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Sample records for washington university genome

  1. University of Washington

    Data.gov (United States)

    Federal Laboratory Consortium — The theme of the University of Washington based Center for Child Environmental Health Risks Research (CHC) is understanding the biochemical, molecular and exposure...

  2. University of Washington Center for Child Environmental Health Risks Research

    Data.gov (United States)

    Federal Laboratory Consortium — The theme of the University of Washington based Center for Child Environmental Health Risks Research (CHC) is understanding the biochemical, molecular and exposure...

  3. Washington State University Algae Biofuels Research

    Energy Technology Data Exchange (ETDEWEB)

    chen, Shulin [Washington State Univ., Pullman, WA (United States). Dept. of Biological Systems Engineering; McCormick, Margaret [Targeted Growth, Inc., Seattle, WA (United States); Sutterlin, Rusty [Inventure Renewables, Inc., Gig Harbor, WA (United States)

    2012-12-29

    The goal of this project was to advance algal technologies for the production of biofuels and biochemicals by establishing the Washington State Algae Alliance, a collaboration partnership among two private companies (Targeted Growth, Inc. (TGI), Inventure Chemicals (Inventure) Inc (now Inventure Renewables Inc) and Washington State University (WSU). This project included three major components. The first one was strain development at TGI by genetically engineering cyanobacteria to yield high levels of lipid and other specialty chemicals. The second component was developing an algal culture system at WSU to produce algal biomass as biofuel feedstock year-round in the northern states of the United States. This system included two cultivation modes, the first one was a phototrophic process and the second a heterotrophic process. The phototrophic process would be used for algae production in open ponds during warm seasons; the heterotrophic process would be used in cold seasons so that year-round production of algal lipid would be possible. In warm seasons the heterotrophic process would also produce algal seeds to be used in the phototrophic culture process. Selected strains of green algae and cyanobacteria developed by TGI were tested in the system. The third component was downstream algal biomass processing by Inventure that included efficiently harvesting the usable fuel fractions from the algae mass and effectively isolating and separating the usable components into specific fractions, and converting isolated fractions into green chemicals.

  4. 75 FR 52023 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2010-08-24

    ... DEPARTMENT OF THE INTERIOR National Park Service Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service... of the Thomas Burke Memorial Washington State Museum (Burke Museum), University of Washington...

  5. 75 FR 36672 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2010-06-28

    ... DEPARTMENT OF THE INTERIOR National Park Service Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service... of the Thomas Burke Memorial Washington State Museum (Burke Museum), University of Washington...

  6. Nonproliferation Education at the University of Washington

    International Nuclear Information System (INIS)

    Jones, Chris D.; Leek, K.M.

    2006-01-01

    The nonproliferation curriculum at the University of Washington (UW) is the product of collaboration between Pacific Northwest Center for Global Security (PNWCGS) at the Pacific Northwest National Laboratory (PNNL) and the Jackson School of International Studies (JSIS) and Department of Political Science at the University of Washington. This collaboration began in 2001 with the establishment the Institute for Global and Regional Security Studies (IGRSS). IGRSS is housed in the Jackson School, which will celebrate its centenary in 2008 as a center for the study of world regions. PNNL also engages in a number of collaborative relationships with UW units in the natural and applied sciences. The principal goal of IGRSS has been to develop courses that draw graduates and undergraduates into careers in the field of nonproliferation. Since offering its first courses in 2002, IGRSS has assisted a substantial number of UW graduate students in submitting successful applications for nonproliferation positions in U.S. government agencies, including the Nonproliferation Graduate Program at the National Nuclear Security Administration. Since 2001, several UW undergraduates have begun careers in the field of nonproliferation, either by working at national laboratories or enrolling in non-UW graduate programs. The UW brought to its nonproliferation partnership with PNNL long-established programs in a wide range of professional programs and academic disciplines, including the 14 interdisciplinary regional and topical programs of the Jackson School of International Studies. The JSIS is an interdisciplinary and interdepartmental enterprise that brings together faculty and students from across the UW. Since the late 1940s the UW has trained experts for the nation's foreign policy community in programs focused in the languages, cultures, and histories of regions deemed critical to U.S. national security. However, since the termination of its program in nuclear engineering several

  7. 77 FR 11582 - Notice of Inventory Completion: Central Washington University Department of Anthropology...

    Science.gov (United States)

    2012-02-27

    ...: Central Washington University Department of Anthropology, Ellensburg, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Central Washington University Department of Anthropology has... Central Washington University Department of Anthropology. Repatriation of the human remains and associated...

  8. 77 FR 15802 - Notice of Inventory Completion: Central Washington University Department of Anthropology...

    Science.gov (United States)

    2012-03-16

    ...: Central Washington University Department of Anthropology, Ellensburg, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Central Washington University Department of Anthropology has... contact the Central Washington University Department of Anthropology. Repatriation of the human remains to...

  9. 75 FR 14462 - Notice of Inventory Completion: Central Washington University, Department of Anthropology...

    Science.gov (United States)

    2010-03-25

    ... Washington University, Department of Anthropology, Ellensburg, WA, and Thomas Burke Memorial Washington State... Washington University, Department of Anthropology, Ellensburg, WA, and the Thomas Burke Memorial Washington... Anthropology, Central Washington University, Ellensburg, WA 98926-7544, telephone (509) 963-2671 or Dr. Peter...

  10. 75 FR 14463 - Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA

    Science.gov (United States)

    2010-03-25

    ... Washington, Department of Anthropology, Seattle, WA AGENCY: National Park Service, Interior. ACTION: Notice... University of Washington, Department of Anthropology, Seattle, WA. The human remains were removed from... University of Washington, Department of Anthropology and Burke Museum staff in consultation with...

  11. History of Cardiothoracic Surgery at Washington University in Saint Louis.

    Science.gov (United States)

    Moon, Marc R

    2016-01-01

    The Division of Cardiothoracic Surgery at Washington University evolved a century ago to address what many considered to be the last surgical frontier, diseases of the chest. In addition, as one of the first training programs in thoracic surgery, Washington University has been responsible for educating more thoracic surgeons than nearly any other program in the world. Beginning with Evarts A. Graham and continuing through to Ralph J. Damiano Jr., the leaders of the division have had a profound impact on the field of cardiothoracic surgery. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Composition at Washington State University: Building a Multimodal Bricolage

    Science.gov (United States)

    Ericsson, Patricia; Hunter, Leeann Downing; Macklin, Tialitha Michelle; Edwards, Elizabeth Sue

    2016-01-01

    Multimodal pedagogy is increasingly accepted among composition scholars. However, putting such pedagogy into practice presents significant challenges. In this profile of Washington State University's first-year composition program, we suggest a multi-vocal and multi-theoretical approach to addressing the challenges of multimodal pedagogy. Patricia…

  13. Universal pacemaker of genome evolution.

    Science.gov (United States)

    Snir, Sagi; Wolf, Yuri I; Koonin, Eugene V

    2012-01-01

    A fundamental observation of comparative genomics is that the distribution of evolution rates across the complete sets of orthologous genes in pairs of related genomes remains virtually unchanged throughout the evolution of life, from bacteria to mammals. The most straightforward explanation for the conservation of this distribution appears to be that the relative evolution rates of all genes remain nearly constant, or in other words, that evolutionary rates of different genes are strongly correlated within each evolving genome. This correlation could be explained by a model that we denoted Universal PaceMaker (UPM) of genome evolution. The UPM model posits that the rate of evolution changes synchronously across genome-wide sets of genes in all evolving lineages. Alternatively, however, the correlation between the evolutionary rates of genes could be a simple consequence of molecular clock (MC). We sought to differentiate between the MC and UPM models by fitting thousands of phylogenetic trees for bacterial and archaeal genes to supertrees that reflect the dominant trend of vertical descent in the evolution of archaea and bacteria and that were constrained according to the two models. The goodness of fit for the UPM model was better than the fit for the MC model, with overwhelming statistical significance, although similarly to the MC, the UPM is strongly overdispersed. Thus, the results of this analysis reveal a universal, genome-wide pacemaker of evolution that could have been in operation throughout the history of life.

  14. 77 FR 51564 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2012-08-24

    ... Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Thomas Burke Memorial Washington... of human remains under the control of the Thomas Burke Memorial Washington State Museum (Burke Museum...

  15. 78 FR 59964 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2013-09-30

    ....S.C. 3003, of the completion of an inventory of human remains under the control of the Burke Museum....R50000] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of... Washington (Burke Museum), and Central Washington University have completed an inventory of human remains, in...

  16. 78 FR 64006 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2013-10-25

    ... inventory of human remains under the control of the Burke Museum. The human remains were removed from Island....R50000] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of... Memorial Washington State Museum, University of Washington (Burke Museum), has completed an inventory of...

  17. 78 FR 59955 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2013-09-30

    ... completion of an inventory of human remains under the control of the Burke Museum, Seattle, WA. The human....R50000] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of... Memorial Washington State Museum, University of Washington (Burke Museum), has completed an inventory of...

  18. 77 FR 51563 - Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA

    Science.gov (United States)

    2012-08-24

    ... Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA AGENCY: National... Anthropology, has completed an inventory of human remains and associated funerary objects, in consultation with... of Washington, Department of Anthropology. Disposition of the human remains and associated funerary...

  19. The FLIP fuel experience at Washington State University

    International Nuclear Information System (INIS)

    Lovas, Thomas A.

    1977-01-01

    The Washington State University TRIGA-fueled modified G.E. reactor was refueled with a partial TRIGA-FLIP core in February, 1976. The final core loading consisted of 35 FLIP and 75 Standard TRIGA fuel rods and provided a core excess reactivity of $7.98. The observed performance of the reactor did not deviate significantly from the design predictions and specifications. Pulsing tests revealed a maximum power output of 1850 MW with a fuel temperature of 449 deg. C from a $2.50 pulse. Slight power fluctuations at 1 Megawatt steady-state operation and post-pulse power oscillations were observed. (author)

  20. 76 FR 58033 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2011-09-19

    ... DEPARTMENT OF THE INTERIOR National Park Service [2253-665] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Thomas Burke Memorial Washington State Museum (Burke...

  1. 77 FR 46117 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2012-08-02

    ... DEPARTMENT OF THE INTERIOR National Park Service [NPS-WASO-NAGPRA-10823; 2200-1100-665] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Thomas Burke Memorial Washington...

  2. 78 FR 11675 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2013-02-19

    ... DEPARTMENT OF THE INTERIOR National Park Service [NPS-WASO-NAGPRA-12080;2200-1100-665] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Thomas Burke Memorial Washington...

  3. 75 FR 36671 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2010-06-28

    ... DEPARTMENT OF THE INTERIOR National Park Service Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA; Correction AGENCY: National Park... human remains and associated funerary objects in the possession of the Thomas Burke Memorial Washington...

  4. 76 FR 58034 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2011-09-19

    ... DEPARTMENT OF THE INTERIOR National Park Service [2253-665] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Thomas Burke Memorial Washington State Museum (Burke...

  5. 76 FR 58039 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2011-09-19

    ... DEPARTMENT OF THE INTERIOR National Park Service [2253-665] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Thomas Burke Memorial Washington State Museum (Burke...

  6. 76 FR 73664 - Notice of Inventory Completion: Washington State University, Museum of Anthropology, Pullman, WA

    Science.gov (United States)

    2011-11-29

    ...: Washington State University, Museum of Anthropology, Pullman, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Washington State University, Museum of Anthropology (WSU) has completed an... University, Museum of Anthropology, Pullman, WA 99164-4910, telephone (509) 335-4314. SUPPLEMENTARY...

  7. University of Washington, Nuclear Physics Laboratory annual report, 1995

    International Nuclear Information System (INIS)

    1995-04-01

    The Nuclear Physics Laboratory of the University of Washington supports a broad program of experimental physics research. The current program includes in-house research using the local tandem Van de Graff and superconducting linac accelerators and non-accelerator research in double beta decay and gravitation as well as user-mode research at large accelerator and reactor facilities around the world. This book is divided into the following areas: nuclear astrophysics; neutrino physics; nucleus-nucleus reactions; fundamental symmetries and weak interactions; accelerator mass spectrometry; atomic and molecular clusters; ultra-relativistic heavy ion collisions; external users; electronics, computing, and detector infrastructure; Van de Graff, superconducting booster and ion sources; nuclear physics laboratory personnel; degrees granted for 1994--1995; and list of publications from 1994--1995

  8. Nuclear Physics Laboratory, University of Washington annual report

    International Nuclear Information System (INIS)

    1998-04-01

    The Nuclear Physics Laboratory at the University of Washington in Seattle pursues a broad program of nuclear physics. These activities are conducted locally and at remote sites. The current programs include in-house research using the local tandem Van de Graaff and superconducting linac accelerators and non-accelerator research in solar neutrino physics at the Sudbury Neutrino Observatory in Canada and at SAGE in Russia, and gravitation as well as user-mode research at large accelerators and reactor facilities around the world. Summaries of the individual research projects are included. Areas of research covered are: fundamental symmetries, weak interactions and nuclear astrophysics; neutrino physics; nucleus-nucleus reactions; ultra-relativistic heavy ions; and atomic and molecular clusters

  9. The power professorship program at Washington State University

    International Nuclear Information System (INIS)

    Mosher, C.C.; Shamash, Y.

    1993-01-01

    As with most electric power programs, Washington State University's has existed since the beginning of the engineering program 100 years ago. It has grown and developed largely through the efforts of a few dedicated individuals. The Power Professorship Program has existed since 1972. The Power Professor has been Dr. Clifford C. Mosher until his recent semi-retirement. The Power Professorship was conceived of as an avenue for joint university-industry interaction. Considerable time and ingenuity by visionary engineers and others have resulted in development of a financial base for the Power Professorship Program. The program has been funded equally by public and investor-utility sectors. Following financial difficulties stemming from the Washington Public Power Supply System financial default on public utility bonds for several nuclear projects, funding for the program from the public sector was canceled. After several lean years, public-sector support was again restored by WSU's electrical engineering department offering a contract for services to the utilities in exchange for funding. This contract has been renewed annually, with costs and benefits firmly established through careful analysis and consultation. Problems facing the power industry in the early 1970s with regard to establishing a pipeline of future human resources, were almost identical with those of the present time: indifferent feelings about the industry in general, students being attracted to more glamorous disciplines, and a decline in educational opportunities available in the power area. A 1985 article in the IEEE Power Engineering Review describing today's declining enrollment in power engineering applies equally well to previous periods. A major driving force for initiating utility-industry participation in the Power Professorship Program was the concern for maintaining a source of entry-level engineers with a background in power engineering

  10. 78 FR 25471 - Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA

    Science.gov (United States)

    2013-05-01

    ....R50000] Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA..., Department of Anthropology, has completed an inventory of human remains and associated funerary objects, in... Burke Museum acting on behalf of the University of Washington, Department of Anthropology. Disposition...

  11. 78 FR 5200 - Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA

    Science.gov (United States)

    2013-01-24

    ... Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA AGENCY: National... Anthropology, has completed an inventory of human remains and associated funerary objects, in consultation with... acting on behalf of the University of Washington, Department of Anthropology. Disposition of the human...

  12. 78 FR 19297 - Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA

    Science.gov (United States)

    2013-03-29

    ...-PPWOCRADN0] Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA..., Department of Anthropology, has completed an inventory of human remains and associated funerary objects, in... Burke Museum acting on behalf of the University of Washington, Department of Anthropology. Disposition...

  13. 78 FR 22286 - Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA

    Science.gov (United States)

    2013-04-15

    ....R50000] Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA..., Department of Anthropology, has completed an inventory of human remains, in consultation with the appropriate... acting on behalf of the University of Washington, Department of Anthropology. If no additional requestors...

  14. 77 FR 74871 - Notice of Inventory Completion: The Museum of Anthropology at Washington State University...

    Science.gov (United States)

    2012-12-18

    ... Inventory Completion: The Museum of Anthropology at Washington State University, Pullman, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Museum of Anthropology has completed an... objects may contact the Museum of Anthropology at Washington State University. Repatriation of the human...

  15. 78 FR 2432 - Notice of Inventory Completion: The Museum of Anthropology at Washington State University...

    Science.gov (United States)

    2013-01-11

    ... Inventory Completion: The Museum of Anthropology at Washington State University, Pullman, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Museum of Anthropology has completed an... objects may contact the Museum of Anthropology at Washington State University. Repatriation of the human...

  16. 78 FR 59963 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2013-09-30

    ... DEPARTMENT OF THE INTERIOR National Park Service [NPS-WASO-NAGPRA-13770; PPWOCRADN0-PCU00RP14.R50000] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of..., Interior. ACTION: Notice. SUMMARY: The Thomas Burke Memorial Washington State Museum, University of...

  17. University of Washington Lab Report to SNEAP, 1999

    International Nuclear Information System (INIS)

    Amsbaugh, J.F.; Harper, G.C.; Linder, C.E.; Myers, A.W.; Storns, D.W.; Wechel, T.D. van; Will, D.I.

    2000-01-01

    OAK-B135 University of Washington Lab Report to SNEAP, 1999. The NPL tandem Van de Graaff accelerator chains ran 1869 hours between 9/1/98 and 8/31/99. The DEIS ran 356 hours and the SpIS ran 667. There were 28 experiment-days in which the LINAC and tandem were used together and seven days when the tandem was used, with one of the external ion sources, as a tandem. Four of these were with light ions and three with heavy ions. There were 68 days of Tandem Terminal Ion Source (TIS) development or repair, and 46 days of TIS installation or removal or changing TIS ion species. The TIS/tandem was used a total of 70 days to deliver p, d, 3 He, or 4 He beams for use by an experimenter. There were 47 experiment-days during which the injector deck was used to generate C 60 or LiF 3 clusters, which were then investigated without further acceleration. They had 25 tank openings over the year. There were three scheduled openings for the installation or removal of the TIS, and seven to change the TIS ion species. There were 10 openings for 4 He ion source and column resistor gradient development. There were four openings for various repairs other than ion source, and one to replace the LE grid, which was found undamaged after all

  18. 78 FR 19298 - Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA

    Science.gov (United States)

    2013-03-29

    ...-PPWOCRADN0] Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA..., Department of Anthropology, has completed an inventory of human remains, in consultation with the appropriate... Washington, Department of Anthropology. Disposition of the human remains to the Indian tribes stated below...

  19. 78 FR 5198 - Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA

    Science.gov (United States)

    2013-01-24

    ... Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA AGENCY: National... Anthropology, has completed an inventory of human remains and associated funerary objects, in consultation with... of Washington, Department of Anthropology. Disposition of the human remains to the Indian tribes...

  20. Collection Development Policy: Federal Government Publications at Eastern Washington University Libraries.

    Science.gov (United States)

    Roselle, Ann; Chan, Karen

    This collection development policy serves as a guide for the selection and retention of depository government documents by the Government Publications Unit of the Kennedy Memorial Library of Eastern Washington University (EWU) in Cheney, Washington. The library selects approximately 65 percent of the depository items distributed by the U.S.…

  1. 78 FR 45958 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2013-07-30

    ... DEPARTMENT OF THE INTERIOR National Park Service [NPS-WASO-NAGPRA-13406; PPWOCRADN0-PCU00RP14.R50000] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Thomas Burke...

  2. 78 FR 44595 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2013-07-24

    ... DEPARTMENT OF THE INTERIOR National Park Service [NPS-WASO-NAGPRA-13407; PPWOCRADN0-PCU00RP14.R50000] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Thomas Burke...

  3. Annual report of the Nuclear Physics Laboratory, University of Washington

    International Nuclear Information System (INIS)

    Snover, K.; Fulton, B.

    1996-04-01

    The Nuclear Physics Laboratory of the University of Washington has for over 40 years supported a broad program of experimental physics research. Some highlights of the research activities during the past year are given. Work continues at a rapid pace toward completion of the Sudbury Neutrino Observatory in January 1997. Following four years of planning and development, installation of the acrylic vessel began last July and is now 50% complete, with final completion scheduled for September. The Russian-American Gallium Experiment (SAGE) has completed a successful 51 Cr neutrino source experiment. The first data from 8 B decay have been taken in the Mass-8 CVC/Second Class Current study. The analysis of the measured barrier distributions for Ca-induced fission of prolate 192 Os and oblate 194 Pt has been completed. In a collaboration with a group from the Bhabha Atomic Research Centre they have shown that fission anisotropies at energies well above the barrier are not influenced by the mass asymmetry of the entrance channel relative to the Businaro-Gallone critical asymmetry. They also have preliminary evidence at higher bombarding energy that noncompound nucleus fission scales with the mean square angular momentum, in contrast to previous suggestions. The authors have measured proton and alpha particle emission spectra from the decay of A ∼ 200 compound nuclei at excitation energies of 50--100 MeV, and used these measurements to infer the nuclear temperature. The investigations of multiparticle Bose-Einstein interferometry have led to a new algorithm for putting Bose-Einstein and Coulomb correlations of up to 6th order into Monte Carlo simulations of ultra-relativistic collision events, and to a new fast algorithm for extracting event temperatures

  4. Sulfates, Clouds and Radiation Brazil (SCAR-B) University of Washington C131A Data

    Data.gov (United States)

    National Aeronautics and Space Administration — SCAR_B_UWC131A data are Smoke/Sulfates, Clouds and Radiation Experiment in Brazil data from instruments on board the University of Washington C131A aircraft in...

