics, Population ; Human Activities ; Humans ; North America ; Phylogeny ; Population Dynamics ; Sequence Analysis, DNA ; Time
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    A virus reveals population structure and recent demographic history of its carnivore host (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-01-28
    Description: Directly transmitted parasites often provide substantial information about the temporal and spatial characteristics of host-to-host contact. Here, we demonstrate that a fast-evolving virus (feline immunodeficiency virus, FIV) can reveal details of the contemporary population structure and recent demographic history of its natural wildlife host (Puma concolor) that were not apparent from host genetic data and would be impossible to obtain by other means. We suggest that rapidly evolving pathogens may provide a complementary tool for studying population dynamics of their hosts in "shallow" time.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Biek, Roman -- Drummond, Alexei J -- Poss, Mary -- New York, N.Y. -- Science. 2006 Jan 27;311(5760):538-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wildlife Biology Program, University of Montana, Missoula, MT 59812, USA. rbiek@emory.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16439664" target="_blank"〉PubMed〈/a〉
    Keywords: Alberta/epidemiology ; Animals ; Bayes Theorem ; British Columbia/epidemiology ; Ecosystem ; *Evolution, Molecular ; Genes, env ; Genes, pol ; Geography ; Immunodeficiency Virus, Feline/*classification/*genetics ; Lentivirus Infections/epidemiology/*veterinary/virology ; Microsatellite Repeats ; Molecular Sequence Data ; Montana/epidemiology ; Phylogeny ; Population Dynamics ; *Puma/genetics/virology ; Time Factors ; Wyoming/epidemiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-10-30
    Description: Pancreatic cancer is a highly lethal malignancy with few effective therapies. We performed exome sequencing and copy number analysis to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (stage I and II) sporadic pancreatic ductal adenocarcinoma. Detailed analysis of 99 informative tumours identified substantial heterogeneity with 2,016 non-silent mutations and 1,628 copy-number variations. We define 16 significantly mutated genes, reaffirming known mutations (KRAS, TP53, CDKN2A, SMAD4, MLL3, TGFBR2, ARID1A and SF3B1), and uncover novel mutated genes including additional genes involved in chromatin modification (EPC1 and ARID2), DNA damage repair (ATM) and other mechanisms (ZIM2, MAP2K4, NALCN, SLC16A4 and MAGEA6). Integrative analysis with in vitro functional data and animal models provided supportive evidence for potential roles for these genetic aberrations in carcinogenesis. Pathway-based analysis of recurrently mutated genes recapitulated clustering in core signalling pathways in pancreatic ductal adenocarcinoma, and identified new mutated genes in each pathway. We also identified frequent and diverse somatic aberrations in genes described traditionally as embryonic regulators of axon guidance, particularly SLIT/ROBO signalling, which was also evident in murine Sleeping Beauty transposon-mediated somatic mutagenesis models of pancreatic cancer, providing further supportive evidence for the potential involvement of axon guidance genes in pancreatic carcinogenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530898/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530898/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Biankin, Andrew V -- Waddell, Nicola -- Kassahn, Karin S -- Gingras, Marie-Claude -- Muthuswamy, Lakshmi B -- Johns, Amber L -- Miller, David K -- Wilson, Peter J -- Patch, Ann-Marie -- Wu, Jianmin -- Chang, David K -- Cowley, Mark J -- Gardiner, Brooke B -- Song, Sarah -- Harliwong, Ivon -- Idrisoglu, Senel -- Nourse, Craig -- Nourbakhsh, Ehsan -- Manning, Suzanne -- Wani, Shivangi -- Gongora, Milena -- Pajic, Marina -- Scarlett, Christopher J -- Gill, Anthony J -- Pinho, Andreia V -- Rooman, Ilse -- Anderson, Matthew -- Holmes, Oliver -- Leonard, Conrad -- Taylor, Darrin -- Wood, Scott -- Xu, Qinying -- Nones, Katia -- Fink, J Lynn -- Christ, Angelika -- Bruxner, Tim -- Cloonan, Nicole -- Kolle, Gabriel -- Newell, Felicity -- Pinese, Mark -- Mead, R Scott -- Humphris, Jeremy L -- Kaplan, Warren -- Jones, Marc D -- Colvin, Emily K -- Nagrial, Adnan M -- Humphrey, Emily S -- Chou, Angela -- Chin, Venessa T -- Chantrill, Lorraine A -- Mawson, Amanda -- Samra, Jaswinder S -- Kench, James G -- Lovell, Jessica A -- Daly, Roger J -- Merrett, Neil D -- Toon, Christopher -- Epari, Krishna -- Nguyen, Nam Q -- Barbour, Andrew -- Zeps, Nikolajs -- Australian Pancreatic Cancer Genome Initiative -- Kakkar, Nipun -- Zhao, Fengmei -- Wu, Yuan Qing -- Wang, Min -- Muzny, Donna M -- Fisher, William E -- Brunicardi, F Charles -- Hodges, Sally E -- Reid, Jeffrey G -- Drummond, Jennifer -- Chang, Kyle -- Han, Yi -- Lewis, Lora R -- Dinh, Huyen -- Buhay, Christian J -- Beck, Timothy -- Timms, Lee -- Sam, Michelle -- Begley, Kimberly -- Brown, Andrew -- Pai, Deepa -- Panchal, Ami -- Buchner, Nicholas -- De Borja, Richard -- Denroche, Robert E -- Yung, Christina K -- Serra, Stefano -- Onetto, Nicole -- Mukhopadhyay, Debabrata -- Tsao, Ming-Sound -- Shaw, Patricia A -- Petersen, Gloria M -- Gallinger, Steven -- Hruban, Ralph H -- Maitra, Anirban -- Iacobuzio-Donahue, Christine A -- Schulick, Richard D -- Wolfgang, Christopher L -- Morgan, Richard A -- Lawlor, Rita T -- Capelli, Paola -- Corbo, Vincenzo -- Scardoni, Maria -- Tortora, Giampaolo -- Tempero, Margaret A -- Mann, Karen M -- Jenkins, Nancy A -- Perez-Mancera, Pedro A -- Adams, David J -- Largaespada, David A -- Wessels, Lodewyk F A -- Rust, Alistair G -- Stein, Lincoln D -- Tuveson, David A -- Copeland, Neal G -- Musgrove, Elizabeth A -- Scarpa, Aldo -- Eshleman, James R -- Hudson, Thomas J -- Sutherland, Robert L -- Wheeler, David A -- Pearson, John V -- McPherson, John D -- Gibbs, Richard A -- Grimmond, Sean M -- 13031/Cancer Research UK/United Kingdom -- 2P50CA101955/CA/NCI NIH HHS/ -- P01CA134292/CA/NCI NIH HHS/ -- P50 CA101955/CA/NCI NIH HHS/ -- P50 CA102701/CA/NCI NIH HHS/ -- P50CA062924/CA/NCI NIH HHS/ -- R01 CA097075/CA/NCI NIH HHS/ -- R01 CA97075/CA/NCI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Cancer Research UK/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2012 Nov 15;491(7424):399-405. doi: 10.1038/nature11547. Epub 2012 Oct 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, Sydney, New South Wales 2010, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23103869" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Axons/*metabolism ; Carcinoma, Pancreatic Ductal/*genetics/*pathology ; Gene Dosage ; Gene Expression Regulation, Neoplastic ; Genome/*genetics ; Humans ; Kaplan-Meier Estimate ; Mice ; Mutation ; Pancreatic Neoplasms/*genetics/*pathology ; Proteins/genetics ; Signal Transduction
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    Enhancement of Mixing and Reaction in High-speed Combustor Flowfields (1997)
    In:  CASI
    Details
    Publication Date: 2019-07-13
    Description: Research has been underway for a number of years, both in the United States and abroad, to develop advanced aerospace propulsion systems for use late in this century and beyond. One program is now underway at the NASA Langley Research Research has been underway for a number of years, both in the United States and abroad, to develop advanced aerospace propulsion systems for use late in this century and beyond. One program is now underway at the NASA Langley Research Center to develop a hydrogen-fueled supersonic combustion ramjet (scramjet) that is capable of propelling a vehicle at hypersonic speeds in the atmosphere. A part of that research has been directed toward the optimization of the scramjet combustor and, in particular, the efficiency of fuel-air mixing and reaction taking place in the engine. In the high-speed vehicle configurations currently being considered, achieving a high combustor efficiency becomes particularly difficult. With increasing combustor Mach number, the degree of fuel-air mixing that can be achieved through natural convective and diffusive processes is reduced leading to an overall decrease in combustion efficiency and thrust. Compressible shear layers and jets provide a good model for studying the physical processes occurring in high speed mixing and combustion in a scramjet. Mixing layers are characterized by large scale eddies that form due to the high shear that is present between the fuel and the air streams. These eddies entrain the fuel and air into the mixing region between the fluids leading to increased surface area and locally steep concentration gradients. Molecular diffusion then occurs across the strained interfaces. In an early study of high-speed mixing, Brown and Roshko show that the spreading rate of a supersonic mixing layer decreases with increasing Mach number, exhibiting a factor of three decrease in spread rate as compared with an incompressible mixing layer with the same density ratio. They conclude that the reduced spread rate is primarily due to compressibility. Papamoschou and Roshko also observe that the spreading rate of compressible mixing layers is significantly reduced over that of incompressible layers. To characterize the structure of the flow quantitatively, they define a convective Mach number. The reduction in mixing layer spreading rate is shown in these experiments to correlate well with increasing convective Mach number.
