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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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    A Resonant Pulse Detonation Actuator for High-Speed Boundary Layer Separation Control (2004)
    In:  CASI
    Details
    Publication Date: 2019-07-13
    Description: A variety of different types of actuators have been previously investigated as flow control devices. Potential applications include the control of boundary layer separation in external flows, as well as jet engine inlet and diffuser flow control. The operating principles for such devices are typically based on either mechanical deflection of control surfaces (which include MEMS flap devices), mass injection (which includes combustion driven jet actuators), or through the use of synthetic jets (diaphragm devices which produce a pulsating jet with no net mass flow). This paper introduces some of the initial flow visualization work related to the development of a relatively new type of combustion-driven jet actuator that has been proposed based on a pulse detonation principle. The device is designed to utilize localized detonation of a premixed fuel (Hydrogen)-air mixture to periodically inject a jet of gas transversely into the primary flow. Initial testing with airflow successfully demonstrated resonant conditions within the range of acoustic frequencies expected for the design. Schlieren visualization of the pulsating air jet structure revealed axially symmetric vortex flow, along with the formation of shocks. Flow visualization of the first successful sustained oscillation condition is also demonstrated for one configuration of the current test section. Future testing will explore in more detail the onset of resonant combustion and the approach to conditions of sustained resonant detonation.
    Keywords: Fluid Mechanics and Thermodynamics
    Type: 2004-11ISV-BTB , 11th International Symposium on Flow Visualization; Aug 09, 2004 - Aug 12, 2004; Notre Dame, IN; United States
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  • 6
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    CFD Analysis of Mixing Characteristics of Several Fuel Injectors at Hypervelocity Flow Conditions (2016)
    In:  CASI
    Details
    Publication Date: 2019-07-13
    Description: CFD analysis is presented of the mixing characteristics and performance of three fuel injectors at hypervelocity flow conditions. The calculations were carried out using the VULCAN-CFD solver and Reynolds-Averaged Simulations (RAS). The high Mach number flow conditions match those proposed for the planned experiments conducted as a part of the Enhanced Injection and Mixing Project (EIMP) at the NASA Langley Research Center. The EIMP aims to investigate scramjet fuel injection and mixing physics, improve the understanding of underlying physical processes, and develop enhancement strategies and functional relationships relevant to flight Mach numbers greater than eight. Because of the high Mach number flow considered, the injectors consist of a fuel placement device, a strut; and a fluidic vortical mixer, a ramp. These devices accomplish the necessary task of distributing and mixing fuel into the supersonic cross-flow albeit via different strategies. Both of these devices were previously studied at lower flight Mach numbers where they exhibited promising performance in terms of mixing efficiency and total pressure recovery. For comparison, a flush-wall injector is also included. This type of injector generally represents the simplest method of introducing fuel into a scramjet combustor, however, at high flight Mach number conditions, the dynamic pressure needed to induce sufficient fuel penetration may be difficult to achieve along with other requirements such as achieving desired levels of fuel-to-air mixing at the required equivalence ratio. The three injectors represent the baseline configurations planned for the experiments. The current work discusses the mixing flow field behavior and differences among the three fuel injectors, mixing performance as described by the mixing efficiency and the total pressure recovery, and performance considerations based on the thrust potential.