  5. Ethical issues in human genome epidemiology: a case study based on the Japanese American Family Study in Seattle, Washington.

    Science.gov (United States)

    Austin, Melissa A

    2002-04-01

    Recent completion of the draft sequence of the human genome has been greeted with both excitement and skepticism, and the potential of this accomplishment for advancing public health has been tempered by ethical concerns about the protection of human subjects. This commentary explores ethical issues arising in human genome epidemiology by using a case study approach based on the ongoing Japanese American Family Study at the University of Washington in Seattle (1994-2003). Ethical issues encountered in designing the study, collecting the data, and reporting the study results are considered. When developing studies, investigators must consider whether to restrict the study to specific racial or ethnic groups and whether community involvement is appropriate. Once the study design is in place, further ethical issues emerge, including obtaining informed consent for DNA banking and protecting the privacy and confidentiality of family members. Finally, investigators must carefully consider whether to report genotype results to study participants and whether pedigrees illustrating the results of the study will be published. Overall, the promise of genomics for improving public health must be pursued based on the fundamental ethical principles of respect for persons, beneficence, and justice.

  6. Total body composition measurements using in vivo neutron activation at the University of Washington

    International Nuclear Information System (INIS)

    Lewellen, T.L.

    1986-01-01

    The University of Washington Division of Nuclear Medicine has been using in vivo irradiation to study whole body calcium since 1969. Over 350 patients have been studied and currently five patients per week are being measured in support of research programs on bone wasting disease. (author)

  7. 78 FR 11673 - Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA

    Science.gov (United States)

    2013-02-19

    ... Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA AGENCY: National... Anthropology, has completed an inventory of human remains and associated funerary objects, in consultation with... Anthropology. Disposition of the human remains and associated funerary objects to the Indian tribes stated...

  8. 78 FR 5201 - Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA

    Science.gov (United States)

    2013-01-24

    ... Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA AGENCY: National... Anthropology, has completed an inventory of human remains, in consultation with the appropriate Indian tribes..., Department of Anthropology. Disposition of the human remains to the Indian tribes stated below may occur if...

  9. Sociology at Washington University in St. Louis: History and Reflections, 1906-1989.

    Science.gov (United States)

    Pittman, David J.; Boden, Deirdre

    1990-01-01

    Traces the history of sociology at Washington University (Missouri) from 1906 to 1989 in relation to the decision to abolish the department. Maintains that this decision began in 1968. Defines the contours of the sociology department, including a discussion of prominent scholars, contending that the decision will harm the discipline in the long…

  10. 76 FR 73663 - Notice of Intent To Repatriate Cultural Items: Washington State University, Museum of...

    Science.gov (United States)

    2011-11-29

    ... below by December 29, 2011. ADDRESSES: Mary Collins, Director, Washington State University, Museum of... ethnographic collection from the Conner Museum to the Museum of Anthropology. In June of 2011, the curator of collections at the Conner Museum found four unassociated funerary items in the museum storage area and...

  11. Now It's Necessary: Virtual Reference Services at Washington State University, Pullman

    Science.gov (United States)

    Nicol, Erica Carlson; Crook, Linda

    2013-01-01

    While virtual reference services (VRS) are becoming more and more common in academic libraries, implementing and maintaining well-used and effective VRS can be a challenge in the face of competing demands on time, staffing, and funding. Between 2011 and 2012, librarians at Washington State University, Pullman (WSU) have overhauled and reorganized…

  12. 78 FR 78379 - Notice of Inventory Completion: Museum of Anthropology at Washington State University, Pullman, WA

    Science.gov (United States)

    2013-12-26

    ....R50000] Notice of Inventory Completion: Museum of Anthropology at Washington State University, Pullman, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Museum of Anthropology at... Indian tribes or Native Hawaiian organizations, and has determined that there is a cultural affiliation...

  13. Sample preparation for accelerator mass spectrometry at the University of Washington

    International Nuclear Information System (INIS)

    Grootes, P.M.; Stuiver, M.; Farwell, G.W.; Schmidt, F.H.

    1981-01-01

    The adaptation of the University of Washington FN tandem Van de Graaff to accelerator mass spectrometry (AMS), as well as some of the results obtained, are described in another paper in this volume (Farwell et al., 1981). Here we discuss our experiences in preparing carbon and beryllium samples that give large and stable ion beams when used in our Extrion cesium sputter source with an inverted cesium beam geometry

  14. Tropospheric Aerosol Radiative Forcing Observational eXperiment - University of Washington instrumented C-131A aircraft Data Set

    Data.gov (United States)

    National Aeronautics and Space Administration — TARFOX_UWC131A is the Tropospheric Aerosol Radiative Forcing Observational eXperiment (TARFOX) - University of Washington instrumented C-131A aircraft data set. The...

  15. Radiochemistry Education at Washington State University: Sustaining Academic Radiochemistry for the Nation

    International Nuclear Information System (INIS)

    Clark, Sue B.; Nash, Ken; Benny, Paul; Clark, Aurora; Wall, Nathalie; Wall, Don; Yoo, Choong-Shik

    2009-01-01

    Since 2002, Washington State University has been building radiochemistry as a component of its overall chemistry program. Using an aggressive hiring strategy and leveraged funds from the state of Washington and federal agencies, six radiochemistry faculty members have been added to give a total of seven radiochemists out of a department of twenty-five faculty members. These faculty members contribute to a diverse curriculum in radiochemistry, and the Chemistry Department now enjoys a significant increase in the number of trainees, the quantity of research expenditures, and the volume and quality of peer-reviewed scientific literature generated by the radiochemistry faculty and the trainees. These three factors are essential for sustaining the radiochemistry education and research program at any academic institution.

  16. A universal genomic coordinate translator for comparative genomics.

    Science.gov (United States)

    Zamani, Neda; Sundström, Görel; Meadows, Jennifer R S; Höppner, Marc P; Dainat, Jacques; Lantz, Henrik; Haas, Brian J; Grabherr, Manfred G

    2014-06-30

    Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N. Here, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of expression levels across

  17. 78 FR 2429 - Notice of Inventory Completion: The Museum of Anthropology at Washington State University...

    Science.gov (United States)

    2013-01-11

    ... construction. Archaeologists working for the Washington Archaeological Research Center at Washington State... Reservation. Historical, ethnographic, linguistic, and archaeological information links the site to the...

  18. The University of Washington Mobile Planetarium: A Do-it-yourself Guide

    Science.gov (United States)

    Rosenfield, P.; Gaily, J.; Fraser, O.; Wisniewski, J.

    2014-07-01

    The University of Washington mobile planetarium project is a student-driven effort to bring astronomy to secondary schools, and the community, in Seattle, USA. This paper presents the solution that was designed and built in order to use the World- Wide Telescope — a computer program created by Microsoft that displays the astronomical sky as maps, the 3D Universe, and earth science data — from a laptop and an off-the-shelf high-definition (HD) projector located in an inflatable plane- tarium. In the first six months of operation, undergraduates at the University of Washington presented planetarium shows to over 1500 people, and 150 secondary school students created and presented their own astronomy projects in our dome, at their school. This paper aims to share the technical aspects of the project so that others can replicate the model or adapt it to their needs. This project was made possible thanks to a NASA/ESA Hubble Space Telescope education/public outreach grant.

  19. Epithermal neutron beam for BNCT research at the Washington State University TRIGA research reactor

    International Nuclear Information System (INIS)

    Nigg, D.W.; Venhuizen, J.R.; Wheeler, F.J.; Wemple, C.A.; Tripard, G.E.; Gavin, P.R.

    2000-01-01

    A new epithermal-neutron beam facility for BNCT (Boron Neutron Capture Therapy) research and boronated agent screening in animal models is in the final stages of construction at Washington State University (WSU). A key distinguishing feature of the design is the incorporation of a new, high-efficiency, neutron moderating and filtering material, Fluental, developed by the Technical Research Centre of Finland. An additional key feature is the provision for adjustable filter-moderator thickness to systematically explore the radiobiological consequences of increasing the fast-neutron contamination above the nominal value associated with the baseline system. (author)

  20. The Installation of a P.E.T. Pharmacy at Washington University

    International Nuclear Information System (INIS)

    Gaehle, G.; Schwarz, S.; Mueller, M.; Margenau, B.; Welch, M.J.

    2003-01-01

    Washington University has produced radioisotopes for medical application since the early 1960s. In order to serve seven PET scanners and to meet more stringent government regulations we have installed a new PET pharmacy based on our past years of experiences. The new pharmacy was installed at the site of the 3.7 MeV tandem cascade accelerator that was decommissioned in April of 2001. The pharmacy consists of a production lab, quality control lab, reagent preparation lab, shipping and storage area and an office. Security and safety was a main consideration in the design of this PET pharmacy

  1. Promoting academic excellence through leadership development at the University of Washington: the Teaching Scholars Program.

    Science.gov (United States)

    Robins, Lynne; Ambrozy, Donna; Pinsky, Linda E

    2006-11-01

    The University of Washington Teaching Scholars Program (TSP) was established in 1995 to prepare faculty for local and national leadership and promote academic excellence by fostering a community of educational leaders to innovate, enliven, and enrich the environment for teaching and learning at the University of Washington (UW). Faculty in the Department of Medical Education and Biomedical Informatics designed and continue to implement the program. Qualified individuals from the UW Health Sciences Professional Schools and foreign scholars who are studying at the UW are eligible to apply for acceptance into the program. To date, 109 faculty and fellows have participated in the program, the majority of whom have been physicians. The program is committed to interprofessional education and seeks to diversify its participants. The curriculum is developed collaboratively with each cohort and comprises topics central to medical education and an emergent set of topics related to the specific interests and teaching responsibilities of the participating scholars. Core sessions cover the history of health professions education, learning theories, educational research methods, assessment, curriculum development, instructional methods, professionalism, and leadership. To graduate, scholars must complete a scholarly project in curriculum development, faculty development, or educational research; demonstrate progress towards construction of a teaching portfolio; and participate regularly and actively in program sessions. The TSP has developed and nurtured an active cadre of supportive colleagues who are transforming educational practice, elevating the status of teaching, and increasing the recognition of teachers. Graduates fill key teaching and leadership positions at the UW and in national and international professional organizations.

  2. Development of the University of Washington Biofuels and Biobased Chemicals Process Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Gustafson, Richard [University of Washington

    2014-02-04

    The funding from this research grant enabled us to design and build a bioconversion steam explosion reactor and ancillary equipment such as a high pressure boiler and a fermenter to support the bioconversion process research. This equipment has been in constant use since its installation in 2012. Following are research projects that it has supported: • Investigation of novel chip production method in biofuels production • Investigation of biomass refining following steam explosion • Several studies on use of different biomass feedstocks • Investigation of biomass moisture content on pretreatment efficacy. • Development of novel instruments for biorefinery process control Having this equipment was also instrumental in the University of Washington receiving a $40 million grant from the US Department of Agriculture for biofuels development as well as several other smaller grants. The research that is being done with the equipment from this grant will facilitate the establishment of a biofuels industry in the Pacific Northwest and enable the University of Washington to launch a substantial biofuels and bio-based product research program.

  3. The pre-history of the University of Washington Astronomy Department: 1891-1965

    Science.gov (United States)

    Sullivan, Woodruff T.

    2015-01-01

    The University of Washington (UW) created its first Professor of Astronomy (within the Mathematics Department) in 1891, only two years after Washington itself became a state. Joseph Taylor bought a Warner & Swasey refractor with a 6-inch John Brashear lens, and installed it in a dome in 1895 when the university moved to a new campus outside of downtown Seattle. The small observatory became only the second building on the present campus, and is listed on the State Register of Historical Buildings. Over succeeding decades, Taylor was followed, amongst others, by Samuel Boothroyd (who after nine years left for Cornell in 1921) and for two years by Herman Zanstra (of "Zanstra method" fame). In 1928 Theodor Jacobsen joined the faculty after having obtained his Ph.D. at the University of California (Berkeley) and spending two years as a staff member at Lick Observatory. Jacobsen's research over the years focused on the spectra and motions of variable stars, especially of the Cepheid type. In the 1970s Jacobsen published a paper about secular changes in one particular Cepheid variable still using his own data extending as far back as the 1920s. For 42 years until his retirement, Jacobsen taught courses in astronomy (although there never was an astronomy major and only two graduate degrees were ever awarded), navigation, and a variety of mathematical topics. In the decade following Sputnik and the birth of NASA, UW astronomy ceased to be a one-man effort with the creation of a modern department, founding of a graduate program, and hiring of two new faculty members: George Wallerstein and Paul Hodge came from Berkeley in 1965 and are both still engaged in research 50 years later.

  4. Interview with David Tauben: University of Washington, Chief of the Division of Pain Medicine.

    Science.gov (United States)

    Tauben, David

    2017-07-01

    Dr Tauben is Clinical Professor jointly appointed in the Departments of Medicine and Anesthesia & Pain Medicine, and is the Hughes M & Katherine G Blake Endowed Professor, board certified in both Internal Medicine and Pain Medicine. He is also University of Washington (UW) Director of Medical Student and Resident Education in Pain Medicine, and Medical Director of UW TelePain, a tele-video-conferencing program intended to provide innovative pain education and consultative support to a five-state northwest regional primary care providers. He served as a member of the NIH National Pain Strategy task force on pain education and is principal investigator for the UW's prestigious NIH Pain Consortium Center of Excellence for Pain Education, leading curriculum development to extend the pain proficiency qualifications of interprofessional primary care providers. Dr Tauben is a member of the American Pain Society and the International Association for the Study of Pain special interest study groups on Pain Education. He is a founding member of the State of Washington Agency Medical Directors panel of medical experts developing opioid prescription guidelines for the state, and a regular clinical and content expert for regulatory and legislative bodies involved in public policy regarding pain medicine practice and standards. He speaks as a clinical expert in medical management of chronic pain, especially as it applies to primary care practices. Dr Tauben served as an expert for several US Centers for Disease Control clinical outreach programs and policy reviews advising primary care providers on how to prescribe opioids for chronic noncancer pain. He is annually recognized by his peers as recipient of regional awards in care of pain patients, and brings decades of clinical experience of best practice medication management of acute and chronic pain. Dr Tauben received his bachelors degree in philosophy from Yale University, medical degree from Tufts University School of

  5. Psychometric Properties of the Persian Version of the Padua Inventory: Washington State University Revision (PI-WSUR)

    OpenAIRE

    Shams, Giti; Kaviani, Hosein; Esmaili, Yaghob; Ebrahimkhani, Narges; Manesh, Alireza Amin

    2011-01-01

    Objective The psychometric properties and factor structure of the Persian Padua Inventory Washington State University Revision (PI-WSUR), a measure of obsessive- compulsive phenomena, was examined in a non-clinical sample of 348 Iranian university students. Method The PI-WSUR was translated into Persian, and its back translation was controlled by the author inventory. A pilot study based on cultural differences was carried out on twenty students. The study subjects consisted of 348 university...

  6. Outreach at Washington State University: a case study in costs and attendance

    Science.gov (United States)

    Bernhardt, Elizabeth A.; Bollen, Viktor; Bersano, Thomas M.; Mossman, Sean M.

    2016-09-01

    Making effective and efficient use of outreach resources can be difficult for student groups in smaller rural communities. Washington State University's OSA/SPIE student chapter desires well attended yet cost-effective ways to educate and inform the public. We designed outreach activities focused on three different funding levels: low upfront cost, moderate continuing costs, and high upfront cost with low continuing costs. By featuring our activities at well attended events, such as a pre-football game event, or by advertising a headlining activity, such as a laser maze, we take advantage of large crowds to create a relaxed learning atmosphere. Moreover, participants enjoy casual learning while waiting for a main event. Choosing a particular funding level and associating with well-attended events makes outreach easier. While there are still many challenges to outreach, such as motivating volunteers or designing outreach programs, we hope overcoming two large obstacles will lead to future outreach success.

  7. MRFM (Magnetic Resonance Force Microscopy) MURI ARO Final Report (Grant W911NF-05-1-0403, University of Washington)

    Science.gov (United States)

    2012-10-14

    University of Michigan; Ann Arbor, Michigan. • Faculty: 4 – Prof. John A. Sidles Department of Orthopaedics and Sports Medicine; University of Washington...electric field in the sample [17]; over a silicon sample the dissipation was shown to be proportional to the sample’s doping level [26]. 21 filename...nm thick film of perdeuterated polystyrene was doped with the free-radical TEMPAMINE at a concentration of 40 mM. An attonewton-sensitivity

  8. Structures of the major capsid proteins of the human Karolinska Institutet and Washington University polyomaviruses.

    Science.gov (United States)

    Neu, Ursula; Wang, Jianbo; Macejak, Dennis; Garcea, Robert L; Stehle, Thilo

    2011-07-01

    The Karolinska Institutet and Washington University polyomaviruses (KIPyV and WUPyV, respectively) are recently discovered human viruses that infect the respiratory tract. Although they have not yet been linked to disease, they are prevalent in populations worldwide, with initial infection occurring in early childhood. Polyomavirus capsids consist of 72 pentamers of the major capsid protein viral protein 1 (VP1), which determines antigenicity and receptor specificity. The WUPyV and KIPyV VP1 proteins are distant in evolution from VP1 proteins of known structure such as simian virus 40 or murine polyomavirus. We present here the crystal structures of unassembled recombinant WUPyV and KIPyV VP1 pentamers at resolutions of 2.9 and 2.55 Å, respectively. The WUPyV and KIPyV VP1 core structures fold into the same β-sandwich that is a hallmark of all polyomavirus VP1 proteins crystallized to date. However, differences in sequence translate into profoundly different surface loop structures in KIPyV and WUPyV VP1 proteins. Such loop structures have not been observed for other polyomaviruses, and they provide initial clues about the possible interactions of these viruses with cell surface receptors.

  9. The Impact of NSF-funded Physics Education Research at the University of Washington

    Science.gov (United States)

    Heron, Paula

    2015-03-01

    It is now well known that many students who complete introductory physics courses are unable to apply fundamental concepts in situations that involve qualitative reasoning. Systematic investigations have helped researchers understand why so many students fail to develop robust and coherent conceptual frameworks, and have led to the development of new teaching practices and materials that are far more effective than conventional ones. The Physics Education Group at the University of Washington has played a leading role in raising awareness of the need to improve instruction, and in supporting physics faculty in their efforts to do so. With support from the National Science Foundation, the group has helped build a research base that instructors can draw on, and has produced practical, flexible instructional materials that promote deeper learning in physics classrooms. Both ``Tutorials in Introductory Physics'' (Pearson, 2002) and ``Physics by Inquiry'' (Wiley, 1996) have been developed in an iterative process in which ongoing assessment of student learning plays an integral role. These materials have had a widespread and significant impact on physics teaching and on student learning from kindergarten through graduate school. In this talk I will describe the role of research in curriculum development, and speculate on the next generation of tools and resources to support physics teaching and learning.

  10. Migration to Alma/Primo: A Case Study of Central Washington University

    Directory of Open Access Journals (Sweden)

    Ping Fu

    2015-12-01

    Full Text Available This paper describes how Central Washington University Libraries (CWUL interacted and collaborated with the Orbis Cascade Alliance (OCA Shared Integrated Library System’s (SILS Implementation Team and Ex Libris to process systems and data migration from Innovative Interfaces Inc.’s Millennium integrated library system to Alma/Primo, Ex Libris’ next-generation library management solution and discovery and delivery solution. A chronological review method was used for this case study to provide an overall picture of key migration events, tasks, and implementation efforts, including pre-migration cleanup, migration forms, integration with external systems, testing, cutover, post-migration cleanup, and reporting and fixing outstanding issues. A three-phase migration model was studied, and a questionnaire was designed to collect data from functional leads to determine staff time spent on the migration tasks. Staff time spent on each phase was analyzed and quantitated, with some top essential elements for the success of the migration identified through the case review and data analysis. An analysis of the Ex Libris’ Salesforce cases created during the migration and post-migration was conducted to be used for identifying roles of key librarians and staff functional leads during the migration.