    Keywords: Aircraft Propulsion and Power
    Type: International Colloquium on Advanced Computation and Analysis of Combustion; May 12, 1997 - May 15, 1997; Moscow; Russia
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  • 6
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    Thrust Enhancement in Hypervelocity Nozzles by Chemical Catalysis (1997)
    In:  CASI
    Details
    Publication Date: 2019-07-13
    Description: In the hypersonic flight regime, the air-breathing supersonic combustion ramjet (scramjet) has been shown to be a viable propulsion system. The current designs of scramjet engines provide performance benefits only up to a Mach number of 14. Performance losses increase rapidly as the Mach number increases. To extend the applicability of scram'jets beyond Mach 14, research is being conducted in the area of inlet and wave drag reduction, skin-friction and heat-transfer reduction, nozzle loss minimization, low-loss mixing, and combustion enhancement. For high Mach number applications, hydrogen is the obvious fuel choice because of its high energy content per unit mass in comparison with conventional fuels. These flight conditions require engines to operate at supersonic internal velocities, high combustor temperatures, and low static pressures. The high static temperature condition enhances the production of radicals such as H and OH, and the low-pressure condition slows the reaction rates, particularly the recombination reactions. High-temperature and low-pressure constraints, in combination with a small residence time, result in a radical-rich exhaust gas mixture exiting the combustor. At high Mach number conditions (due to low residence time), H and OH do not have enough time to recombine ; thus, a significant amount of energy is lost as these high-energy free radical are exhausted. The objective of the present study is to conduct a flowfield analysis for a typical nozzle geometry for NASP-type vehicle to assess for thrust enhancement in hypervelocity nozzles by substituting small amount of phosphine for hydrogen.
    Keywords: Aircraft Propulsion and Power
    Type: NASA/TM-1997-208084 , NAS 1.15:208084 , Journal of Propulsion and Power; 13; 4; 574-576
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  • 7
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    Filtered Mass Density Function for Design Simulation of High Speed Airbreathing Propulsion Systems (2002)
    In:  CASI
    Details
    Publication Date: 2019-07-13
    Description: The objective of this research is to develop and implement a new methodology for large eddy simulation of (LES) of high-speed reacting turbulent flows. We have just completed 2 1/2 years of Phase I of this research. The work within the past six months was concentrated on the following two subjects: (1) Development of the joint velocity-scalar filtered density function (VSFDF) scheme for LES. (2) Implementation of our previously developed scalar filtered density function (SFDF) for flame simulations.
    Keywords: Aircraft Propulsion and Power
    Format: text
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  • 8
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    Research in Hypersonic Airbreathing Propulsion at the NASA Langley Research Center (2001)
    In:  CASI
    Details
    Publication Date: 2019-07-13
    Description: The NASA Langley Research Center has been conducting research for over four decades to develop technology for an airbreathing-propelled vehicle. Several other organizations within the United States have also been involved in this endeavor. Even though significant progress has been made over this period, a hypersonic airbreathing vehicle has not yet been realized due to low technology maturity. One of the major reasons for the slow progress in technology development has been the low level and cyclic nature of funding. The paper provides a brief historical overview of research in hypersonic airbreathing technology and then discusses current efforts at NASA Langley to develop various analytical, computational, and experimental design tools and their application in the development of future hypersonic airbreathing vehicles. The main focus of this paper is on the hypersonic airbreathing propulsion technology.
    Keywords: Aircraft Propulsion and Power
    Type: ISABE-2001-4 , Fifteenth International Symposium on Airbreathing Engines; Sep 02, 2001 - Sep 07, 2001; Bangalore; India
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  • 9
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    Predicting the Effects of Test Media in Ground-Based Propulsion Testing (2006)
    In:  CASI
    Details
    Publication Date: 2019-07-13
    Description: This paper discusses the progress of work which began in mid-2004 sponsored by the Office of the Secretary of Defense (OSD) Test & Evaluation/Science & Technology (T&E/S&T) Program. The purpose of the work is to improve the state of the art of CFD capabilities for predicting the effects of the test media on the flameholding characteristics in scramjet engines. The program has several components including the development of advance algorithms and models for simulating engine flowpaths as well as a fundamental experimental and diagnostic development effort to support the formulation and validation of the mathematical models. The paper will provide details of current work involving the development of phenomenological models for Reynolds averaged Navier-Stokes codes, large-eddy simulation techniques and reduced-kinetics models. Experiments that will provide data for the modeling efforts will also be described, along with with the associated nonintrusive diagnostics used to collect the data.
    Keywords: Aircraft Propulsion and Power
    Type: 2006 Annual ITEA Technology Review; Aug 07, 2006 - Aug 10, 2006; Cambridge, MA; United States
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  • 10
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    Supersonic Combustion Research at NASA (2007)
    In:  CASI
    Details
    Publication Date: 2019-07-13
    Description: This paper discusses the progress of work to model high-speed supersonic reacting flow. The purpose of the work is to improve the state of the art of CFD capabilities for predicting the flow in high-speed propulsion systems, particularly combustor flowpaths. The program has several components including the development of advanced algorithms and models for simulating engine flowpaths as well as a fundamental experimental and diagnostic development effort to support the formulation and validation of the mathematical models. The paper will provide details of current work on experiments that will provide data for the modeling efforts along with the associated nonintrusive diagnostics used to collect the data from the experimental flowfield. Simulation of a recent experiment to partially validate the accuracy of a combustion code is also described.
    Keywords: Aircraft Propulsion and Power
    Type: 2007 Fall Technical Meeting - Eastern States Section of the Combustion Institute; Oct 21, 2007 - Oct 24, 2007; Charlotesville, VA; United States
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