    Keywords: Fluid Mechanics and Thermodynamics
    Type: NF1676L-23413 , AIAA Propulsion and Energy Forum and Exposition; Jul 25, 2016 - Jul 27, 2016; Salt Lake, UT; United States
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  • 7
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    Impact of Flight Enthalpy, Fuel Simulant, and Chemical Reactions on the Mixing Characteristics of Several Injectors at Hypervelocity Flow Conditions (2016)
    In:  CASI
    Details
    Publication Date: 2019-08-13
    Description: The high total temperatures or total enthalpies required to duplicate the high-speed flight conditions in ground experiments often place stringent requirements on the material selection and cooling needs for the test articles and intrusive flow diagnostic equipment. Furthermore, for internal flows, these conditions often complicate the use of nonintrusive diagnostics that need optical access to the test section and interior portions of the flowpath. Because of the technical challenges and increased costs associated with experimentation at high values of total enthalpy, an attempt is often made to reduce it. This is the case for the Enhanced Injection and Mixing Project (EIMP) currently underway in the Arc-Heated Scramjet Test Facility at the NASA Langley Research Center. The EIMP aims to investigate supersonic combustion ramjet (scramjet) fuel injection and mixing physics, improve the understanding of underlying physical processes, and develop enhancement strategies and functional relationships between mixing performance and losses relevant to flight Mach numbers greater than 8. The experiments will consider a "direct-connect" approach and utilize a Mach 6 nozzle to simulate the combustor entrance flow of a scramjet engine. However, while the value of the Mach number is matched to that expected at the combustor entrance in flight, the maximum value of the total enthalpy for these experiments is limited by the thermal-structural limits of the uncooled experimental hardware. Furthermore, the fuel simulant is helium, not hydrogen. The use of "cold" flows and non-reacting mixtures of fuel simulants for mixing experiments is not new and has been extensively utilized as a screening technique for scramjet fuel injectors. In this study, Reynolds-averaged simulations are utilized (RAS) to systematically verify the implicit assumptions used by the EIMP. This is accomplished by first performing RAS of mixing for two injector configurations at planned nominal experimental conditions. The mixing parameters of interest, such as mixing efficiency and total pressure recovery, are then computed and compared to the values obtained from RAS under the true enthalpy conditions and using helium and hydrogen. Finally, the impact of combustion on mixing, often deemed small enough to neglect at hypervelocity conditions, is assessed by comparing the results obtained from the hydrogen-fueled reacting and non-reacting RAS. For reacting flows, in addition to mixing efficiency and total pressure recovery, the combustion efficiency and thrust potential are also considered. In all of the simulations, the incoming air Mach number and the fuel-to-air ratio are the same, while the total pressure, total enthalpy, and the fuel simulant vary depending on the case considered. It is found that under some conditions the "cold" flow experiments are a good approximation of the flight.
    Keywords: Fluid Mechanics and Thermodynamics
    Type: NF1676L-23113 , JANNAF Propulsion Meeting (JPM); May 16, 2016 - May 20, 2016; Newport News, VA; United States
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  • 8
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    Development of a Pulsed Combustion Actuator For High-Speed Flow Control (2005)
    In:  CASI
    Details
    Publication Date: 2019-07-13
    Description: This paper describes the flow within a prototype actuator, energized by pulsed combustion or detonations, that provides a pulsed jet suitable for flow control in high-speed applications. A high-speed valve, capable of delivering a pulsed stream of reactants a mixture of H2 and air at rates of up to 1500 pulses per second, has been constructed. The reactants burn in a resonant chamber, and the products exit the device as a pulsed jet. High frequency pressure transducers have been used to monitor the pressure fluctuations in the device at various reactant injection frequencies, including both resonant and off-resonant conditions. The combustion chamber has been constructed with windows, and the flow inside it has been visualized using Planar Laser-Induced Fluorescence (PLIF). The pulsed jet at the exit of the device has been observed using schlieren.
    Keywords: Fluid Mechanics and Thermodynamics
    Type: AIAA Paper 2005-1084 , 43rd AIAA Aerospace Sciences Meeting and Exhibit; Jan 10, 2005 - Jan 13, 2005; Reno, NV; United States
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  • 9
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    Modeling Combustion in Supersonic Flows (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 flow-paths. 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 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: Fluid Mechanics and Thermodynamics
    Type: 3rd International Symposium on Non-Equilibrium Processes, Plasma, Combustion, and Atmospheric Phenomena (NEPCAP 2007); Jun 25, 2007 - Jun 29, 2007; Sochi; Russia
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  • 10
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    Toward a High-Frequency Pulsed-Detonation Actuator (2006)
    In:  CASI
    Details
    Publication Date: 2019-07-12
    Description: This paper describes the continued development of an actuator, energized by pulsed detonations, that provides a pulsed jet suitable for flow control in high-speed applications. A high-speed valve, capable of delivering a pulsed stream of reactants a mixture of H2 and air at rates of up to 1500 pulses per second, has been constructed. The reactants burn in a resonant tube and the products exit the tube as a pulsed jet. High frequency pressure transducers have been used to monitor the pressure fluctuations in the device at various reactant injection frequencies, including both resonant and off-resonant conditions. Pulsed detonations have been demonstrated in the lambda/4 mode of an 8 inch long tube at approx. 600 Hz. The pulsed jet at the exit of the device has been observed using shadowgraph and an infrared camera.
    Keywords: Fluid Mechanics and Thermodynamics
    Type: AIAA 2006-0555 , LAR-16967-1
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