  11. Overcoming institutional challenges through continuous professionalism improvement: the University of Washington experience.

    Science.gov (United States)

    Fryer-Edwards, Kelly; Van Eaton, Erik; Goldstein, Erika A; Kimball, Harry R; Veith, Richard C; Pellegrini, Carlos A; Ramsey, Paul G

    2007-11-01

    The University of Washington (UW) School of Medicine is in the midst of an emerging ecology of professionalism. This initiative builds on prior work focusing on professionalism at the student level and moves toward the complete integration of a culture of professionalism within the UW medical community of including staff, faculty, residents, and students. The platform for initiating professionalism as institutional culture is the Committee on Continuous Professionalism Improvement, established in November 2006. This article reviews three approaches to organizational development used within and outside medicine and highlights features that are useful for enhancing an institutional culture of professionalism: organizational culture, safety culture, and appreciative inquiry. UW Medicine has defined professional development as a continuous process, built on concrete expectations, using mechanisms to facilitate learning from missteps and highlighting strengths. To this end, the school of medicine is working toward improvements in feedback, evaluation, and reward structures at all levels (student, resident, faculty, and staff) as well as creating opportunities for community dialogues on professionalism issues within the institution. Throughout all the Continuous Professionalism Improvement activities, a two-pronged approach to cultivating a culture of professionalism is taken: celebration of excellence and attention to accountability.

  12. Promoting fundamental clinical skills: a competency-based college approach at the University of Washington.

    Science.gov (United States)

    Goldstein, Erika A; Maclaren, Carol F; Smith, Sherilyn; Mengert, Terry J; Maestas, Ramoncita R; Foy, Hugh M; Wenrich, Marjorie D; Ramsey, Paul G

    2005-05-01

    The focus on fundamental clinical skills in undergraduate medical education has declined over the last several decades. Dramatic growth in the number of faculty involved in teaching and increasing clinical and research commitments have contributed to depersonalization and declining individual attention to students. In contrast to the close teaching and mentoring relationship between faculty and students 50 years ago, today's medical students may interact with hundreds of faculty members without the benefit of a focused program of teaching and evaluating clinical skills to form the core of their four-year curriculum. Bedside teaching has also declined, which may negatively affect clinical skills development. In response to these and other concerns, the University of Washington School of Medicine has created an integrated developmental curriculum that emphasizes bedside teaching and role modeling, focuses on enhancing fundamental clinical skills and professionalism, and implements these goals via a new administrative structure, the College system, which consists of a core of clinical teachers who spend substantial time teaching and mentoring medical students. Each medical student is assigned a faculty mentor within a College for the duration of his or her medical school career. Mentors continuously teach and reflect with students on clinical skills development and professionalism and, during the second year, work intensively with them at the bedside. They also provide an ongoing personal faculty contact. Competency domains and benchmarks define skill areas in which deepening, progressive attention is focused throughout medical school. This educational model places primary focus on the student.

  13. Exploratory Factor Analysis of NRG Oncology's University of Washington Quality of Life Questionnaire – RTOG Modification

    Science.gov (United States)

    Pugh, Stephanie L.; Wyatt, Gwen; Wong, Raimond K. W.; Sagar, Stephen M.; Yueh, Bevan; Singh, Anurag K.; Yao, Min; Nguyen-Tan, Phuc Felix; Yom, Sue S.; Cardinale, Francis S.; Sultanem, Khalil; Hodson, D. Ian; Krempl, Greg A.; Chavez, Ariel; Yeh, Alexander M.; Bruner, Deborah W.

    2016-01-01

    Context The 15-item University of Washington Quality of Life questionnaire – Radiation Therapy Oncology Group (RTOG) modification (UW-QOL-RTOG modification) has been used in several trials of head and neck cancer conducted by NRG Oncology such as RTOG 9709, RTOG 9901, RTOG 0244, and RTOG 0537. Objectives This study is an exploratory factor analysis (EFA) to establish validity and reliability of the instrument subscales. Methods EFA on the UW-QOL - RTOG modification was conducted using baseline data from NRG Oncology's RTOG 0537, a trial of acupuncture-like transcutaneous electrical nerve stimulation in treating radiation-induced xerostomia. Cronbach's α coefficient was calculated to measure reliability; correlation with the University of Michigan Xerostomia Related Quality of Life Scale (XeQOLS) was used to evaluate concurrent validity; and correlations between consecutive time points were used to assess test-retest reliability. Results The 15-item EFA of the modified tool resulted in 11 items split into 4 factors: mucus, eating, pain, and activities. Cronbach's α ranged from 0.71 to 0.93 for the factors and total score, consisting of all 11 items. There were strong correlations (ρ≥0.60) between consecutive time points and between total score and the XeQOLS total score (ρ>0.65). Conclusion The UW-QOL-RTOG modification is a valid tool that can be used to assess symptom burden of head and neck cancer patients receiving radiation therapy or those who have recently completed radiation. The modified tool has acceptable reliability, concurrent validity, and test-retest reliability in this patient population, as well as the advantage of having being shortened from 15 to 11 items. PMID:27899312

  14. Climate Change Education at the University of Washington: Bridging Academic Degrees, Departments and Disciplines

    Science.gov (United States)

    Thompson, L.; Bertram, M. A.

    2012-12-01

    Education on climate change occurs in many departments at large research universities, but providing a coordinated educational experience for students in this topic is challenging. Departmental boundaries, accounting for student credit hours, and curricula inertia create roadblocks to the creation of interdisciplinary curriculum for both graduate and undergraduate students. We describe a hierarchy of interdisciplinary programs that reach students from seniors in high school to graduate students, targeting students from a variety of disciplines. The UWHS (University of Washington in the High School) program allows high school teachers to be trained to teach UW courses to their own high school students at their own school. The students who enroll receive a UW grade and credit for the course (as well as high school credit). A UWHS course on Climate and Climate Change (Atmospheric Sciences 211) was created in 2011 supported by training to high school science teachers on the fundamentals of climate science. For the 2012-13 academic year we anticipate at least 5 schools in Washington State will be offering this course. Once students matriculate at UW, 211 serves as a prerequisite for the Climate Minor that began in 2011. The minor is hosted by the departments of Atmospheric Sciences, Earth and Space Sciences and Oceanography, offering instruction in three focus areas: climate chemistry and biology, the physical climate, and past climate and ice. Students also take an integrative seminar where they are required to communicate to both scientific and non-scientific audiences some topic in climate science. Students enrolled in graduate programs at UW can participate in the Graduate Certificate in Climate Science that began 2008. The certificate gives students instruction in climate science covering the same topic areas as the minor and with a capstone project where student communicate some aspect of climate science to a non-physical science audience. Projects have included

  15. A new era in science at Washington University, St. Louis: Viktor Hamburger's zoology department in the 1940's.

    Science.gov (United States)

    Carson, H L

    2001-04-01

    In the early 1940s, the administration of the College of Arts and Sciences at Washington University, St. Louis was firmly in the hands of classical scholars who were not inclined to promote the development of modern research on scientific subjects. Funds supporting research in biology favored the School of Medicine and the Missouri Botanical Garden. Viktor Hamburger arrived at Washington University in 1935. At about the time he became the Acting Chairman of Zoology in 1942, research work in the biological departments began a dramatic surge that has continued to this day. For 65 years under his counsel and leadership, basic biology has thrived at this fine institution. As an early faculty recruit, I recount here a few personal recollections from those formative years.

  16. The Zoology Department at Washington University (1944-1954): from undergraduate to graduate studies with Viktor Hamburger.

    Science.gov (United States)

    Dunnebacke, T H

    2001-04-01

    Beginning from an undergraduate's perspective and continuing through graduate school, this student's experiences in the Department of Zoology at Washington University in St. Louis, Missouri was a time of many rewarding experiences. Now, on this occasion of his 100th birthday, I wish to express my appreciation to the Chairman, Dr. Viktor Hamburger, for his teachings, his encouragement, and his friendship that has lasted over the past 56 years.

  17. 78 FR 59955 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2013-09-30

    ... responsibilities under NAGPRA, 25 U.S.C. 3003(d)(3). The determinations in this notice are the sole responsibility... Reservation, Washington) that this notice has been published. Dated: August 20, 2013. Sherry Hutt, Manager...

  18. University of Washington's radioecological studies in the Marshall Islands, 1946-1977.

    Science.gov (United States)

    Donaldson, L R; Seymour, A H; Nevissi, A E

    1997-07-01

    Since 1946, personnel from the School of Fisheries, University of Washington (Applied Fisheries Laboratory, 1943-1958; Laboratory of Radiation Biology, 1958-1967; and Laboratory of Radiation Ecology, since 1967), have studied the effects of nuclear detonations and the ensuing radioactivity on the marine and terrestrial environments throughout the Central Pacific. A collection of reports and publications about these activities plus a collection of several thousand samples from these periods are kept at the School of Fisheries. General findings from the surveys show that (1) fission products were prevalent in organisms of the terrestrial environment whereas activation products were prevalent in marine organisms; (2) the best biological indicators of fallout radionuclides by environments were (a) terrestrial-coconuts, land crabs; (b) reef-algae, invertebrates; and (c) marine-plankton, fish. Studies of plutonium and americium in Bikini Atoll showed that during 1971-1977 the highest concentrations of 241Am, 2.85 Bq g(-1) (77 pCi g(-1)) and 239,240Pu, 4.44 Bq g(-1) (120 pCi g(-1)), in surface sediments were found in the northwest part of the lagoon. The concentrations in the bomb craters were substantially lower than these values. Concentrations of soluble and particulate plutonium and americium in surface and deep water samples showed distributions similar to the sediment samples. That is, the highest concentration of these radionuclides in the water column were at locations with highest sediment concentration. Continuous circulation of water in the lagoon and exchange of water with open ocean resulted in removal of 111 G Bq y(-1) (3 Ci y(-1)) 241Am and 222 G Bq y(-1) (6 Ci y(-1)) 239,240Pu into the North Equatorial Current. A summary of the surveys, findings, and the historical role of the Laboratory in radioecological studies of the Marshall Islands are presented.

  19. University of Washington's eScience Institute Promotes New Training and Career Pathways in Data Science

    Science.gov (United States)

    Stone, S.; Parker, M. S.; Howe, B.; Lazowska, E.

    2015-12-01

    Rapid advances in technology are transforming nearly every field from "data-poor" to "data-rich." The ability to extract knowledge from this abundance of data is the cornerstone of 21st century discovery. At the University of Washington eScience Institute, our mission is to engage researchers across disciplines in developing and applying advanced computational methods and tools to real world problems in data-intensive discovery. Our research team consists of individuals with diverse backgrounds in domain sciences such as astronomy, oceanography and geology, with complementary expertise in advanced statistical and computational techniques such as data management, visualization, and machine learning. Two key elements are necessary to foster careers in data science: individuals with cross-disciplinary training in both method and domain sciences, and career paths emphasizing alternative metrics for advancement. We see persistent and deep-rooted challenges for the career paths of people whose skills, activities and work patterns don't fit neatly into the traditional roles and success metrics of academia. To address these challenges the eScience Institute has developed training programs and established new career opportunities for data-intensive research in academia. Our graduate students and post-docs have mentors in both a methodology and an application field. They also participate in coursework and tutorials to advance technical skill and foster community. Professional Data Scientist positions were created to support research independence while encouraging the development and adoption of domain-specific tools and techniques. The eScience Institute also supports the appointment of faculty who are innovators in developing and applying data science methodologies to advance their field of discovery. Our ultimate goal is to create a supportive environment for data science in academia and to establish global recognition for data-intensive discovery across all fields.

  20. Carotid Consensus Panel duplex criteria can replace modified University of Washington criteria without affecting accuracy.

    Science.gov (United States)

    Kim, Ann H; Augustin, Gener; Shevitz, Andrew; Kim, Hannah; Trivonovich, Michael R; Powell, Alexis R; Kumins, Norman; Tarr, Robert; Kashyap, Vikram S

    2018-04-01

    The decision to intervene for internal carotid stenosis often depends on the degree of stenosis seen on duplex ultrasound (US). The aim of this study is to compare the diagnostic accuracy of two criteria: modified University of Washington (UW) and 2003 Carotid Consensus Panel (CCP). All patients undergoing US in an accredited (IAC) vascular laboratory from January 2010 to June 2015 were reviewed ( n=18,772 US exams). Patients receiving a neck computed tomography angiography (CTA) within 6 months of the US were included in the study ( n=254). The degree of stenosis was determined by UW/CCP criteria and confirmed on CTA images using North American Symptomatic Carotid Endarterectomy Trial (NASCET)/European Carotid Surgery Trial (ECST) schema. Kappa analysis with 95% confidence intervals (CIs) were utilized to determine duplex-CTA agreement. A total of 417 carotid arteries from 221 patients were assessed in this study. The modified UW criteria accurately classified 266 (63.9%, kappa = 0.321, 95% CI 0.255 to 0.386) cases according to NASCET-derived measurements. The sensitivity, specificity, and accuracy at ≥ 60% stenosis were 65.7%, 81.3%, and 81.9%. The CCP criteria resulted in 296 (70.9%) accurate diagnoses (kappa = 0.359, 95% CI 0.280 to 0.437). At ≥ 70% stenosis, the sensitivity, specificity and accuracy were 38.8%, 91.6%, and 87.1% for NASCET. Comparison of the duplex results to ECST-derived CTA measurements revealed a similar trend (UW 53.1%, κ = 0.301 vs CCP 62.1%, κ = 0.315). The CCP criteria demonstrate a higher concordance rate with measurements taken from CTAs. The CCP criteria may be more sensitive in classifying clinically significant degrees of stenosis without a loss in diagnostic accuracy.

  1. Universal and idiosyncratic characteristic lengths in bacterial genomes

    Science.gov (United States)

    Junier, Ivan; Frémont, Paul; Rivoire, Olivier

    2018-05-01

    In condensed matter physics, simplified descriptions are obtained by coarse-graining the features of a system at a certain characteristic length, defined as the typical length beyond which some properties are no longer correlated. From a physics standpoint, in vitro DNA has thus a characteristic length of 300 base pairs (bp), the Kuhn length of the molecule beyond which correlations in its orientations are typically lost. From a biology standpoint, in vivo DNA has a characteristic length of 1000 bp, the typical length of genes. Since bacteria live in very different physico-chemical conditions and since their genomes lack translational invariance, whether larger, universal characteristic lengths exist is a non-trivial question. Here, we examine this problem by leveraging the large number of fully sequenced genomes available in public databases. By analyzing GC content correlations and the evolutionary conservation of gene contexts (synteny) in hundreds of bacterial chromosomes, we conclude that a fundamental characteristic length around 10–20 kb can be defined. This characteristic length reflects elementary structures involved in the coordination of gene expression, which are present all along the genome of nearly all bacteria. Technically, reaching this conclusion required us to implement methods that are insensitive to the presence of large idiosyncratic genomic features, which may co-exist along these fundamental universal structures.

  2. Program and curriculum development in radiochemistry at Washington State University to educate the next generation of radiochemists in the US

    International Nuclear Information System (INIS)

    Clark, S.B.; Nash, K.; Benny, P.; Elliston, J.; Buckely, P.

    2005-01-01

    Washington State University (WSU) has -been the recipient of grant funds from the U.S. Department of Energy's Office of Nuclear Science and Technology to enhance its curriculum and service activities in radiochemistry. These funds have been used to hire new faculty, redesign undergraduate and graduate courses in radiochemistry, and initiate summer programs in radiochemistry for regional college faculty and high school teachers. The funds received from the federal government were matched by investments from the state of Washington. These investments have resulted in many positive changes in the Chemistry Department and the Nuclear Radiation Center at WSU. The number of students graduating from our radiochemistry programs has increased markedly, and the level of additional extra mural funding for our programs has also increased. These activities will be described, and feedback from employers of our radiochemistry graduates will be provided. Plans for future radiochemistry program development will also be discussed.

  3. Safety evaluation report related to the renewal of the operating license for the Washington State University TRIGA reactor. Docket No. 50-27

    International Nuclear Information System (INIS)

    1982-05-01

    This Safety Evaluation Report for the application filed by the Washington State University (WSU) for a renewal of operating license number R-76 to continue to operate a research reactor has been prepared by the Office of Nuclear Reactor Regulation of the US Nuclear Regulatory Commission. The facility is owned and operated by the Washington State University and is located on the WSU campus in Pullman, Whitman County, Washington. The staff concludes that the TRIGA reactor facility can continue to be operated by WSU without endangering the health and safety of the public

  4. Perception of Natural Hazards and Risk among University of Washington Students

    Science.gov (United States)

    Herr, K.; Brand, B.; Hamlin, N.; Ou, J.; Thomas, B.; Tudor, E.

    2012-12-01

    Familiarity with a given population's perception of natural hazards and the threats they present is vital for the development of effective education prior to and emergency management response after a natural event. While much work has been done in other active tectonic regions, perception of natural hazards and risk among Pacific Northwest (PNW) residents is poorly constrained. The objective of this work is to assess the current perception of earthquake and volcanic hazards and risk in the PNW, and to better understand the factors which drive the public's behavior concerning preparedness and response. We developed a survey to assess the knowledge of natural hazards common to the region, their perception of risk concerning these hazards, and their level of preparedness should a natural hazard occur. The survey was distributed to University of Washington students and employees via an internet link as part of a class project in 'Living with Volcanoes' (ESS 106) in March of 2012, which returned more than 900 responses. The UW student population was chosen as our first "population" to assess because of their uniqueness as a large, semi-transient population (typical residence of less than 5 years). Only 50% of participants correctly reported their proximity to an active volcano, indicating either lack of knowledge of active volcanoes in the region or poor spatial awareness. When asked which area were most at risk to lahars, respondents indicated that all areas close to the hazard source, including topographically elevated regions, were at a higher risk than more distal and low-lying localities that are also at high risk, indicating a lack of knowledge concerning the topographic dependency of this hazard. Participants perceived themselves to be able to cope better with an earthquake than a volcanic event. This perception may be due to lack of knowledge of volcanic hazards and their extent or due to a false sense of security concerning earthquakes fostered by regular

  5. MCNP6 model of the University of Washington clinical neutron therapy system (CNTS).

    Science.gov (United States)

    Moffitt, Gregory B; Stewart, Robert D; Sandison, George A; Goorley, John T; Argento, David C; Jevremovic, Tatjana

    2016-01-21

    A MCNP6 dosimetry model is presented for the Clinical Neutron Therapy System (CNTS) at the University of Washington. In the CNTS, fast neutrons are generated by a 50.5 MeV proton beam incident on a 10.5 mm thick Be target. The production, scattering and absorption of neutrons, photons, and other particles are explicitly tracked throughout the key components of the CNTS, including the target, primary collimator, flattening filter, monitor unit ionization chamber, and multi-leaf collimator. Simulations of the open field tissue maximum ratio (TMR), percentage depth dose profiles, and lateral dose profiles in a 40 cm × 40 cm × 40 cm water phantom are in good agreement with ionization chamber measurements. For a nominal 10 × 10 field, the measured and calculated TMR values for depths of 1.5 cm, 5 cm, 10 cm, and 20 cm (compared to the dose at 1.7 cm) are within 0.22%, 2.23%, 4.30%, and 6.27%, respectively. For the three field sizes studied, 2.8 cm × 2.8 cm, 10.4 cm × 10.3 cm, and 28.8 cm × 28.8 cm, a gamma test comparing the measured and simulated percent depth dose curves have pass rates of 96.4%, 100.0%, and 78.6% (depth from 1.5 to 15 cm), respectively, using a 3% or 3 mm agreement criterion. At a representative depth of 10 cm, simulated lateral dose profiles have in-field (⩾ 10% of central axis dose) pass rates of 89.7% (2.8 cm × 2.8 cm), 89.6% (10.4 cm × 10.3 cm), and 100.0% (28.8 cm × 28.8 cm) using a 3% and 3 mm criterion. The MCNP6 model of the CNTS meets the minimum requirements for use as a quality assurance tool for treatment planning and provides useful insights and information to aid in the advancement of fast neutron therapy.

