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  • 1
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    Mapping the origins and expansion of the Indo-European language family (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-08-28
    Description: There are two competing hypotheses for the origin of the Indo-European language family. The conventional view places the homeland in the Pontic steppes about 6000 years ago. An alternative hypothesis claims that the languages spread from Anatolia with the expansion of farming 8000 to 9500 years ago. We used Bayesian phylogeographic approaches, together with basic vocabulary data from 103 ancient and contemporary Indo-European languages, to explicitly model the expansion of the family and test these hypotheses. We found decisive support for an Anatolian origin over a steppe origin. Both the inferred timing and root location of the Indo-European language trees fit with an agricultural expansion from Anatolia beginning 8000 to 9500 years ago. These results highlight the critical role that phylogeographic inference can play in resolving debates about human prehistory.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4112997/" 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/PMC4112997/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bouckaert, Remco -- Lemey, Philippe -- Dunn, Michael -- Greenhill, Simon J -- Alekseyenko, Alexander V -- Drummond, Alexei J -- Gray, Russell D -- Suchard, Marc A -- Atkinson, Quentin D -- 260864/European Research Council/International -- R01 GM086887/GM/NIGMS NIH HHS/ -- R01 HG006139/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2012 Aug 24;337(6097):957-60. doi: 10.1126/science.1219669.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Computer Science, University of Auckland, Auckland 1142, New Zealand.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22923579" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/history ; Bayes Theorem ; *Cultural Evolution ; History, Ancient ; Humans ; Language/*history ; Linguistics/history ; Phylogeography ; Turkey ; Vocabulary
    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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    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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  • 4
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    Language phylogenies reveal expansion pulses and pauses in Pacific settlement (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-01-24
    Description: Debates about human prehistory often center on the role that population expansions play in shaping biological and cultural diversity. Hypotheses on the origin of the Austronesian settlers of the Pacific are divided between a recent "pulse-pause" expansion from Taiwan and an older "slow-boat" diffusion from Wallacea. We used lexical data and Bayesian phylogenetic methods to construct a phylogeny of 400 languages. In agreement with the pulse-pause scenario, the language trees place the Austronesian origin in Taiwan approximately 5230 years ago and reveal a series of settlement pauses and expansion pulses linked to technological and social innovations. These results are robust to assumptions about the rooting and calibration of the trees and demonstrate the combined power of linguistic scholarship, database technologies, and computational phylogenetic methods for resolving questions about human prehistory.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gray, R D -- Drummond, A J -- Greenhill, S J -- New York, N.Y. -- Science. 2009 Jan 23;323(5913):479-83. doi: 10.1126/science.1166858.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Psychology, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19164742" target="_blank"〉PubMed〈/a〉
    Keywords: Bayes Theorem ; Databases, Factual ; *Emigration and Immigration/history ; History, Ancient ; Humans ; *Language ; Linguistics ; *Oceanic Ancestry Group/history ; Pacific Islands ; Philippines ; Phylogeny ; Polynesia ; Population Dynamics ; Taiwan ; Vocabulary
    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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  • 5
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    Mixing and mixing enhancement in supersonic reacting flowfields (1991)
    In:  Other Sources
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    Publication Date: 2011-08-24
    Description: Propulsion systems planned for use late in this century and beyond will require appropriate physical models for describing supersonic combustion and numerical techniques for solving the model governing equations. A computer program to study these flows is reported which considers the multicomponent diffusion and convection of important chemical species, the finite-rate reaction of these species, and the resulting interaction of the field mechanics and the chemistry. The application of the program to a spatially developing and reacting mixing layer, which serves an an excellent physical model for the mixing and reaction processes that take place in a scramjet combustor, is reported. Several techniques to enhance the fuel-air mixing and growth of that layer and improve its overall combustion efficiency are considered.
    Keywords: FLUID MECHANICS AND HEAT TRANSFER
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  • 6
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    A numerical model for supersonic reacting mixing layers (1987)
    In:  Other Sources
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    Publication Date: 2011-08-19
    Description: A current research effort is underway at the NASA Langley Research Center to achieve a detailed understanding of important phenomena present when a supersonic flow undergoes a chemical reaction. A computer program has been developed to study the details of such flows. The program has been constructed to consider the multicomponent diffusion and convection of important species, the finite-rate reaction of these species, and the resulting interaction between the fluid mechanics and chemistry. Code results from the analysis of a spatially developing and reacting mixing layer are presented, and conclusions are drawn regarding the structure of the evolving layer and its associated flame.