  6. Legume Genome Initiative at the University of Oklahoma

    Energy Technology Data Exchange (ETDEWEB)

    Bruce A. Roe

    2004-02-27

    Consolidated Appropriations Resolution, 2003 Conference Report for the Department of Energy's Biological and Environmental Research (BER) program provided $481,000 for the Legume Genome Initiative at the University of Oklahoma. These funds were used to support our research that is aimed at determining the entire sequence of the gene rich regions of the genome of the legume, Medicago truncatula, by allowing us to obtain a greater degree of finished BAC sequences from the draft sequences we have already obtained through research funded by the Noble Foundation. During the funding period we increased the number of Medicago truncatula BACs with finished (Bermuda standard) sequences from 109 to 359, and the total number of BACs for which we collected sequence data from 584 to 842, 359 of which reached phase 2 (ordered and oriented contigs). We also sequenced a series of pooled BAC clones that cover additional euchromatic (gene rich) genomic regions. This work resulted in 6 refereed publications, see below. Genes whose sequence was determined during this study included multiple members of the plant disease resistance (R-gene) family as well as several genes involved in flavinoid biosynthesis, nitrogen fixation and plant-microbial symbosis. This work also served as a prelude to obtaining NSF funding for the international collaborative effort to complete the entire sequence of the Medicago truncatula genomic euchromatic regions using a BAC based approach.

  7. Toward a Modern Science of Obesity at Washington University: How We Do It and What is the Payoff?

    Science.gov (United States)

    Colditz, Graham A; Gehlert, Sarah; Bowen, Deborah J; Carson, Kenneth; Hovmand, Peter S; Lee, Jung Ae; Moley, Kelle H

    2016-07-01

    In our Cancer Prevention Program at Washington University in Saint Louis (WUSTL), we have made extraordinary efforts to create the kind of cancer prevention and control program that is both translational and transdisciplinary in nature, to accelerate the march from basic discoveries to population change. Here we present an overview of our obesity-related research currently ongoing in our Center, paying particular attention to both the translational- transdisciplinary process and to community-based participatory research. We end with our future directions for improving obesity-related cancer outcomes research. Cancer Prev Res; 9(7); 503-8. ©2016 AACR. ©2016 American Association for Cancer Research.

  8. Training the teachers. The clinician-educator track of the University of Washington Pulmonary and Critical Care Medicine Fellowship Program.

    Science.gov (United States)

    Adamson, Rosemary; Goodman, Richard B; Kritek, Patricia; Luks, Andrew M; Tonelli, Mark R; Benditt, Joshua

    2015-04-01

    The University of Washington was the first pulmonary and critical care medicine fellowship training program accredited by the Accreditation Council for Graduate Medical Education to create a dedicated clinician-educator fellowship track that has its own National Residency Matching Program number. This track was created in response to increasing demand for focused training in medical education in pulmonary and critical care. Through the Veterans Health Administration we obtained a stipend for a clinician-educator fellow to dedicate 12 months to training in medical education. This takes place predominantly in the second year of fellowship and is composed of several core activities: fellows complete the University of Washington's Teaching Scholars Program, a professional development program designed to train leaders in medical education; they teach in a variety of settings and receive feedback on their work from clinician-educator faculty and the learners; and they engage in scholarly activity, which may take the form of scholarship of teaching, integration, or investigation. Fellows are guided throughout this process by a primary mentor and a mentoring committee. Since funding became available in 2009, two of the three graduates to date have successfully secured clinician-educator faculty positions. Graduates uniformly believe that the clinician-educator track met their training goals better than the research-based track would have.

  9. Going from Microbial Ecology to Genome Data and Back: Studies on a Haloalkaliphilic Bacterium Isolated from Soap Lake, Washington State

    Directory of Open Access Journals (Sweden)

    Melanie R. Mormile

    2014-11-01

    Full Text Available Soap Lake is a meromictic, alkaline (~pH 9.8 and saline (~14 to 140 g liter-1 lake located in the semiarid area of eastern Washington State. Of note is the length of time it has been meromictic (at least 2000 years and the extremely high sulfide level (~140 mM in its monimolimnion. As expected, the microbial ecology of this lake is greatly influenced by these conditions. A bacterium, Halanaerobium hydrogeniformans, was isolated from the mixolimnion region of this lake. H. hydrogeniformans is a haloalkaliphilic bacterium capable of forming hydrogen from 5- and 6-carbon sugars derived from hemicellulose and cellulose. Due to its ability to produce hydrogen under saline and alkaline conditions, in amounts that rival genetically modified organisms, its genome was sequenced. This sequence data provides an opportunity to explore the unique metabolic capabilities of this organism, including the mechanisms for tolerating the extreme conditions of both high salinity and alkalinity of its environment.

  10. Grassroots Engagement and the University of Washington: Evaluating Science Communication Training Created by Graduate Students for Graduate Students

    Science.gov (United States)

    Rohde, J. A.; Clarkson, M.; Houghton, J.; Chen, W.

    2016-12-01

    Science graduate students increasingly seek science communication training, yet many do not have easy access to training programs. Students often rely on a "do it yourself" approach to gaining communication skills, and student created science communication programs are increasingly found at universities and institutions across the U.S. In 2010, graduate students at the University of Washington led a grassroots effort to improve their own communication and outreach by creating "The Engage Program." With a focus on storytelling and public speaking, this graduate level course not only trains students in science communication but also gives them real world experience practicing that training at a public speaker series at Town Hall Seattle. The Engage Program was fortunate in that it was able to find institutional champions at University of Washington and secure funding to sustain the program over the long-term. However, many grassroots communication programs find it difficult to gain institutional support if there is a perceived lack of alignment with university priorities or lack of return on investment. In order to justify and incentivize institutional support for instruction in science communication, student leaders within the program initiated, designed and carried out an evaluation of their own program focused on assessing the impact of student communication, evaluating the effectiveness of the program in teaching communication skills, and quantifying the benefits of communication training to both the students and their institution. Project leaders created the opportunity for this evaluation by initiating a crowdfunding campaign, which has helped to further engage public support of science communication and incentivized student participation in the program, and may also inspire future program leaders to pursue similar program optimizations.

  11. Work-based learning experiences help students with disabilities transition to careers: a case study of University of Washington projects.

    Science.gov (United States)

    Bellman, Scott; Burgstahler, Sheryl; Ladner, Richard

    2014-01-01

    This case study describes evidence-based practices employed by a collection of University of Washington projects that engage high school and postsecondary students with disabilities in work-based learning experiences such as industry and research internships, career development activities, job shadows, field trips, and mock interviews. The purpose of the article is two-fold. First, authors share best practices with others who wish to increase the participation of students with disabilities in work-based learning and thereby contribute to their academic and career success. The article discusses methods used to recruit students, employers and mentors, match students with specific opportunities, and prepare students for success. Second, authors share outcomes from studies regarding participation in these work-based learning opportunities, which include increased employment success, motivation to work toward a career, knowledge about careers and the workplace, job-related skills, ability to work with supervisors and coworkers, skills in self-advocating for accommodations, and perceived career options.

  12. Development and design of a computer-assisted information management system for radiation safety management at the University of Washington

    International Nuclear Information System (INIS)

    Riches, C.G.; Riordan, F.J.; Robb, D.; Grieb, C.; Pence, G.; O'Brien, M.J.

    1984-01-01

    The Radiation Safety Office (RSO) at the University of Washington (UW) found that it needed a computerized information system to help manage the campus radiation safety program and to help provide the records necessary to show compliance with regulations and license requirements. The John L. Locke Computer Center at the UW had just developed the GLAMOR system to aid information entry and query for their computer when the RSO turned to them for assistance. The module that was developed provided a mechanism for controlling and monitoring radioactive materials on campus. This became one part of a multi-faceted system that registers users, employees, sealed sources and radiation-producing machines. The system is designed to be interactive, for immediate information recall, and powerful enough to provide routine and special reports on compliance status. The RSO information system is designed to be flexible and can easily incorporate additional features. Some future features include an interactive SNM control program, an interface to the information system currently being developed for the occupational safety and health program and an interface to the database provided by the commercial film badge service used by the University. Development of this program lead the RSO to appreciate the usefulness of having health physics professionals on the staff who were also knowledgeable about computers and who could develop programs and reports necessary to their activities

  13. 30 years of Physics Education Research at the University of Washington

    Science.gov (United States)

    Shaffer, Peter S.

    2017-01-01

    Over the past 30 years, members of the UW Physics Education Group have examined student learning in courses serving a wide range of populations. Most of the focus has been on elementary, middle, and high school teachers and students in introductory university physics courses, but more recently, the effort has expanded to include physics majors in upper-division courses on quantum mechanics and electrodynamics. In general, the group has taken a practical approach that focuses on identifying instructional strategies that are effective at promoting conceptual understanding and student reasoning ability. Examples will be drawn from across these courses to illustrate common themes and connections.

  14. Procurement of Human Tissues for Research Banking in the Surgical Pathology Laboratory: Prioritization Practices at Washington University Medical Center

    Science.gov (United States)

    Chernock, Rebecca D.; Leach, Tracey A.; Kahn, Ajaz A.; Yip, James H.; Rossi, Joan; Pfeifer, John D.

    2011-01-01

    Academic hospitals and medical schools with research tissue repositories often derive many of their internal human specimen acquisitions from their site's surgical pathology service. Typically, such acquisitions come from appropriately consented tissue discards sampled from surgical resections. Because the practice of surgical pathology has patient care as its primary mission, competing needs for tissue inevitably arise, with the requirement to preserve adequate tissue for clinical diagnosis being paramount. A set of best-practice gross pathology guidelines are summarized here, focused on the decision for tissue banking at the time specimens are macroscopically evaluated. These reflect our collective experience at Washington University School of Medicine, and are written from the point of view of our site biorepository. The involvement of trained pathology personnel in such procurements is very important. These guidelines reflect both good surgical pathology practice (including the pathologic features characteristic of various anatomic sites) and the typical objectives of research biorepositories. The guidelines should be helpful to tissue bank directors, and others charged with the procurement of tissues for general research purposes. We believe that appreciation of these principles will facilitate the partnership between surgical pathologists and biorepository directors, and promote both good patient care and strategic, value-added banking procurements. PMID:23386925

  15. Program in Functional Genomics of Autoimmunity and Immunology of yhe University of Kentucky and the University of Alabama

    Energy Technology Data Exchange (ETDEWEB)

    Alan M Kaplan

    2012-10-12

    This grant will be used to augment the equipment infrastructure and core support at the University of Kentucky and the University of Alabama particularly in the areas of genomics/informatics, molecular analysis and cell separation. In addition, we will promote collaborative research interactions through scientific workshops and exchange of scientists, as well as joint exploration of the role of immune receptors as targets in autoimmunity and host defense, innate and adaptive immune responses, and mucosal immunity in host defense.

  16. A universal, rapid, and inexpensive method for genomic DNA ...

    Indian Academy of Sciences (India)

    MOHAMMED BAQUR SAHIB A. AL-SHUHAIB

    gels, containing 7% glycerol, and 1×TBE buffer. The gels were run under 200 .... Inc. Germany, GeneaidTM DNA Isolation Kit, Geneaid. Biotech., New Taipei City, .... C. L. and Arsenos G. 2015 Comparison of eleven methods for genomic DNA ...

  17. A Universal Genome Array and Transcriptome Atlas for Brachypodium Distachyon

    Energy Technology Data Exchange (ETDEWEB)

    Mockler, Todd [Oregon State Univ., Corvallis, OR (United States)

    2017-04-17

    Brachypodium distachyon is the premier experimental model grass platform and is related to candidate feedstock crops for bioethanol production. Based on the DOE-JGI Brachypodium Bd21 genome sequence and annotation we designed a whole genome DNA microarray platform. The quality of this array platform is unprecedented due to the exceptional quality of the Brachypodium genome assembly and annotation and the stringent probe selection criteria employed in the design. We worked with members of the international community and the bioinformatics/design team at Affymetrix at all stages in the development of the array. We used the Brachypodium arrays to interrogate the transcriptomes of plants grown in a variety of environmental conditions including diurnal and circadian light/temperature conditions and under a variety of environmental conditions. We examined the transciptional responses of Brachypodium seedlings subjected to various abiotic stresses including heat, cold, salt, and high intensity light. We generated a gene expression atlas representing various organs and developmental stages. The results of these efforts including all microarray datasets are published and available at online public databases.

  18. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques.

    OpenAIRE

    Aljanabi, S M; Martinez, I

    1997-01-01

    A very simple, fast, universally applicable and reproducible method to extract high quality megabase genomic DNA from different organisms is described. We applied the same method to extract high quality complex genomic DNA from different tissues (wheat, barley, potato, beans, pear and almond leaves as well as fungi, insects and shrimps' fresh tissue) without any modification. The method does not require expensive and environmentally hazardous reagents and equipment. It can be performed even i...

  19. Global-Service Learning and Student-Athletes: A Model for Enhanced Academic Inclusion at the University of Washington.

    Science.gov (United States)

    Barker, Holly M

    The University of Washington (UW) continues to create opportunities to engage all students in transformational undergraduate educational opportunities, such as study abroad. This article describes specific efforts to increase inclusion for student-athletes in study abroad, particularly for first-generation students, including low-income students of color. Given the overrepresentation of students of color in sports vis-à-vis the larger student body at predominantly white institutions (PWIs), like UW, service-learning in communities beyond campus boundaries provides opportunities to apply international learning to a local context and to create a continuum of learning. By coupling educational theories from the classroom-particularly theories related to power and privilege-with community-based leadership in local communities, students are better prepared to actively engage in improving their own institutions. During the summers of 2013, 2014, and 2015, the author was the instructor for study abroad courses to French Polynesia with student-athletes. The courses were for 12 days (10 days on the ground and 2 days of flying), the maximum time that football players could be away from required summer workouts. This paper examines student evaluations from the French Polynesia trip in 2015. Student-athlete evaluations of a study abroad experience underscored: the transformative impact of study abroad to their academic, social, and athletic lives; the benefit of creating family-like relationships outside the confines of their sport; an appreciation for the many forms where indigenous knowledge resides, such as in navigation, dance, fishing, weaving, and cooking; intense feelings of culture shock upon return to the US, even when the trip is short in duration; a desire to engage with the diverse communities in Seattle beyond the scope of the program's structure, and; frustration, particularly for the male student-athletes, about the ways coaches, family, and friends wanted to

  20. Washington State Biofuels Industry Development

    Energy Technology Data Exchange (ETDEWEB)

    Gustafson, Richard [Univ. of Washington, Seattle, WA (United States)

    2017-04-09

    The funding from this research grant enabled us to design, renovate, and equip laboratories to support University of Washington biofuels research program. The research that is being done with the equipment from this grant will facilitate the establishment of a biofuels industry in the Pacific Northwest and enable the University of Washington to launch a substantial biofuels and bio-based product research program.

  1. Universal global imprints of genome growth and evolution--equivalent length and cumulative mutation density.

    Directory of Open Access Journals (Sweden)

    Hong-Da Chen

    Full Text Available BACKGROUND: Segmental duplication is widely held to be an important mode of genome growth and evolution. Yet how this would affect the global structure of genomes has been little discussed. METHODS/PRINCIPAL FINDINGS: Here, we show that equivalent length, or L(e, a quantity determined by the variance of fluctuating part of the distribution of the k-mer frequencies in a genome, characterizes the latter's global structure. We computed the L(es of 865 complete chromosomes and found that they have nearly universal but (k-dependent values. The differences among the L(e of a chromosome and those of its coding and non-coding parts were found to be slight. CONCLUSIONS: We verified that these non-trivial results are natural consequences of a genome growth model characterized by random segmental duplication and random point mutation, but not of any model whose dominant growth mechanism is not segmental duplication. Our study also indicates that genomes have a nearly universal cumulative "point" mutation density of about 0.73 mutations per site that is compatible with the relatively low mutation rates of (1-5 x 10(-3/site/Mya previously determined by sequence comparison for the human and E. coli genomes.

  2. An expanding universe of the non-coding genome in cancer biology.

    Science.gov (United States)

    Xue, Bin; He, Lin

    2014-06-01

    Neoplastic transformation is caused by accumulation of genetic and epigenetic alterations that ultimately convert normal cells into tumor cells with uncontrolled proliferation and survival, unlimited replicative potential and invasive growth [Hanahan,D. et al. (2011) Hallmarks of cancer: the next generation. Cell, 144, 646-674]. Although the majority of the cancer studies have focused on the functions of protein-coding genes, emerging evidence has started to reveal the importance of the vast non-coding genome, which constitutes more than 98% of the human genome. A number of non-coding RNAs (ncRNAs) derived from the 'dark matter' of the human genome exhibit cancer-specific differential expression and/or genomic alterations, and it is increasingly clear that ncRNAs, including small ncRNAs and long ncRNAs (lncRNAs), play an important role in cancer development by regulating protein-coding gene expression through diverse mechanisms. In addition to ncRNAs, nearly half of the mammalian genomes consist of transposable elements, particularly retrotransposons. Once depicted as selfish genomic parasites that propagate at the expense of host fitness, retrotransposon elements could also confer regulatory complexity to the host genomes during development and disease. Reactivation of retrotransposons in cancer, while capable of causing insertional mutagenesis and genome rearrangements to promote oncogenesis, could also alter host gene expression networks to favor tumor development. Taken together, the functional significance of non-coding genome in tumorigenesis has been previously underestimated, and diverse transcripts derived from the non-coding genome could act as integral functional components of the oncogene and tumor suppressor network. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  3. Universal features in the genome-level evolution of protein domains.

    Science.gov (United States)

    Cosentino Lagomarsino, Marco; Sellerio, Alessandro L; Heijning, Philip D; Bassetti, Bruno

    2009-01-01

    Protein domains can be used to study proteome evolution at a coarse scale. In particular, they are found on genomes with notable statistical distributions. It is known that the distribution of domains with a given topology follows a power law. We focus on a further aspect: these distributions, and the number of distinct topologies, follow collective trends, or scaling laws, depending on the total number of domains only, and not on genome-specific features. We present a stochastic duplication/innovation model, in the class of the so-called 'Chinese restaurant processes', that explains this observation with two universal parameters, representing a minimal number of domains and the relative weight of innovation to duplication. Furthermore, we study a model variant where new topologies are related to occurrence in genomic data, accounting for fold specificity. Both models have general quantitative agreement with data from hundreds of genomes, which indicates that the domains of a genome are built with a combination of specificity and robust self-organizing phenomena. The latter are related to the basic evolutionary 'moves' of duplication and innovation, and give rise to the observed scaling laws, a priori of the specific evolutionary history of a genome. We interpret this as the concurrent effect of neutral and selective drives, which increase duplication and decrease innovation in larger and more complex genomes. The validity of our model would imply that the empirical observation of a small number of folds in nature may be a consequence of their evolution.

  4. Genome-wide screen for universal individual identification SNPs based on the HapMap and 1000 Genomes databases.

    Science.gov (United States)

    Huang, Erwen; Liu, Changhui; Zheng, Jingjing; Han, Xiaolong; Du, Weian; Huang, Yuanjian; Li, Chengshi; Wang, Xiaoguang; Tong, Dayue; Ou, Xueling; Sun, Hongyu; Zeng, Zhaoshu; Liu, Chao

    2018-04-03

    Differences among SNP panels for individual identification in SNP-selecting and populations led to few common SNPs, compromising their universal applicability. To screen all universal SNPs, we performed a genome-wide SNP mining in multiple populations based on HapMap and 1000Genomes databases. SNPs with high minor allele frequencies (MAF) in 37 populations were selected. With MAF from ≥0.35 to ≥0.43, the number of selected SNPs decreased from 2769 to 0. A total of 117 SNPs with MAF ≥0.39 have no linkage disequilibrium with each other in every population. For 116 of the 117 SNPs, cumulative match probability (CMP) ranged from 2.01 × 10-48 to 1.93 × 10-50 and cumulative exclusion probability (CEP) ranged from 0.9999999996653 to 0.9999999999945. In 134 tested Han samples, 110 of the 117 SNPs remained within high MAF and conformed to Hardy-Weinberg equilibrium, with CMP = 4.70 × 10-47 and CEP = 0.999999999862. By analyzing the same number of autosomal SNPs as in the HID-Ion AmpliSeq Identity Panel, i.e. 90 randomized out of the 110 SNPs, our panel yielded preferable CMP and CEP. Taken together, the 110-SNPs panel is advantageous for forensic test, and this study provided plenty of highly informative SNPs for compiling final universal panels.

  5. Universal Internucleotide Statistics in Full Genomes: A Footprint of the DNA Structure and Packaging?

    OpenAIRE

    Bogachev, Mikhail I.; Kayumov, Airat R.; Bunde, Armin

    2014-01-01

    Uncovering the fundamental laws that govern the complex DNA structural organization remains challenging and is largely based upon reconstructions from the primary nucleotide sequences. Here we investigate the distributions of the internucleotide intervals and their persistence properties in complete genomes of various organisms from Archaea and Bacteria to H. Sapiens aiming to reveal the manifestation of the universal DNA architecture. We find that in all considered organisms the internucleot...

  6. [Overview of patents on targeted genome editing technologies and their implications for innovation and entrepreneurship education in universities].

    Science.gov (United States)

    Fan, Xiang-yu; Lin, Yan-ping; Liao, Guo-jian; Xie, Jian-ping

    2015-12-01

    Zinc finger nuclease, transcription activator-like effector nuclease, and clustered regularly interspaced short palindromic repeats/Cas9 nuclease are important targeted genome editing technologies. They have great significance in scientific research and applications on aspects of functional genomics research, species improvement, disease prevention and gene therapy. There are past or ongoing disputes over ownership of the intellectual property behind every technology. In this review, we summarize the patents on these three targeted genome editing technologies in order to provide some reference for developing genome editing technologies with self-owned intellectual property rights and some implications for current innovation and entrepreneurship education in universities.

  7. Universal internucleotide statistics in full genomes: a footprint of the DNA structure and packaging?

    Directory of Open Access Journals (Sweden)

    Mikhail I Bogachev

    Full Text Available Uncovering the fundamental laws that govern the complex DNA structural organization remains challenging and is largely based upon reconstructions from the primary nucleotide sequences. Here we investigate the distributions of the internucleotide intervals and their persistence properties in complete genomes of various organisms from Archaea and Bacteria to H. Sapiens aiming to reveal the manifestation of the universal DNA architecture. We find that in all considered organisms the internucleotide interval distributions exhibit the same [Formula: see text]-exponential form. While in prokaryotes a single [Formula: see text]-exponential function makes the best fit, in eukaryotes the PDF contains additionally a second [Formula: see text]-exponential, which in the human genome makes a perfect approximation over nearly 10 decades. We suggest that this functional form is a footprint of the heterogeneous DNA structure, where the first [Formula: see text]-exponential reflects the universal helical pitch that appears both in pro- and eukaryotic DNA, while the second [Formula: see text]-exponential is a specific marker of the large-scale eukaryotic DNA organization.

  8. Promoting Inclusivity in STEM through Active Recruiting and Mentoring: The Pre-Major in Astronomy Program (Pre-MAP) at the University of Washington

    Science.gov (United States)

    Schwieterman, Edward; Binder, Breanna A.; Pre-Major in Astronomy Program

    2016-01-01

    The Pre-Major in Astronomy Program (Pre-MAP) is a research and mentoring program for entering undergraduate students offered by the University of Washington Astronomy Department since 2005. The primary goal of Pre-MAP is to recruit and retain students from groups traditionally underrepresented in science, technology, engineering, and mathematics (STEM) through early exposure to guided research projects. The Pre-MAP seminar is the core component of the program and offers instruction in computing skills, data manipulation, science writing, statistical analysis, and scientific speaking and presentation skills. Students choose research projects proposed by faculty, post-docs and graduate students in areas related to astrophysics, planetary science, and astrobiology. Pre-MAP has been successful in retaining underrepresented students in STEM fields relative to the broader UW population, and we've found these students are more likely to graduate and excel academically than their peers. As of fall 2015, more than one hundred students have taken the Pre-MAP seminar, and both internal and external evaluations have shown that all groups of participating students report an increased interest in astronomy and science careers at the end of the seminar. This talk will provide an overview of the program and the structure of the core seminar. In particular, the talk will focus on additions and revisions to the seminar course over the last few years, such as the introduction of a public speaking coach, career and internship modules, and the formalization of external lab tours.

  9. Structural genomics: keeping up with expanding knowledge of the protein universe

    Science.gov (United States)

    Grabowski, Marek; Joachimiak, Andrzej; Otwinowski, Zbyszek; Minor, Wladek

    2010-01-01

    Structural characterization of the protein universe is the main mission of Structural Genomics (SG) programs. However, progress in gene sequencing technology, set in motion in the 1990s, has resulted in rapid expansion of protein sequence space — a twelvefold increase in the past seven years. For the SG field, this creates new challenges and necessitates a reassessment of its strategies. Nevertheless, despite the growth of sequence space, at present nearly half of the content of the Swiss-Prot database and over 40% of Pfam protein families can be structurally modeled based on structures determined so far, with SG projects making an increasingly significant contribution. The SG contribution of new Pfam structures nearly doubled from 27.2% in 2003 to 51.6% in 2006. PMID:17587562

  10. Structural genomics: keeping up with expanding knowledge of the protein universe.

    Science.gov (United States)

    Grabowski, Marek; Joachimiak, Andrzej; Otwinowski, Zbyszek; Minor, Wladek

    2007-06-01

    Structural characterization of the protein universe is the main mission of Structural Genomics (SG) programs. However, progress in gene sequencing technology, set in motion in the 1990s, has resulted in rapid expansion of protein sequence space--a twelvefold increase in the past seven years. For the SG field, this creates new challenges and necessitates a re-assessment of its strategies. Nevertheless, despite the growth of sequence space, at present nearly half of the content of the Swiss-Prot database and over 40% of Pfam protein families can be structurally modeled based on structures determined so far, with SG projects making an increasingly significant contribution. The SG contribution of new Pfam structures nearly doubled from 27.2% in 2003 to 51.6% in 2006.

  11. Xerostomia After Treatment for Oral and Oropharyngeal Cancer Using the University of Washington Saliva Domain and a Xerostomia-Related Quality-of-Life Scale

    International Nuclear Information System (INIS)

    Rogers, Simon N.; Johnson, Ian A.; Lowe, Derek

    2010-01-01

    Purpose: The first aim of this study was to identify which clinical factors are associated with xerostomia in patients after treatment for oral and oropharyngeal squamous cell carcinoma, using the Xerostomia-Related Quality-of-Life Scale (XeQoLS) and the University of Washington Quality-of-Life Questionnaire Version 4 dry mouth item (UW-QOL v4). The second aim was to compare these two questionnaires and postulate a cutoff in the UW-QOL below which patients are doing sufficient badly to warrant further evaluation and support. Methods and Materials: In all, 371 patients alive and disease free treated between 1992 and 2005 were sent the survey, of whom 250 (67%) responded. Various clinical factors correlated with xerostomia, particularly adjuvant radiotherapy and Pstage. Results: In logistic regression analyses to predict three or more problems on the XeQoLS, only adjuvant radiotherapy (p < 0.001) was significant at the 5% level. There were significant (p < 0.001) correlations between the XeQoLS scores (total average and domain) with all the UW-QOL domain scores, the strongest with swallowing (-0.69), taste (-0.64), chewing (-0.64), mood (-0.60), and saliva (-0.59) domains. Patients scoring <70 (i.e., 0 or 30) on the UW-QOL could be used as a screening cutoff because it formed 1 in 5 of all patients (49/242) but accounted for half (299/566) of the significant problems generated by the XeQoLS. This also identified 13/21 patients with 10 or more problems. Conclusion: The UW-QOL saliva domain seems to be a suitable means of screening for dry mouth in head-and-neck clinics and could be used to trigger interventions.

  12. Promoting Diversity in STEM through Active Recruiting and Mentoring: The Pre-Major in Astronomy Program (Pre-MAP) at the University of Washington

    Science.gov (United States)

    Schwieterman, Edward; Binder, Breanna; Tremmel, Michael; Garofali, Kristen; Agol, Eric; Meadows, Victoria

    2015-11-01

    The Pre-Major in Astronomy Program (Pre-MAP) is a research and mentoring program for underclassmen and transfer students offered by the University of Washington Astronomy Department since 2005. The primary goal of Pre-MAP is to recruit and retain students from groups traditionally underrepresented in science, technology, engineering, and mathematics (STEM) through early exposure to research. The Pre-MAP seminar is the core component of the program and offers instruction in computing skills, data manipulation, science writing, statistical analysis, and scientific speaking and presentation skills. Students choose research projects proposed by faculty, post-docs and graduate students in areas related to astrophysics, planetary science, and astrobiology. Pre-MAP has been successful in retaining underrepresented students in STEM fields relative to the broader UW population, and we've found these students are more likely to graduate and excel academically than their peers. As of spring 2015, more than one hundred students have taken the Pre-MAP seminar, and both internal and external evaluations have shown that all groups of participating students report an increased interest in astronomy and science careers at the end of the seminar. Several former Pre-MAP students have obtained or are pursuing doctoral and master’s degrees in STEM fields; many more work at NASA centers, teaching colleges, or as engineers or data analysts. Pre- MAP student research has produced dozens of publications in peer-reviewed research journals. This talk will provide an overview of the program: the structure of the seminar, examples of projects completed by students, cohort-building activities outside the seminar, funding sources, recruitment strategies, and the aggregate demographic and achievement data of our students. It is our hope that similar programs may be adopted successfully at other institutions.

  13. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  14. A universe of dwarfs and giants: genome size and chromosome evolution in the monocot family Melanthiaceae.

    Science.gov (United States)

    Pellicer, Jaume; Kelly, Laura J; Leitch, Ilia J; Zomlefer, Wendy B; Fay, Michael F

    2014-03-01

    • Since the occurrence of giant genomes in angiosperms is restricted to just a few lineages, identifying where shifts towards genome obesity have occurred is essential for understanding the evolutionary mechanisms triggering this process. • Genome sizes were assessed using flow cytometry in 79 species and new chromosome numbers were obtained. Phylogenetically based statistical methods were applied to infer ancestral character reconstructions of chromosome numbers and nuclear DNA contents. • Melanthiaceae are the most diverse family in terms of genome size, with C-values ranging more than 230-fold. Our data confirmed that giant genomes are restricted to tribe Parideae, with most extant species in the family characterized by small genomes. Ancestral genome size reconstruction revealed that the most recent common ancestor (MRCA) for the family had a relatively small genome (1C = 5.37 pg). Chromosome losses and polyploidy are recovered as the main evolutionary mechanisms generating chromosome number change. • Genome evolution in Melanthiaceae has been characterized by a trend towards genome size reduction, with just one episode of dramatic DNA accumulation in Parideae. Such extreme contrasting profiles of genome size evolution illustrate the key role of transposable elements and chromosome rearrangements in driving the evolution of plant genomes. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  15. Plasma Science and Innovation Center at Washington, Wisconsin, and Utah State: Final Scientific Report for the University of Wisconsin-Madison

    Energy Technology Data Exchange (ETDEWEB)

    Sovinec, Carl R. [Univ. of Wisconsin, Madison, WI (United States)

    2016-11-28

    The University of Wisconsin-Madison component of the Plasma Science and Innovation Center (PSI Center) contributed to modeling capabilities and algorithmic efficiency of the Non-Ideal Magnetohydrodynamics with Rotation (NIMROD) Code, which is widely used to model macroscopic dynamics of magnetically confined plasma. It also contributed to the understanding of direct-current (DC) injection of electrical current for initiating and sustaining plasma in three spherical torus experiments: the Helicity Injected Torus-II (HIT-II), the Pegasus Toroidal Experiment, and the National Spherical Torus Experiment (NSTX). The effort was funded through the PSI Center's cooperative agreement with the University of Washington and Utah State University over the period of March 1, 2005 - August 31, 2016. In addition to the computational and physics accomplishments, the Wisconsin effort contributed to the professional education of four graduate students and two postdoctoral research associates. The modeling for HIT-II and Pegasus was directly supported by the cooperative agreement, and contributions to the NSTX modeling were in support of work by Dr. Bickford Hooper, who was funded through a separate grant. Our primary contribution to model development is the implementation of detailed closure relations for collisional plasma. Postdoctoral associate Adam Bayliss implemented the temperature-dependent effects of Braginskii's parallel collisional ion viscosity. As a graduate student, John O'Bryan added runtime options for Braginskii's models and Ji's K2 models of thermal conduction with magnetization effects and thermal equilibration. As a postdoctoral associate, O'Bryan added the magnetization effects for ion viscosity. Another area of model development completed through the PSI-Center is the implementation of Chodura's phenomenological resistivity model. Finally, we investigated and tested linear electron parallel viscosity, leveraged by support from

  16. Modeling the Risk of Radiation-Induced Acute Esophagitis for Combined Washington University and RTOG Trial 93-11 Lung Cancer Patients

    International Nuclear Information System (INIS)

    Huang, Ellen X.; Bradley, Jeffrey D.; El Naqa, Issam; Hope, Andrew J.; Lindsay, Patricia E.; Bosch, Walter R.; Matthews, John W.; Sause, William T.; Graham, Mary V.; Deasy, Joseph O.

    2012-01-01

    Purpose: To construct a maximally predictive model of the risk of severe acute esophagitis (AE) for patients who receive definitive radiation therapy (RT) for non–small-cell lung cancer. Methods and Materials: The dataset includes Washington University and RTOG 93-11 clinical trial data (events/patients: 120/374, WUSTL = 101/237, RTOG9311 = 19/137). Statistical model building was performed based on dosimetric and clinical parameters (patient age, sex, weight loss, pretreatment chemotherapy, concurrent chemotherapy, fraction size). A wide range of dose–volume parameters were extracted from dearchived treatment plans, including Dx, Vx, MOHx (mean of hottest x% volume), MOCx (mean of coldest x% volume), and gEUD (generalized equivalent uniform dose) values. Results: The most significant single parameters for predicting acute esophagitis (RTOG Grade 2 or greater) were MOH85, mean esophagus dose (MED), and V30. A superior–inferior weighted dose-center position was derived but not found to be significant. Fraction size was found to be significant on univariate logistic analysis (Spearman R = 0.421, p < 0.00001) but not multivariate logistic modeling. Cross-validation model building was used to determine that an optimal model size needed only two parameters (MOH85 and concurrent chemotherapy, robustly selected on bootstrap model-rebuilding). Mean esophagus dose (MED) is preferred instead of MOH85, as it gives nearly the same statistical performance and is easier to compute. AE risk is given as a logistic function of (0.0688 ∗ MED+1.50 ∗ ConChemo-3.13), where MED is in Gy and ConChemo is either 1 (yes) if concurrent chemotherapy was given, or 0 (no). This model correlates to the observed risk of AE with a Spearman coefficient of 0.629 (p < 0.000001). Conclusions: Multivariate statistical model building with cross-validation suggests that a two-variable logistic model based on mean dose and the use of concurrent chemotherapy robustly predicts acute esophagitis

  17. Modeling the Risk of Radiation-Induced Acute Esophagitis for Combined Washington University and RTOG Trial 93-11 Lung Cancer Patients

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Ellen X.; Bradley, Jeffrey D.; El Naqa, Issam [Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO (United States); Hope, Andrew J.; Lindsay, Patricia E. [Princess Margaret Hospital, Toronto, ON (Canada); Bosch, Walter R.; Matthews, John W. [Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO (United States); Sause, William T. [Department of Radiation Oncology, LDS Hospital, Salt Lake City, UT (United States); Graham, Mary V. [Department of Radiation Oncology, Phelps County Regional Hospital, Rolla, MO (United States); Deasy, Joseph O., E-mail: deasyj@mskcc.org [Department of Medical Physics, Memorial Sloan-Kettering Cancer Center, New York, NY (United States)

    2012-04-01

    Purpose: To construct a maximally predictive model of the risk of severe acute esophagitis (AE) for patients who receive definitive radiation therapy (RT) for non-small-cell lung cancer. Methods and Materials: The dataset includes Washington University and RTOG 93-11 clinical trial data (events/patients: 120/374, WUSTL = 101/237, RTOG9311 = 19/137). Statistical model building was performed based on dosimetric and clinical parameters (patient age, sex, weight loss, pretreatment chemotherapy, concurrent chemotherapy, fraction size). A wide range of dose-volume parameters were extracted from dearchived treatment plans, including Dx, Vx, MOHx (mean of hottest x% volume), MOCx (mean of coldest x% volume), and gEUD (generalized equivalent uniform dose) values. Results: The most significant single parameters for predicting acute esophagitis (RTOG Grade 2 or greater) were MOH85, mean esophagus dose (MED), and V30. A superior-inferior weighted dose-center position was derived but not found to be significant. Fraction size was found to be significant on univariate logistic analysis (Spearman R = 0.421, p < 0.00001) but not multivariate logistic modeling. Cross-validation model building was used to determine that an optimal model size needed only two parameters (MOH85 and concurrent chemotherapy, robustly selected on bootstrap model-rebuilding). Mean esophagus dose (MED) is preferred instead of MOH85, as it gives nearly the same statistical performance and is easier to compute. AE risk is given as a logistic function of (0.0688 Asterisk-Operator MED+1.50 Asterisk-Operator ConChemo-3.13), where MED is in Gy and ConChemo is either 1 (yes) if concurrent chemotherapy was given, or 0 (no). This model correlates to the observed risk of AE with a Spearman coefficient of 0.629 (p < 0.000001). Conclusions: Multivariate statistical model building with cross-validation suggests that a two-variable logistic model based on mean dose and the use of concurrent chemotherapy robustly predicts

  18. Modeling the risk of radiation-induced acute esophagitis for combined Washington University and RTOG trial 93-11 lung cancer patients.

    Science.gov (United States)

    Huang, Ellen X; Bradley, Jeffrey D; El Naqa, Issam; Hope, Andrew J; Lindsay, Patricia E; Bosch, Walter R; Matthews, John W; Sause, William T; Graham, Mary V; Deasy, Joseph O

    2012-04-01

    To construct a maximally predictive model of the risk of severe acute esophagitis (AE) for patients who receive definitive radiation therapy (RT) for non-small-cell lung cancer. The dataset includes Washington University and RTOG 93-11 clinical trial data (events/patients: 120/374, WUSTL = 101/237, RTOG9311 = 19/137). Statistical model building was performed based on dosimetric and clinical parameters (patient age, sex, weight loss, pretreatment chemotherapy, concurrent chemotherapy, fraction size). A wide range of dose-volume parameters were extracted from dearchived treatment plans, including Dx, Vx, MOHx (mean of hottest x% volume), MOCx (mean of coldest x% volume), and gEUD (generalized equivalent uniform dose) values. The most significant single parameters for predicting acute esophagitis (RTOG Grade 2 or greater) were MOH85, mean esophagus dose (MED), and V30. A superior-inferior weighted dose-center position was derived but not found to be significant. Fraction size was found to be significant on univariate logistic analysis (Spearman R = 0.421, p < 0.00001) but not multivariate logistic modeling. Cross-validation model building was used to determine that an optimal model size needed only two parameters (MOH85 and concurrent chemotherapy, robustly selected on bootstrap model-rebuilding). Mean esophagus dose (MED) is preferred instead of MOH85, as it gives nearly the same statistical performance and is easier to compute. AE risk is given as a logistic function of (0.0688 MED+1.50 ConChemo-3.13), where MED is in Gy and ConChemo is either 1 (yes) if concurrent chemotherapy was given, or 0 (no). This model correlates to the observed risk of AE with a Spearman coefficient of 0.629 (p < 0.000001). Multivariate statistical model building with cross-validation suggests that a two-variable logistic model based on mean dose and the use of concurrent chemotherapy robustly predicts acute esophagitis risk in combined-data WUSTL and RTOG 93-11 trial datasets. Copyright

  19. Washington Conference

    International Nuclear Information System (INIS)

    Anon.

    1981-01-01

    The 1981 Particle Accelerator Conference was held in Washington from 11-13 March. It was the ninth in the series of meetings organized in the USA which differ from the 'International' meetings in their coverage of the full range of accelerator engineering and technology, including applications outside e field of high energy physics. The Conference took place under the cloud of further budget cuts for Fiscal Year 1982 in the USA which the Department of Energy has applied in line with the financial policy of the new administration. Coming on top of many years of budget trimming which have reduced the number of high energy physics Laboratories funded by the DOE to three (Brookhaven, Fermilab, Stanford - Cornell is funded by the National Science Foundation) and reduced the exploitation of these Laboratories to less than half of their potential, the new cuts did not exactly help to boost morale. Nevertheless, the huge amount of tailed work in accelerator physics and technology which was presented at the Conference showed how alive the field is

  20. The Significance of UNESCO’s Universal Declaration on the Human Genome & Human Rights

    Directory of Open Access Journals (Sweden)

    Shawn H.E. Harmon

    2005-03-01

    Full Text Available Modern medical research, particularly genetic research, is changing the nature of medicine. Concerns surrounding these changes and their potential negative impact on human rights led UNESCO to spearhead collaboration by experts in the creation of an international instrument intended to provide guidance for the promotion of bioethics and the protection of human rights in the genetic context. The result was the Universal Declaration of the Human Genome and Human Rights. This article briefly highlights the scientific and social setting into which the Declaration was injected. This is followed by a consideration of the drafting body (the IBC so as to assess whether UNESCO was the appropriate body to lead this project. The process by which the Declaration was created is also considered so as to assess whether it represents an example of ethical and democratic drafting. Finally, the substantive content of the Declaration is considered and measured against the pre-existing regime so as to assess whether it represents an intelligible and coherent response to the concerns raised capable of offering guidance now and into the future. By assessing these procedural and substantive matters, one can draw some tentative conclusions about the utility and significance of the Declaration.