    Keywords: FLUID MECHANICS AND HEAT TRANSFER
    Type: Computer Methods in Applied Mechanics and Engineering (ISSN 0045-7825); 64; 39-60
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  • 7
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    Supersonic reacting internal flowfields (1991)
    In:  Other Sources
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    Publication Date: 2011-08-24
    Description: The national program to develop a trans-atmospheric vehicle has kindled a renewed interest in the modeling of supersonic reacting flows. A supersonic combustion ramjet, or scramjet, has been proposed to provide the propulsion system for this vehicle. The development of computational techniques for modeling supersonic reacting flowfields, and the application of these techniques to an increasingly difficult set of combustion problems are studied. Since the scramjet problem has been largely responsible for motivating this computational work, a brief history is given of hypersonic vehicles and their propulsion systems. A discussion is also given of some early modeling efforts applied to high speed reacting flows. Current activities to develop accurate and efficient algorithms and improved physical models for modeling supersonic combustion is then discussed. Some new problems where computer codes based on these algorithms and models are being applied are described.
    Keywords: FLUID MECHANICS AND HEAT TRANSFER
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  • 8
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    Investigation of radiative interactions in chemically reacting supersonic internal flows (1991)
    In:  Other Sources
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    Publication Date: 2019-06-28
    Description: Analyses and numerical procedures are presented to investigate the radiative interactions of absorbing-emitting species in chemically reacting supersonic flow in various ducts. Specific attention is directed in investigating the radiative contributions of H2O, OH, and NO under realistic physical and flow conditions. The radiative interactions in reacting flows are investigated by considering the supersonic flow of premixed hydrogen and air in a channel with a compression corner at the lower boundary. The results indicate that radiation can have significant influence on the flowfield and species production depending on the chemistry model employed.
    Keywords: FLUID MECHANICS AND HEAT TRANSFER
    Type: AIAA PAPER 91-0572
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  • 9
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    Modeling turbulent/chemistry interactions using assumed pdf methods (1992)
    In:  Other Sources
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    Publication Date: 2019-06-28
    Description: Two assumed probability density functions (pdfs) are employed for computing the effect of temperature fluctuations on chemical reaction. The pdfs assumed for this purpose are the Gaussian and the beta densities of the first kind. The pdfs are first used in a parametric study to determine the influence of temperature fluctuations on the mean reaction-rate coefficients. Results indicate that temperature fluctuations significantly affect the magnitude of the mean reaction-rate coefficients of some reactions depending on the mean temperature and the intensity of the fluctuations. The pdfs are then tested on a high-speed turbulent reacting mixing layer. Results clearly show a decrease in the ignition delay time due to increases in the magnitude of most of the mean reaction rate coefficients.
    Keywords: FLUID MECHANICS AND HEAT TRANSFER
    Type: AIAA PAPER 92-3638
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  • 10
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    Development of an algebraic turbulence model for analysis of propulsion flows (1992)
    In:  Other Sources
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    Publication Date: 2019-06-28
    Description: A simple turbulence model that will be applicable to propulsion flows having both wall bounded and unbounded regions was developed and installed within the PARC Navier-Stokes code by linking two existing algebraic turbulence models. The first is the Modified Mixing Length (MML) model which is optimized for wall bounded flows. The second is the Thomas model, the standard algebraic turbulence model in PARC which has been used to calculate both bounded and unbounded turbulent flows but was optimized for the latter. This paper discusses both models and the method employed to link them into one model (referred to as the MMLT model). The PARC code with the MMLT model was applied to two dimensional turbulent flows over a flat plate and over a backward facing step to validate and optimize the model and to compare its predictions to those obtained with the three turbulence models already available in PARC.
    Keywords: FLUID MECHANICS AND HEAT TRANSFER
    Type: AIAA PAPER 92-3861
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