  1. Genomic potential hypothesis of evolution: a concept of biogenesis in habitable spaces of the universe.

    Science.gov (United States)

    Schwabe, Christian

    2002-11-01

    The new hypothesis of evolution establishes a contiguity of life sciences with cosmology, physics, and chemistry, and provides a basis for the search for life on other planets. Chemistry is the sole driving force of the assembly of life, under the subtle guidance exerted by bonding orbital geometry. That phenomenon leads to multiple origins that function on the same principles but are different to the extent that their nucleic acid core varies. Thus, thoughts about the origins of life and the development of complexity have been transferred from the chance orientation of the past to the realm of atomic structures, which are subject to the laws of thermodynamics and kinetics. Evolution is a legitimate subject of basic science, and the complexity of life will submit to the laws of chemistry and physics as the problem is viewed from a new perspective. The paradigm connects life to the big events that formed every sphere of our living space and that keeps conditions fine-tuned for life to persist, perhaps a billion years or more. The "genomic potential" hypothesis leads to the prediction that life like ours is likely to exist in galaxies that are as distant from the origin of the universe as the Milky Way, and that the habitable zone of our galaxy harbors other living planets as well. Copyright 2002 Wiley-Liss, Inc.

  2. Draft Genome Sequences of 12 Clinical and Environmental Methicillin-Resistant Strains of Staphylococcus pseudintermedius Isolated from a Veterinary Teaching Hospital in Washington State

    Science.gov (United States)

    Shah, Devendra H.; Jones, Lisa P.; Paul, Narayan

    2018-01-01

    ABSTRACT Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is a globally emergent multidrug-resistant pathogen of dogs associated with nosocomial transmission in dogs and with potential zoonotic impacts. Here, we report the draft whole-genome sequences of 12 hospital-associated MRSP strains and their resistance genotypes and phenotypes. PMID:29650582

  3. Whole genome sequencing analyses of Listeria monocytogenes that persisted in a milkshake machine for a year and caused illnesses in Washington State

    OpenAIRE

    Li, Zhen; P?rez-Osorio, Ailyn; Wang, Yu; Eckmann, Kaye; Glover, William A.; Allard, Marc W.; Brown, Eric W.; Chen, Yi

    2017-01-01

    Background In 2015, in addition to a United States multistate outbreak linked to contaminated ice cream, another outbreak linked to ice cream was reported in the Pacific Northwest of the United States. It was a hospital-acquired outbreak linked to milkshakes, made from contaminated ice cream mixes and milkshake maker, served to patients. Here we performed multiple analyses on isolates associated with this outbreak: pulsed-field gel electrophoresis (PFGE), whole genome single nucleotide polymo...

  4. The Pediatric Cancer Genome Project

    Science.gov (United States)

    Downing, James R; Wilson, Richard K; Zhang, Jinghui; Mardis, Elaine R; Pui, Ching-Hon; Ding, Li; Ley, Timothy J; Evans, William E

    2013-01-01

    The St. Jude Children’s Research Hospital–Washington University Pediatric Cancer Genome Project (PCGP) is participating in the international effort to identify somatic mutations that drive cancer. These cancer genome sequencing efforts will not only yield an unparalleled view of the altered signaling pathways in cancer but should also identify new targets against which novel therapeutics can be developed. Although these projects are still deep in the phase of generating primary DNA sequence data, important results are emerging and valuable community resources are being generated that should catalyze future cancer research. We describe here the rationale for conducting the PCGP, present some of the early results of this project and discuss the major lessons learned and how these will affect the application of genomic sequencing in the clinic. PMID:22641210

  5. Microbial Genomics: The Expanding Universe of Bacterial Defense Systems.

    Science.gov (United States)

    Forsberg, Kevin J; Malik, Harmit S

    2018-04-23

    Bacteria protect themselves against infection using multiple defensive systems that move by horizontal gene transfer and accumulate in genomic 'defense islands'. A recent study exploited these features to uncover ten novel defense systems, substantially expanding the catalog of bacterial defense systems and predicting the discovery of many more. Copyright © 2018 Elsevier Ltd. All rights reserved.

  6. 76 FR 14045 - Notice of Intent To Repatriate a Cultural Item: Museum of Anthropology at Washington State...

    Science.gov (United States)

    2011-03-15

    ...: Museum of Anthropology at Washington State University, Pullman, WA AGENCY: National Park Service... Museum of Anthropology at Washington State University, Pullman, WA, that meets the definition of..., a copper pendant was given to the Museum of Anthropology at Washington State University for intended...

  7. Institutional Responsibility and the Flawed Genomic Biomarkers at Duke University: A Missed Opportunity for Transparency and Accountability.

    Science.gov (United States)

    DeMets, David L; Fleming, Thomas R; Geller, Gail; Ransohoff, David F

    2017-08-01

    When there have been substantial failures by institutional leadership in their oversight responsibility to protect research integrity, the public should demand that these be recognized and addressed by the institution itself, or the funding bodies. This commentary discusses a case of research failures in developing genomic predictors for cancer risk assessment and treatment at a leading university. In its review of this case, the Office of Research Integrity, an agency within the US Department of Health and Human Services, focused their report entirely on one individual faculty member and made no comment on the institution's responsibility and its failure to provide adequate oversight and investigation. These actions missed an important opportunity to emphasize the institution's critical responsibilities in oversight of research integrity and the importance of institutional transparency and accountability.

  8. University of Washington/ Northwest National Marine Renewable Energy Center Tidal Current Technology Test Protocol, Instrumentation, Design Code, and Oceanographic Modeling Collaboration: Cooperative Research and Development Final Report, CRADA Number CRD-11-452

    Energy Technology Data Exchange (ETDEWEB)

    Driscoll, Frederick R. [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2016-11-01

    The University of Washington (UW) - Northwest National Marine Renewable Energy Center (UW-NNMREC) and the National Renewable Energy Laboratory (NREL) will collaborate to advance research and development (R&D) of Marine Hydrokinetic (MHK) renewable energy technology, specifically renewable energy captured from ocean tidal currents. UW-NNMREC is endeavoring to establish infrastructure, capabilities and tools to support in-water testing of marine energy technology. NREL is leveraging its experience and capabilities in field testing of wind systems to develop protocols and instrumentation to advance field testing of MHK systems. Under this work, UW-NNMREC and NREL will work together to develop a common instrumentation system and testing methodologies, standards and protocols. UW-NNMREC is also establishing simulation capabilities for MHK turbine and turbine arrays. NREL has extensive experience in wind turbine array modeling and is developing several computer based numerical simulation capabilities for MHK systems. Under this CRADA, UW-NNMREC and NREL will work together to augment single device and array modeling codes. As part of this effort UW NNMREC will also work with NREL to run simulations on NREL's high performance computer system.

  9. 76 FR 58031 - Notice of Intent To Repatriate Cultural Items: Thomas Burke Memorial Washington State Museum...

    Science.gov (United States)

    2011-09-19

    ... DEPARTMENT OF THE INTERIOR National Park Service [2253-665] Notice of Intent To Repatriate Cultural Items: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Thomas Burke Memorial Washington State Museum...

  10. 76 FR 28066 - Notice of Intent To Repatriate a Cultural Item: Museum of Anthropology at Washington State...

    Science.gov (United States)

    2011-05-13

    ... Cultural Item: Museum of Anthropology at Washington State University, Pullman, WA AGENCY: National Park... possession of the Museum of Anthropology at Washington State University, Pullman, WA, that meets the... notice. One lot of stone, bone, and glass beads was given to the Museum of Anthropology at Washington...

  11. Reactor console replacement at Washington State University

    International Nuclear Information System (INIS)

    Lovas, Thomas A.

    1978-01-01

    A replacement reactor console was installed in 1977 at the W.S.U. 1 MW TRIGA-fueled reactor as the final step in an instrumentation upgrade program. The program was begun circa 1972 with the design, construction and installation of various systems and equipment. Major instruments were installed in the existing console and tested in the course of reactor operation. The culmination of the program was the installation of a cubicle designed and constructed to house the updated instrumentation. (author)

  12. University of Washington Participation in SAFARI-2000

    Science.gov (United States)

    Hobbs, Peter V.

    2005-01-01

    This report presents a summary, of the participation in the 6-week field study in southern Africa. During the field study there were flown 119.02 research hours (31 research flights). In these flights the researchers obtained many unique data sets for evaluating the effects of biomass burning and other sources of particles and gases on the climate of southern Africa, and obtained simultaneous measurements with NASA ER-2 and Terra overflights. They also analyzed portions of the large data sets acquired in SAFARI-2000. They attended several SAFARI-2000 workshops, national and international conferences to present SAFARI-2000 results.

  13. University of Washington superconducting booster linac

    International Nuclear Information System (INIS)

    Storm, D.W.; Amsbaugh, J.F.; Cramer, J.G.; Swanson, H.E.; Trainor, T.A.; Vandenbosch, R.; Weitkamp, W.G.; Will, D.I.

    1985-01-01

    We have begun construction of a superconducting linac designed to accelerate ions from protons through about mass 60. Injected by our 9 MV-terminal tandem van de Graaff accelerator, the linac is expected to double the proton energy and quadruple the energies of heavier ions. The resonators are lead plated copper quarter wave structures. The overall layout and expected performance of the accelerator will be presented, along with a brief status report. 3 refs., 3 figs

  14. Universe

    CERN Document Server

    2009-01-01

    The Universe, is one book in the Britannica Illustrated Science Library Series that is correlated to the science curriculum in grades 5-8. The Britannica Illustrated Science Library is a visually compelling set that covers earth science, life science, and physical science in 16 volumes.  Created for ages 10 and up, each volume provides an overview on a subject and thoroughly explains it through detailed and powerful graphics-more than 1,000 per volume-that turn complex subjects into information that students can grasp.  Each volume contains a glossary with full definitions for vocabulary help and an index.

  15. On the analysis of genome-wide association studies in family-based designs: a universal, robust analysis approach and an application to four genome-wide association studies.

    Directory of Open Access Journals (Sweden)

    Sungho Won

    2009-11-01

    Full Text Available For genome-wide association studies in family-based designs, we propose a new, universally applicable approach. The new test statistic exploits all available information about the association, while, by virtue of its design, it maintains the same robustness against population admixture as traditional family-based approaches that are based exclusively on the within-family information. The approach is suitable for the analysis of almost any trait type, e.g. binary, continuous, time-to-onset, multivariate, etc., and combinations of those. We use simulation studies to verify all theoretically derived properties of the approach, estimate its power, and compare it with other standard approaches. We illustrate the practical implications of the new analysis method by an application to a lung-function phenotype, forced expiratory volume in one second (FEV1 in 4 genome-wide association studies.

  16. Recent developments: Washington focus

    International Nuclear Information System (INIS)

    Anon.

    1990-01-01

    November was a quiet month in Washington. Although Congress has recessed until 1991, the Senate filled vacancies in party leadership positions created by November's elections. The House is expected to proceed with its changes in early December. The Nuclear Energy Forum was held in Washington, DC on November 11-14 to discuss the status of the nuclear industry in the USA. The Forum, held in conjunction with the American Nuclear Society's annual meeting, assembled a large number of CEO's from US, European, and Far Eastern utilities and vendors. The meeting concluded with an announcement by Philip Bayne, President of NYPA and chairman of the Nuclear Power Oversight Committee (NPOC), of the results of a year-long NPOC study entitled a open-quotes Strategic Plan for Building New Nuclear Power Plants.close quotes

  17. The expanding universe of cohesin functions: a new genome stability caretaker involved in human disease and cancer.

    Science.gov (United States)

    Mannini, Linda; Menga, Stefania; Musio, Antonio

    2010-06-01

    Cohesin is responsible for sister chromatid cohesion, ensuring the correct chromosome segregation. Beyond this role, cohesin and regulatory cohesin genes seem to play a role in preserving genome stability and gene transcription regulation. DNA damage is thought to be a major culprit for many human diseases, including cancer. Our present knowledge of the molecular basis underlying genome instability is extremely limited. Mutations in cohesin genes cause human diseases such as Cornelia de Lange syndrome and Roberts syndrome/SC phocomelia, and all the cell lines derived from affected patients show genome instability. Cohesin mutations have also been identified in colorectal cancer. Here, we will discuss the human disorders caused by alterations of cohesin function, with emphasis on the emerging role of cohesin as a genome stability caretaker.

  18. Genomic Data Commons launches

    Science.gov (United States)

    The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

  19. Origins of the Human Genome Project.

    Science.gov (United States)

    Watson, J D; Cook-Deegan, R M

    1991-01-01

    Caenorhabditis elegans by a collaboration between Washington University and the Medical Research Council laboratory in Cambridge, U.K. This project is now turning to sequencing C. elegans DNA as a logical extension of this work. These are but the first fruits of the genome project. There is much more to come.

  20. High Quality Genomic Copy Number Data from Archival Formalin-Fixed Paraffin-Embedded Leiomyosarcoma: Optimisation of Universal Linkage System Labelling

    Science.gov (United States)

    Salawu, Abdulazeez; Ul-Hassan, Aliya; Hammond, David; Fernando, Malee; Reed, Malcolm; Sisley, Karen

    2012-01-01

    Most soft tissue sarcomas are characterized by genetic instability and frequent genomic copy number aberrations that are not subtype-specific. Oligonucleotide microarray-based Comparative Genomic Hybridisation (array CGH) is an important technique used to map genome-wide copy number aberrations, but the traditional requirement for high-quality DNA typically obtained from fresh tissue has limited its use in sarcomas. Although large archives of Formalin-fixed Paraffin-embedded (FFPE) tumour samples are available for research, the degradative effects of formalin on DNA from these tissues has made labelling and analysis by array CGH technically challenging. The Universal Linkage System (ULS) may be used for a one-step chemical labelling of such degraded DNA. We have optimised the ULS labelling protocol to perform aCGH on archived FFPE leiomyosarcoma tissues using the 180k Agilent platform. Preservation age of samples ranged from a few months to seventeen years and the DNA showed a wide range of degradation (when visualised on agarose gels). Consistently high DNA labelling efficiency and low microarray probe-to-probe variation (as measured by the derivative log ratio spread) was seen. Comparison of paired fresh and FFPE samples from identical tumours showed good correlation of CNAs detected. Furthermore, the ability to macro-dissect FFPE samples permitted the detection of CNAs that were masked in fresh tissue. Aberrations were visually confirmed using Fluorescence in situ Hybridisation. These results suggest that archival FFPE tissue, with its relative abundance and attendant clinical data may be used for effective mapping for genomic copy number aberrations in such rare tumours as leiomyosarcoma and potentially unravel clues to tumour origins, progression and ultimately, targeted treatment. PMID:23209738

  1. Emory University: High-Throughput Protein-Protein Interaction Dataset for Lung Cancer-Associated Genes | Office of Cancer Genomics

    Science.gov (United States)

    To discover novel PPI signaling hubs for lung cancer, CTD2 Center at Emory utilized large-scale genomics datasets and literature to compile a set of lung cancer-associated genes. A library of expression vectors were generated for these genes and utilized for detecting pairwise PPIs with cell lysate-based TR-FRET assays in high-throughput screening format. Read the abstract.

  2. 76 FR 21928 - Washington State University; Facility Operating License No. R-76; Washington State University...

    Science.gov (United States)

    2011-04-19

    ... late 2008, the site was surrounded for a distance of 400 meters (1300 feet) in all directions by... course is separated from the NRCR by 100 to 200 meters (330 to 660 feet) of land. There is a parcel of land abutting the NRCR of about 10,000 square meters (109,000 square feet) of virgin prairie land which...

  3. From the Bench to the Clinic Part 1: Martin McIntosh, Ph.D., Introduces His Lab's Immunotherapy Research | Office of Cancer Genomics

    Science.gov (United States)

    The field of immunotherapy is rapidly advancing and genomics techniques are being incorporated to add a “precision” approach. OCG spoke with two CTD2 investigators from the Fred Hutchinson Cancer Research Center (FHCRC) about new advances in immunotherapy. For the first article of this two-part series, we interviewed Martin McIntosh, Ph.D., member of the Fred Hutchinson Translational Research program and previously Program Head in Computational Biology at FHCRC/University of Washington Comprehensive Cancer Center.

  4. A Partnership for Modeling the Marine Environment of Puget Sound, Washington

    Science.gov (United States)

    2009-03-30

    Northwest National Marine Renewable Energy Center, a joint University of Washington - Oregon State project funded by the U.S. Department of Energy. e. A... Marine Renewable Energy Center (NNMREC), a joint Washington - Oregon State project to investigate extraction of wave and tidal energy sponsored by

  5. Congress in Washington

    International Nuclear Information System (INIS)

    Anon.

    1993-01-01

    Full text: Over 1200 accelerator physicists and engineers gathered in Washington mid-May for the 15th in the series of biennial Particle Accelerator Conferences (PAC) - the major US forum for accelerator physics and technology. For the first time since their inception, actual attendance declined, however the number of contributed papers stayed around 1500. CERN Director General designate Chris Llewellyn Smith spelled out the challenges with an opening talk underlining the deficiencies in today's Standard Model. From many directions comes the message that collision in the 1 TeV range must tell us something new - wherefore art thou SSC and LHC? The secondary shock waves of last year's (fortunately overturned) bid to cancel the SSC Superconducting Supercollider project still ripple around the USA, while progress towards authorization of CERN's LHC Large Hadron Collider has been slower than initially hoped. The new US administration has indicated a constant rate of SSC funding over the next four years; the figure is higher than the present budget but considerably below the originally proposed budget profile, implying that completion will be retarded by some three years beyond the end of the decade. The SSC Laboratory will clearly have problems to fight increased overall cost and sustain enthusiasm. CERN hopes for LHC blessing in time to allow machine completion by the year 2000. Pride of place at Washington went to DESY's HERA electron-proton collider - the major new facility since the previous PAC. Commissioning has been impressive and physics is well underway, with luminosity climbing towards the design figure. The varied user community of the ubiquitous synchrotron radiation facilities is now considerably larger than that of particle physics and has extensive industrial involvement. Three such machines have come into operation since the previous PAC - the 6 GeV European Synchrotron Radiation Facility at Grenoble, the 1.5 GeV Advanced Light Source

  6. Characterization of near full-length genomes of HIV type 1 strains in Denmark: Basis for a universal therapeutic vaccine

    DEFF Research Database (Denmark)

    Andresen, Betina S.; Vinner, Lasse; Tang, Sheila Tuyet

    2007-01-01

    We report here the near full-length sequence characterization of 17 Danish clinical HIV-1 strains isolated from HLA-A02 patients not in need of ART, with relatively low viral loads and normal CD4 cell counts. Sequencing was performed directly on DNA extracted from short-term cocultures of PBMCs...... of a universal immunotherapeutic vaccine construct based on these epitopes....

  7. Washington Accelerator Conference

    International Nuclear Information System (INIS)

    Anon.

    1993-01-01

    Highlights of the 1993 Particle Accelerator Conference, held in Washington in May, were picked out in the previous issue (page 18). Talks on the big hadron colliders reflected the sea-change in the accelerator world where the scale, complexity and cost of the front-line projects has slowed the pace of developments (not unlike the scene in particle physics itself). Speaking before the anti-SSC vote in the House of Representatives in June, Dick Briggs reviewed the situation at the SSC Superconducting Supercollider in Ellis County, Texas. The linac building is near completion and the Low Energy Booster will be ready to receive components early next year. Tunnelling for the Main Ring is advancing rapidly with four boring machines in action. Five miles of tunnel have been completed since January and the pace has now stepped up to nearly a mile each week. The superconducting magnet news is good. Following the successful initial string test of a half cell of the magnet lattice, a two-ring full cell with all associated services is being assembled. The mechanical robustness of the magnet design was confirmed when a dipole was taken to 9.7 T when cooled to 1.8 K. In the Magnet Test Lab itself, ten test stands are installed and equipped

  8. Recent developments: Washington focus

    International Nuclear Information System (INIS)

    Anon.

    1990-01-01

    Congress reconvened on January 23, but most of Washington's January new involves the Administration. DOE sent two letters to USEC customers, awarded a contract for the independent financial review of the enrichment program, and released a plan for demonstrating AVLIS by 1992. A General Accounting Office (GAO) report investigating the impact of imports of Soviet EUP into the US was made public. Both Congress and the administration are reportedly considering a full-scope US-Soviet Agreement for Nuclear Cooperation. Finally, published reports indicate Congress may consider ending the customs user fee which levies a charge of 0.17% on the value of all imported goods. The fee is felt to violate the General Agreement on Tariffs and Trade (GATT) and is not based on recovering actual Customs costs for processing a good. The fee brings the Treasury over $700 million per year, but the business community plans to lobby hard for its outright elimination or a change in authority to collect the fee based on actual costs

  9. Washington Accelerator Conference

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    1993-09-15

    Highlights of the 1993 Particle Accelerator Conference, held in Washington in May, were picked out in the previous issue (page 18). Talks on the big hadron colliders reflected the sea-change in the accelerator world where the scale, complexity and cost of the front-line projects has slowed the pace of developments (not unlike the scene in particle physics itself). Speaking before the anti-SSC vote in the House of Representatives in June, Dick Briggs reviewed the situation at the SSC Superconducting Supercollider in Ellis County, Texas. The linac building is near completion and the Low Energy Booster will be ready to receive components early next year. Tunnelling for the Main Ring is advancing rapidly with four boring machines in action. Five miles of tunnel have been completed since January and the pace has now stepped up to nearly a mile each week. The superconducting magnet news is good. Following the successful initial string test of a half cell of the magnet lattice, a two-ring full cell with all associated services is being assembled. The mechanical robustness of the magnet design was confirmed when a dipole was taken to 9.7 T when cooled to 1.8 K. In the Magnet Test Lab itself, ten test stands are installed and equipped.

  10. The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

    Science.gov (United States)

    Shaffer, Christopher D.; Alvarez, Consuelo; Bailey, Cheryl; Barnard, Daron; Bhalla, Satish; Chandrasekaran, Chitra; Chandrasekaran, Vidya; Chung, Hui-Min; Dorer, Douglas R.; Du, Chunguang; Eckdahl, Todd T.; Poet, Jeff L.; Frohlich, Donald; Goodman, Anya L.; Gosser, Yuying; Hauser, Charles; Hoopes, Laura L.M.; Johnson, Diana; Jones, Christopher J.; Kaehler, Marian; Kokan, Nighat; Kopp, Olga R.; Kuleck, Gary A.; McNeil, Gerard; Moss, Robert; Myka, Jennifer L.; Nagengast, Alexis; Morris, Robert; Overvoorde, Paul J.; Shoop, Elizabeth; Parrish, Susan; Reed, Kelynne; Regisford, E. Gloria; Revie, Dennis; Rosenwald, Anne G.; Saville, Ken; Schroeder, Stephanie; Shaw, Mary; Skuse, Gary; Smith, Christopher; Smith, Mary; Spana, Eric P.; Spratt, Mary; Stamm, Joyce; Thompson, Jeff S.; Wawersik, Matthew; Wilson, Barbara A.; Youngblom, Jim; Leung, Wilson; Buhler, Jeremy; Mardis, Elaine R.; Lopatto, David

    2010-01-01

    Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students. PMID:20194808

  11. Simple, quick and cost-efficient: A universal RT-PCR and sequencing strategy for genomic characterisation of foot-and-mouth disease viruses.

    Science.gov (United States)

    Dill, V; Beer, M; Hoffmann, B

    2017-08-01

    Foot-and-mouth disease (FMD) is a major contributor to poverty and food insecurity in Africa and Asia, and it is one of the biggest threats to agriculture in highly developed countries. As FMD is extremely contagious, strategies for its prevention, early detection, and the immediate characterisation of outbreak strains are of great importance. The generation of whole-genome sequences enables phylogenetic characterisation, the epidemiological tracing of virus transmission pathways and is supportive in disease control strategies. This study describes the development and validation of a rapid, universal and cost-efficient RT-PCR system to generate genome sequences of FMDV, reaching from the IRES to the end of the open reading frame. The method was evaluated using twelve different virus strains covering all seven serotypes of FMDV. Additionally, samples from experimentally infected animals were tested to mimic diagnostic field samples. All primer pairs showed a robust amplification with a high sensitivity for all serotypes. In summary, the described assay is suitable for the generation of FMDV sequences from all serotypes to allow immediate phylogenetic analysis, detailed genotyping and molecular epidemiology. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. 12 CFR 4.4 - Washington office.

    Science.gov (United States)

    2010-01-01

    ... 12 Banks and Banking 1 2010-01-01 2010-01-01 false Washington office. 4.4 Section 4.4 Banks and... EXAMINERS Organization and Functions § 4.4 Washington office. The Washington office of the OCC is the main office and headquarters of the OCC. The Washington office directs OCC policy, oversees OCC operations...

  13. Historical changes to Lake Washington and route of the Lake Washington Ship Canal, King County, Washington

    Science.gov (United States)

    Chrzastowski, Michael J.

    1983-01-01

    Lake Washington, in the midst of the greater Seattle metropolitan area of the Puget Sound region (fig. 1), is an exceptional commercial, recreational, and esthetic resource for the region . In the past 130 years, Lake Washington has been changed from a " wild " lake in a wilderness setting to a regulated lake surrounded by a growing metropolis--a transformation that provides an unusual opportunity to study changes to a lake's shoreline and hydrologic characteristics -resulting from urbanization.

  14. Ensembl Genomes 2016: more genomes, more complexity.

    Science.gov (United States)

    Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

    2016-01-04

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Development of genomic microsatellite multiplex PCR using dye-labeled universal primer and its validation in pedigree analysis of Pacific oyster ( Crassostrea gigas)

    Science.gov (United States)

    Liu, Ting; Li, Qi; Song, Junlin; Yu, Hong

    2017-02-01

    There is an increasing requirement for traceability of aquaculture products, both for consumer protection and for food safety. There are high error rates in the conventional traceability systems depending on physical labels. Genetic traceability technique depending on DNA-based tracking system can overcome this problem. Genealogy information is essential for genetic traceability, and microsatellite DNA marker is a good choice for pedigree analysis. As increasing genotyping throughput of microsatellites, microsatellite multiplex PCR has become a fast and cost-effective technique. As a commercially important cultured aquatic species, Pacific oyster Crassostrea gigas has the highest global production. The objective of this study was to develop microsatellite multiplex PCR panels with dye-labeled universal primer for pedigree analysis in C. gigas, and these multiplex PCRs were validated using 12 full-sib families with known pedigrees. Here we developed six informative multiplex PCRs using 18 genomic microsatellites in C. gigas. Each multiplex panel contained a single universal primer M13(-21) used as a tail on each locus-specific forward primer and a single universal primer M13(-21) labeled with fluorophores. The polymorphisms of the markers were moderate, with an average of 10.3 alleles per locus and average polymorphic information content of 0.740. The observed heterozygosity per locus ranged from 0.492 to 0.822. Cervus simulations revealed that the six panels would still be of great value when massive families were analysed. Pedigree analysis of real offspring demonstrated that 100% of the offspring were unambiguously allocated to their parents when two multiplex PCRs were used. The six sets of multiplex PCRs can be an important tool for tracing cultured individuals, population genetic analysis, and selective breeding program in C. gigas.

  16. Is autoinducer-2 a universal signal for interspecies communication: a comparative genomic and phylogenetic analysis of the synthesis and signal transduction pathways

    Directory of Open Access Journals (Sweden)

    Wagner-Döbler Irene

    2004-09-01

    Full Text Available Abstract Background Quorum sensing is a process of bacterial cell-to-cell communication involving the production and detection of extracellular signaling molecules called autoinducers. Recently, it has been proposed that autoinducer-2 (AI-2, a furanosyl borate diester derived from the recycling of S-adenosyl-homocysteine (SAH to homocysteine, serves as a universal signal for interspecies communication. Results In this study, 138 completed genomes were examined for the genes involved in the synthesis and detection of AI-2. Except for some symbionts and parasites, all organisms have a pathway to recycle SAH, either using a two-step enzymatic conversion by the Pfs and LuxS enzymes or a one-step conversion using SAH-hydrolase (SahH. 51 organisms including most Gamma-, Beta-, and Epsilonproteobacteria, and Firmicutes possess the Pfs-LuxS pathway, while Archaea, Eukarya, Alphaproteobacteria, Actinobacteria and Cyanobacteria prefer the SahH pathway. In all 138 organisms, only the three Vibrio strains had strong, bidirectional matches to the periplasmic AI-2 binding protein LuxP and the central signal relay protein LuxU. The initial two-component sensor kinase protein LuxQ, and the terminal response regulator luxO are found in most Proteobacteria, as well as in some Firmicutes, often in several copies. Conclusions The genomic analysis indicates that the LuxS enzyme required for AI-2 synthesis is widespread in bacteria, while the periplasmic binding protein LuxP is only present in Vibrio strains. Thus, other organisms may either use components different from the AI-2 signal transduction system of Vibrio strains to sense the signal of AI-2, or they do not have such a quorum sensing system at all.

  17. Oil spill response issues in Washington State

    International Nuclear Information System (INIS)

    Lempriere, P.R.

    1997-01-01

    Washington State statutes and regulations applicable to oil transport and oil spills were described. Specific provisions of the statutes and regulations and other relevant matters were also discussed. Among these were: (1) Washington State oil spill prevention plans, (2) Washington State oil spill contingency plans, (3) best achievable protection, (4) Intertanko's lawsuit against Washington State, (5) oil spill removal organizations, (6) certificates of financial responsibility in Washington State, (7) extent of potential liability under Washington Law, (8) disposal of cleanup materials, and (9) definition of 'qualified individuals' on marine vessels having the authority to implement removal actions

  18. Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

    Directory of Open Access Journals (Sweden)

    Galperin Michael Y

    2003-01-01

    Full Text Available Abstract Background Comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (HGT, at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more common in evolution. This complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task. Results We addressed the problem of constructing parsimonious scenarios for individual sets of orthologous genes given a species tree. The orthologous sets were taken from the database of Clusters of Orthologous Groups of proteins (COGs. We show that the phyletic patterns (patterns of presence-absence in completely sequenced genomes of almost 90% of the COGs are inconsistent with the hypothetical species tree. Algorithms were developed to reconcile the phyletic patterns with the species tree by postulating gene loss, COG emergence and HGT (the latter two classes of events were collectively treated as gene gains. We prove that each of these algorithms produces a parsimonious evolutionary scenario, which can be represented as mapping of loss and gain events on the species tree. The distribution of the evolutionary events among the tree nodes substantially depends on the underlying assumptions of the reconciliation algorithm, e.g. whether or not independent gene gains (gain after loss after gain are permitted. Biological considerations suggest that, on average, gene loss might be a more likely event than gene gain. Therefore different gain penalties were used and the resulting series of reconstructed gene sets for the last universal common ancestor (LUCA of the extant life forms were analysed. The number of genes in the reconstructed LUCA gene sets grows as the gain penalty increases. However, qualitative examination of the LUCA versions reconstructed with different gain penalties

  19. Residential Energy Efficiency Potential: Washington

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, Eric J [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2017-11-27

    Energy used by Washington single-family homes that can be saved through cost-effective improvements. Prepared by Eric Wilson and Noel Merket, NREL, and Erin Boyd, U.S. Department of Energy Office of Energy Policy and Systems Analysis.

  20. Washington Tsunami Hazard Mitigation Program

    Science.gov (United States)

    Walsh, T. J.; Schelling, J.

    2012-12-01

    Washington State has participated in the National Tsunami Hazard Mitigation Program (NTHMP) since its inception in 1995. We have participated in the tsunami inundation hazard mapping, evacuation planning, education, and outreach efforts that generally characterize the NTHMP efforts. We have also investigated hazards of significant interest to the Pacific Northwest. The hazard from locally generated earthquakes on the Cascadia subduction zone, which threatens tsunami inundation in less than hour following a magnitude 9 earthquake, creates special problems for low-lying accretionary shoreforms in Washington, such as the spits of Long Beach and Ocean Shores, where high ground is not accessible within the limited time available for evacuation. To ameliorate this problem, we convened a panel of the Applied Technology Council to develop guidelines for construction of facilities for vertical evacuation from tsunamis, published as FEMA 646, now incorporated in the International Building Code as Appendix M. We followed this with a program called Project Safe Haven (http://www.facebook.com/ProjectSafeHaven) to site such facilities along the Washington coast in appropriate locations and appropriate designs to blend with the local communities, as chosen by the citizens. This has now been completed for the entire outer coast of Washington. In conjunction with this effort, we have evaluated the potential for earthquake-induced ground failures in and near tsunami hazard zones to help develop cost estimates for these structures and to establish appropriate tsunami evacuation routes and evacuation assembly areas that are likely to to be available after a major subduction zone earthquake. We intend to continue these geotechnical evaluations for all tsunami hazard zones in Washington.

  1. 78 FR 15053 - Simpson Lumber Company, LLC, Shelton, Washington; Simpson Lumber Company, LLC, Tacoma, Washington...

    Science.gov (United States)

    2013-03-08

    ...,372B] Simpson Lumber Company, LLC, Shelton, Washington; Simpson Lumber Company, LLC, Tacoma, Washington; Simpson Lumber Company, LLC, Longview, Washington; Notice of Revised Determination on Reconsideration On... Reconsideration for the workers and former workers of Simpson Lumber Company, LLC, Shelton, Washington (TA-W-81...

  2. Structural genomics of infectious disease drug targets: the SSGCID

    International Nuclear Information System (INIS)

    Stacy, Robin; Begley, Darren W.; Phan, Isabelle; Staker, Bart L.; Van Voorhis, Wesley C.; Varani, Gabriele; Buchko, Garry W.; Stewart, Lance J.; Myler, Peter J.

    2011-01-01

    An introduction and overview of the focus, goals and overall mission of the Seattle Structural Genomics Center for Infectious Disease (SSGCID) is given. The Seattle Structural Genomics Center for Infectious Disease (SSGCID) is a consortium of researchers at Seattle BioMed, Emerald BioStructures, the University of Washington and Pacific Northwest National Laboratory that was established to apply structural genomics approaches to drug targets from infectious disease organisms. The SSGCID is currently funded over a five-year period by the National Institute of Allergy and Infectious Diseases (NIAID) to determine the three-dimensional structures of 400 proteins from a variety of Category A, B and C pathogens. Target selection engages the infectious disease research and drug-therapy communities to identify drug targets, essential enzymes, virulence factors and vaccine candidates of biomedical relevance to combat infectious diseases. The protein-expression systems, purified proteins, ligand screens and three-dimensional structures produced by SSGCID constitute a valuable resource for drug-discovery research, all of which is made freely available to the greater scientific community. This issue of Acta Crystallographica Section F, entirely devoted to the work of the SSGCID, covers the details of the high-throughput pipeline and presents a series of structures from a broad array of pathogenic organisms. Here, a background is provided on the structural genomics of infectious disease, the essential components of the SSGCID pipeline are discussed and a survey of progress to date is presented

  3. Graph Structure Theory: Proceedings of a Joint Summer Research Conference on Graph Minors Held June 22 to July 5, 1991, at the University of Washington, Seattle. Contemporary Mathematics 147

    Science.gov (United States)

    1991-01-01

    Rudolf Miiller, A combinatorial approach to obtain bounds for stochastic project neworka, Tech. report, Technische Universitit Berlin, 1991. [Pou851 M...appear). 600 ANDRZEJ PROSKUROWSKI [201 J.A. Wald and C.J. Colbourn, Steiner trees, partial 2-trees, and minimum IFI networks, Networks 13 (1983), 159-167...Colbourn, Steiner trees, partial 2-trees and minimum IFI networks, Networks 13, (1983), 159-167. DEPARTMENT OF COMPUTER SCIENCE, UNIVERSITY OF

  4. GLASS FORMULATION TESTING TO INCREASE SULFATE INCORPORATION - Final Report VSL-04R4960-1, Rev 0, 2/28/05, Vitreous State Laboratory, The Catholic University of American, Washington, D.C.

    Energy Technology Data Exchange (ETDEWEB)

    KRUGER AA; MATLACK KS

    2012-02-07

    About 50 million gallons of high-level mixed waste is currently in storage in underground tanks at The United States Department of Energy's (DOE's) Hanford site in the State of Washington. The Hanford Tank Waste Treatment and Immobilization Plant (WTP) will provide DOE's Office of River Protection (ORP) with a means of treating this waste by vitrification for subsequent disposal. The tank waste will be separated into low- and high-activity fractions, which will then be vitrified respectively into Immobilized Low Activity Waste (ILAW) and Immobilized High Level Waste (IHLW) products. The ILAW product will be disposed of in an engineered facility on the Hanford site while the IHLW product will be directed to the national deep geological disposal facility for high-level nuclear waste. The ILAW and IHLW products must meet a variety of requirements with respect to protection of the environment before they can be accepted for disposal. The Office of River Protection is currently examining options to optimize the Low Activity Waste (LAW) facility and the LAW glass waste form. One option under evaluation is to enhance the waste processing rate of the vitrification plant currently under construction. It is likely that the capacity of the LAW vitrification plant can be increased incrementally by implementation of a variety of low-risk, high-probability changes, either separately or in combination. These changes include: (1) Operating at the higher processing rates demonstrated at the LAW Pilot Melter; (2) Increasing the glass pool surface area within the existing external melter envelope; (3) Increasing plant availability; (4) Increasing the glass waste loading; (5) Removing sulfate from the LAW stream; (6) Operating the melter at slightly higher temperature; (7) Installing the third LAW melter into the WTP plant; and (8) Other smaller impact changes. The melter tests described in this report utilized blended feed (glass formers plus waste simulant) prepared

  5. 78 FR 26249 - Drawbridge Operation Regulation; Lake Washington Ship Canal, Seattle, WA

    Science.gov (United States)

    2013-05-06

    ...The Coast Guard has issued a temporary deviation from the operating schedule that governs the Montlake Bridge across the Lake Washington Ship Canal, mile 5.2, at Seattle, WA, and the University Bridge across the Lake Washington Ship Canal, mile 4.3, at Seattle, WA. This deviation is necessary to accommodate the ``Beat the Bridge'' foot race. This deviation allows the bridges to remain in the closed position to allow safe movement of event participants.

  6. Father Secchi Goes to Washington

    Science.gov (United States)

    McCarthy, M. F.

    1994-12-01

    In 1848 a small group of Jesuit refugees arrived at Georgetown College near Washington, D.C. Among them was a young priest, Angelo Secchi, who had finished theology studies in Rome, but had not been able to complete his final examinations. This done successfully, Secchi turned to astronomy and the new facilities of the Georgetown College Observatory, directed by its founder, Fr. James Curley. During his two years in Washington, Secchi studied physics, wrote an article on Electrical Rheometry for the Smithsonian Institution, and formed a friendship with Matthew Fontaine Maury of the U.S. Navy, who headed the Chart Service and in 1844 was named superintendent of the National Observatory. This was later named the U.S. Naval Observatory. Secchi's friendships formed during the Washington visit proved most helpful for relations between European astronomers and U.S. colleagues. Secchi, after his return to Rome constructed the Observatory of the Collegio Romano atop the baroque Church of St. Ignatius in Rome and began his work in spectral classification of stars.

  7. Physical data collected from Seaglider SG012 during Washington Coast, launched 07 February 2005 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2005-02-07 to 2005-06-08 (NCEI Accession 0156075)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  8. Physical data collected from Seaglider SG005 during Washington Coast June 2004 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2004-06-24 to 2004-07-28 (NCEI Accession 0155971)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  9. Physical data collected from Seaglider SG005 during Washington Coast, September 2002 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2002-09-11 to 2002-11-03 (NCEI Accession 0155983)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  10. Physical data collected from Seaglider SG005 during Washington Coast August 2003 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2003-08-21 to 2004-01-20 (NCEI Accession 0155930)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  11. Physical data collected from Seaglider SG030 during Washington Coast 8 November 2006 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2006-11-09 to 2006-12-17 (NCEI Accession 0156188)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  12. Physical data collected from Seaglider SG012 during Washington Coast, December 2004 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2004-12-23 to 2005-01-25 (NCEI Accession 0156003)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  13. Physical data collected from Seaglider SG005 during Washington Coast, February 2003 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2003-02-08 to 2003-02-12 (NCEI Accession 0155963)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  14. Physical data collected from Seaglider SG002 during Washington Coast, December 2004 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2004-12-23 to 2004-12-30 (NCEI Accession 0155944)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  15. Physical data collected from Seaglider SG002 during Washington Coast, January 2004 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2004-01-20 to 2004-06-24 (NCEI Accession 0155959)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  16. Physical data collected from Seaglider SG005 during Washington Coast, 8 November 2006 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2006-11-09 to 2007-03-15 (NCEI Accession 0155980)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  17. Physical data collected from Seaglider SG005 during Washington Coast, 10 September 2007 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2007-09-10 to 2008-01-17 (NCEI Accession 0155995)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  18. Physical data collected from Seaglider SG014 during Washington Coast, 15 March 2007 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2007-03-15 to 2007-09-10 (NCEI Accession 0156140)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  19. Comprehensive genomic studies: emerging regulatory, strategic, and quality assurance challenges for biorepositories.

    Science.gov (United States)

    McDonald, Sandra A; Mardis, Elaine R; Ota, David; Watson, Mark A; Pfeifer, John D; Green, Jonathan M

    2012-07-01

    As part of the molecular revolution sweeping medicine, comprehensive genomic studies are adding powerful dimensions to medical research. However, their power exposes new regulatory, strategic, and quality assurance challenges for biorepositories. A key issue is that unlike other research techniques commonly applied to banked specimens, nucleic acid sequencing, if sufficiently extensive, yields data that could identify a patient. This evolving paradigm renders the concepts of anonymized and anonymous specimens increasingly outdated. The challenges for biorepositories in this new era include refined consent processes and wording, selection and use of legacy specimens, quality assurance procedures, institutional documentation, data sharing, and interaction with institutional review boards. Given current trends, biorepositories should consider these issues now, even if they are not currently experiencing sample requests for genomic analysis. We summarize our current experiences and best practices at Washington University Medical School, St Louis, MO, our perceptions of emerging trends, and recommendations.

  20. A universal protocol to generate consensus level genome sequences for foot-and-mouth disease virus and other positive-sense polyadenylated RNA viruses using the Illumina MiSeq.

    Science.gov (United States)

    Logan, Grace; Freimanis, Graham L; King, David J; Valdazo-González, Begoña; Bachanek-Bankowska, Katarzyna; Sanderson, Nicholas D; Knowles, Nick J; King, Donald P; Cottam, Eleanor M

    2014-09-30

    Next-Generation Sequencing (NGS) is revolutionizing molecular epidemiology by providing new approaches to undertake whole genome sequencing (WGS) in diagnostic settings for a variety of human and veterinary pathogens. Previous sequencing protocols have been subject to biases such as those encountered during PCR amplification and cell culture, or are restricted by the need for large quantities of starting material. We describe here a simple and robust methodology for the generation of whole genome sequences on the Illumina MiSeq. This protocol is specific for foot-and-mouth disease virus (FMDV) or other polyadenylated RNA viruses and circumvents both the use of PCR and the requirement for large amounts of initial template. The protocol was successfully validated using five FMDV positive clinical samples from the 2001 epidemic in the United Kingdom, as well as a panel of representative viruses from all seven serotypes. In addition, this protocol was successfully used to recover 94% of an FMDV genome that had previously been identified as cell culture negative. Genome sequences from three other non-FMDV polyadenylated RNA viruses (EMCV, ERAV, VESV) were also obtained with minor protocol amendments. We calculated that a minimum coverage depth of 22 reads was required to produce an accurate consensus sequence for FMDV O. This was achieved in 5 FMDV/O/UKG isolates and the type O FMDV from the serotype panel with the exception of the 5' genomic termini and area immediately flanking the poly(C) region. We have developed a universal WGS method for FMDV and other polyadenylated RNA viruses. This method works successfully from a limited quantity of starting material and eliminates the requirement for genome-specific PCR amplification. This protocol has the potential to generate consensus-level sequences within a routine high-throughput diagnostic environment.

  1. Death with dignity in Washington patients with amyotrophic lateral sclerosis.

    Science.gov (United States)

    Wang, Leo H; Elliott, Michael A; Jung Henson, Lily; Gerena-Maldonado, Elba; Strom, Susan; Downing, Sharon; Vetrovs, Jennifer; Kayihan, Paige; Paul, Piper; Kennedy, Kate; Benditt, Joshua O; Weiss, Michael D

    2016-11-15

    To describe the amyotrophic lateral sclerosis (ALS) patients who sought medication under the Washington State Death with Dignity (DWD) Act since its inception in 2009. Chart review at 3 tertiary medical centers in the Seattle/Puget Sound region and comparison to publicly available data of ALS and all-cause DWD cohorts from Washington and Oregon. In Washington State, 39 patients with ALS requested DWD from the University of Washington, Virginia Mason, and Swedish Medical Centers beginning in 2009. The median age at death was 65 years (range 46-86). Seventy-seven percent of the patients used the prescriptions. All of the patients who used the medications passed away without complications. The major reasons for patients to request DWD as reported by participating physicians were loss of autonomy and dignity and decrease in enjoyable activities. Inadequate pain control, financial cost, and loss of bodily control were less commonly indicated. These findings were similar to those of the 92 patients who sought DWD in Oregon. In Washington and Oregon, the percentage of patients with ALS seeking DWD is higher compared to the cancer DWD cohort. Furthermore, compared to the all-cause DWD cohort, patients with ALS are more likely to be non-Hispanic white, married, educated, enrolled in hospice, and to have died at home. Although a small number, ALS represents the disease with the highest proportion of patients seeking to participate in DWD. Patients with ALS who choose DWD are well-educated and have access to palliative or life-prolonging care. The use of the medications appears to be able to achieve the patients' goals without complications. © 2016 American Academy of Neurology.

  2. University of Texas MD Anderson Cancer Center: High-Throughput Screening Identifying Driving Mutations in Endometrial Cancer | Office of Cancer Genomics

    Science.gov (United States)

    Recent advances in next-generation sequencing technology have enabled the unprecedented characterization of a full spectrum of somatic alterations in cancer genomes. Given the large numbers of somatic mutations typically detected by this approach, a key challenge in the downstream analysis is to distinguish “drivers” that functionally contribute to tumorigenesis from “passengers” that occur as the consequence of genomic instability.

  3. Washington: a guide to geothermal energy development

    Energy Technology Data Exchange (ETDEWEB)

    Bloomquist, R.G.; Basescu, N.; Higbee, C.; Justus, D.; Simpson, S.

    1980-06-01

    Washington's geothermal potential is discussed. The following topics are covered: exploration, drilling, utilization, legal and institutional setting, and economic factors of direct use projects. (MHR)

  4. Corrections Education. Washington's Community and Technical Colleges

    Science.gov (United States)

    Washington State Board for Community and Technical Colleges, 2015

    2015-01-01

    The Washington State Department of Corrections contracts with community colleges to provide basic education and job training at each of the state's 12 adult prisons so upon release, individuals are more likely to get jobs and less likely to return. Washington State community colleges build a bridge for offenders to successfully re-enter…

  5. Aerospace Training. Washington's Community and Technical Colleges

    Science.gov (United States)

    Washington State Board for Community and Technical Colleges, 2014

    2014-01-01

    Aerospace is an economic powerhouse that generates jobs and fuels our economy. Washington's community and technical colleges produce the world-class employees needed to keep it that way. With about 1,250 aerospace-related firms employing more than 94,000 workers, Washington has the largest concentration of aerospace expertise in the nation. To…

  6. University of Texas Southwestern Medical Center: High-Throughput siRNA Screening of a Non-Small Cell Lung Cancer (NSCLC) Cell Line Panel | Office of Cancer Genomics

    Science.gov (United States)

    The goal of this project is to use siRNA screens to identify NSCLC-selective siRNAs from two genome-wide libraries that will allow us to functionally define genetic dependencies of subtypes of NSCLC. Using bioinformatics tools, the CTD2 center at the University of Texas Southwestern Medical Center are discovering associations between this functional data (siRNAs) and NSCLC mutational status, methylation arrays, gene expression arrays, and copy number variation data that will help us identify new targets and enrollment biomarkers. 

  7. Washington State biomass data book

    International Nuclear Information System (INIS)

    Deshaye, J.A.; Kerstetter, J.D.

    1991-07-01

    This is the first edition of the Washington State Biomass Databook. It assess sources and approximate costs of biomass fuels, presents a view of current users, identifies potential users in the public and private sectors, and lists prices of competing energy resources. The summary describes key from data from the categories listed above. Part 1, Biomass Supply, presents data increasing levels of detail on agricultural residues, biogas, municipal solid waste, and wood waste. Part 2, Current Industrial and Commercial Use, demonstrates how biomass is successfully being used in existing facilities as an alternative fuel source. Part 3, Potential Demand, describes potential energy-intensive public and private sector facilities. Part 4, Prices of Competing Energy Resources, shows current suppliers of electricity and natural gas and compares utility company rates. 49 refs., 43 figs., 72 tabs

  8. The neutron radiography unit at Washington State University

    International Nuclear Information System (INIS)

    Ogren, J.W.; Burkhart, D.; Hinman, G.

    1972-01-01

    The WSU neutron radiography unit was developed as a student project, but more recently it has been used by our College of Engineering Research Division in a study of mine wall reinforcement by plastic materials

  9. University of Washington Nuclear Physics Data Collection System

    International Nuclear Information System (INIS)

    Green, K.C.

    1981-01-01

    During the past several years, a new data collection system has been developed, replacing a previous system based on an SDS-930 computer. The system is constructed about a PDP 11/60 and an MBD-11 controlled CAMAC crate. The hardware configuration as well as a locally written singles data collection code will be described in some detail. Multiparameter data is taken with an enhanced version of Fermilab Multi. Current capabilities and future plans are discussed

  10. Nuclear Theory Group, University of Washington recent and planned research

    International Nuclear Information System (INIS)

    1993-01-01

    The work of the five staff members is presented individually in turn. (1) Nonperturbative aspects of quantum chromodynamics and its implication for phenomena involving nucleon structure, nuclear structure, and relativistic heavy-ion collisions. (2) Symmetries and the connection of the quark-gluon description of nucleons and nuclei with the nucleon-meson degrees of freedom-parity nonconservation, time reversal invariance, chiral symmetry and charge symmetry, QCD sum rules. (3) The relation between nuclear physics and quantum chromodynamics-physics of color transparency, fundamental symmetries, physics of confinement and hadronic form factors, EMC effect. (4) Chirally invariant chromo-dielectric soliton model, many-nucleon system in models of QCD, flux tube dynamics, anti p-p to anti Λ-Λ and anti Λ-Σ collisions, isotopic effects in atomic parity nonconservation, quantum molecular dynamics. (5) Numerical work related to lattice QCD simulations, and analytical work related to model studies of hadronic phenomenology and the development and understanding of new methods

  11. Nuclear Physics Laboratory, University of Washington annual report, 1989

    International Nuclear Information System (INIS)

    1989-04-01

    This report discusses the following topics: astrophysics; giant resonances; heavy ion induced reactions; fundamental symmetries; nuclear reaction -- polarization; medium energy reactions; accelerator mass spectroscopy; research by outside users; van de Graaff and ion sources; computer systems; instrumentation; and booster linac

  12. Nuclear Physics Laboratory annual report, University of Washington April 1992

    International Nuclear Information System (INIS)

    1992-01-01

    This report contains short discusses on topics in the following areas: astrophysics; giant resonances and photonuclear reactions; nucleus-nucleus reactions; fundamental symmetries; accelerator mass spectrometry; medium energy nuclear physics; ultra-relativistic heavy ion collisions; cluster fusion; instrumentation; van de graaff accelerators and ion sources; and computer data acquisition systems

  13. [University of Washington Nuclear Physics Laboratory] annual report, 1991

    International Nuclear Information System (INIS)

    1991-04-01

    This report contains brief papers on the following topics: giant dipole resonances in excited nuclei; nucleus-nucleus reactions; astrophysics; polarization; fundamental symmetries and interactions; accelerator mass spectrometry; ultra-relativistic heavy ions; medium energy interactions; instrumentation; accelerators and ion sources; and computer systems

  14. Accelerator mass spectrometry at the University of Washington

    International Nuclear Information System (INIS)

    Farwell, G.W.; Schmidt, F.H.; Grootes, P.M.

    1981-01-01

    Our program is directed toward measurement of 10 Be and 14 C using the FN Tandem accelerator of the Nuclear Physics Laboratory. We began work in June 1977. Our progress and results up to August, 1979, were reported at the Tenth International Radiocarbon Conference. The present report covers chiefly our work since then. For 14 C, we are in the final stages of testing a new sample changer and alternator and are comparing three systems of normalizing the rare and abundant ion beams to give isotope ratios. We have successfully prepared graphitized carbon source samples from contemporary and other material; while the graphitized sources have given the largest carbon beams, we are exploring other possibilities, among which the use of C/Ag combinations appears very promising. For 10 Be, we have begun testing and measuring samples prepared from Antarctic and Peruvian snow and ice. In both the carbon and the beryllium programs various technical developments are in progress in addition to those reported here

  15. Nuclear Physics Laboratory annual report, University of Washington April 1992

    Energy Technology Data Exchange (ETDEWEB)

    1992-07-01

    This report contains short discusses on topics in the following areas: astrophysics; giant resonances and photonuclear reactions; nucleus-nucleus reactions; fundamental symmetries; accelerator mass spectrometry; medium energy nuclear physics; ultra-relativistic heavy ion collisions; cluster fusion; instrumentation; van de graaff accelerators and ion sources; and computer data acquisition systems. (LSP)

  16. Nuclear Physics Laboratory annual report, University of Washington April 1992

    Energy Technology Data Exchange (ETDEWEB)

    Cramer, John G.; Ramirez, Maria G.

    1992-01-01

    This report contains short discusses on topics in the following areas: astrophysics; giant resonances and photonuclear reactions; nucleus-nucleus reactions; fundamental symmetries; accelerator mass spectrometry; medium energy nuclear physics; ultra-relativistic heavy ion collisions; cluster fusion; instrumentation; van de graaff accelerators and ion sources; and computer data acquisition systems. (LSP)

  17. P3 microengine development at Washington State University

    International Nuclear Information System (INIS)

    Whalen, Scott; Apblett, Christopher Alan

    2004-01-01

    There is a pressing need for miniaturized power systems for a variety of applications requiring a long life in the field of operations. Such power systems are required to be capable of providing power for months to years of operation, which all but eliminates battery technologies and technologies that bring their own fuel systems (except for nuclear fuel systems, which have their own drawbacks) due to constraints of having the all of the chemical fuel necessary for the entire life of the operational run available at the starting point of the operation. Alternatively, harvesting energy directly from the local environment obviates this need for bringing along all of the fuel necessary for operation. Instead, locally available energy, either in the form of chemical, thermal, light, or motion can be harvested and converted into electrical energy for use in sensor applications. The work from this LDRD is focused on developing a thermal engine that can take scavenged thermal gradients and convert them into direct electrical energy. The converter system is a MEMS based external combustion engine that uses a modified Stirling cycle to generate mechanical work on a piezoelectric generator. This piezoelectric generator then produced an AC voltage and current that can be delivered into an external load. The MEMS engine works on the conversion of a two phase working fluid trapped between two deformable membranes. As heat is added to the system, the liquid working fluid is converted to a gas, which exerts pneumatic pressure on the membranes, expanding them outward. This outward expansion continues after the heat input is removed when the engine is operated at resonance, since the membrane is expanded further due to inertial forces. Finally, the engine cools and heat rejection is accomplished through the membranes, closing the thermodynamic cycle. A piezoelectric generator stack is deposited on one of the membranes, and this generator extracts the strain energy work from the membrane expansion and generates electrical work. The overall system is pulsed by an electrical heater to generate the input heat pulse. Currently, the system has a resonant frequency that is in the low kilohertz regime, but operations under a dynamic damping have demonstrated operation at resonance and the existence of an open mechanical cycle of heat addition, expansion, and heat rejection. Power generation of direct thermal-to-electrical conversion show a 1.45W, 6mJ heat pulse can generate a 0.8 (micro)W power output pulse, and continuous operation generates a sustained power output of 0.8 (micro)W at 240Hz. Future improvements in the device will allow active heat rejection, allowing resonance with external damping to improve the thermal to electrical power efficiency

  18. University of Washington Prostate Cancer Clinical Trials Consortium Application

    Science.gov (United States)

    2011-04-01

    OGX 427 Phase I), 08-005 (HE-3235), 08-015 (Dasatinib PET), 09-046 ( TOK -001), 10-060 (Phase I doc MLN8237), 11-081 (OGX 427 Phase II). Two of these...conference calls to discuss toxicity and efficacy of phase I agents [Montgomery- TOK -001(09-046) and HE-3235 (08-005), Higano-MLN8237 (10-060), Yu OGX-427...part by the repertoire of phase one agents [OGX-427 (07-008), TOK -001 (09-046), MLN-8237 (10-060), HE-3235 (08- 005), KX2-391 (039)] in our program (5

  19. Climate change vulnerability and adaptation in the North Cascades region, Washington

    Science.gov (United States)

    Crystal L. Raymond; David L. Peterson; Regina M. Rochefort

    2014-01-01

    The North Cascadia Adaptation Partnership (NCAP) is a science-management partnership consisting of the U.S. Department of Agriculture Forest Service Mount Baker-Snoqualmie and Okanogan-Wenatchee National Forests and Pacific Northwest Research Station; North Cascades National Park Complex; Mount Rainier National Park; and University of Washington Climate Impacts Group....

  20. University of California San Francisco (UCSF-2): Expression Analysis of Superior Cervical Ganglion from Backcrossed TH-MYCN Transgenic Mice | Office of Cancer Genomics

    Science.gov (United States)

    The CTD2 Center at University of California San Francisco (UCSF-2) used genetic analysis of the peripheral sympathetic nervous system to identify potential therapeutic targets in neuroblastoma. Read the abstract Experimental Approaches Read the detailed Experimental Approaches

  1. Report : public transportation in Washington State, 1984

    Science.gov (United States)

    1984-10-01

    This report is an update of the Public Transportation in Washington State publication, dated December 1981. In order to reflect the changes that have occurred since that time, this report contains the most current data obtainable. Chapter One of this...

  2. Willapa Bay, Washington Benthic Habitats 1995 Biotic

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — In June 1995, the Columbia River Estuary Study Taskforce (CREST) acquired 295 true color aerial photographs (1:12,000) of Willapa Bay, Washington, from the State of...

  3. Willapa Bay, Washington Benthic Habitats 1995 Geoform

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — In June 1995, the Columbia River Estuary Study Taskforce (CREST) acquired 295 true color aerial photographs (1:12,000) of Willapa Bay, Washington, from the State of...

  4. Willapa Bay, Washington Benthic Habitats 1995 Substrate

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — In June 1995, the Columbia River Estuary Study Taskforce (CREST) acquired 295 true color aerial photographs (1:12,000) of Willapa Bay, Washington, from the State of...

  5. Southwestern Washington 6 arc-second DEM

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The 6-second Southwest Washington Elevation Grid provides bathymetric data in ASCII raster format of 6-second resolution in geographic coordinates. This grid is...

  6. Timber resource statistics for southwest Washington.

    Science.gov (United States)

    Patricia M. Bassett; Daniel D. Oswald

    1981-01-01

    This report summarizes a 1978 timber-resource inventory of six counties in southwest Washington: Clark, Cowlitz, Lewis, Pacific, Skamania, and Wahkiakum. Detailed tables of forest area, timber volume, growth, mortality, and harvest are presented.

  7. Timber resource statistics for eastern Washington.

    Science.gov (United States)

    Patricia M. Bassett; Daniel D. Oswald

    1983-01-01

    This report summarizes a 1980 timber resource inventory of the 16 forested counties in Washington east of the crest of the Cascade Range. Detailed tables of forest area, timber volume, growth, mortality, and harvest are presented.

  8. NSA Diana Wueger Published in Washington Quarterly

    OpenAIRE

    Grant, Catherine L.

    2016-01-01

    National Security Affairs (NSA) News NSA Faculty Associate for Research Diana Wueger has recently had an article titled “India’s Nuclear-Armed Submarines: Deterrence or Danger?” published in the Washington Quarterly.

  9. Genomic research perspectives in Kazakhstan

    Directory of Open Access Journals (Sweden)

    Ainur Akilzhanova

    2014-01-01

    Full Text Available Introduction: Technological advancements rapidly propel the field of genome research. Advances in genetics and genomics such as the sequence of the human genome, the human haplotype map, open access databases, cheaper genotyping and chemical genomics, have transformed basic and translational biomedical research. Several projects in the field of genomic and personalized medicine have been conducted at the Center for Life Sciences in Nazarbayev University. The prioritized areas of research include: genomics of multifactorial diseases, cancer genomics, bioinformatics, genetics of infectious diseases and population genomics. At present, DNA-based risk assessment for common complex diseases, application of molecular signatures for cancer diagnosis and prognosis, genome-guided therapy, and dose selection of therapeutic drugs are the important issues in personalized medicine. Results: To further develop genomic and biomedical projects at Center for Life Sciences, the development of bioinformatics research and infrastructure and the establishment of new collaborations in the field are essential. Widespread use of genetic tools will allow the identification of diseases before the onset of clinical symptoms, the individualization of drug treatment, and could induce individual behavioral changes on the basis of calculated disease risk. However, many challenges remain for the successful translation of genomic knowledge and technologies into health advances, such as medicines and diagnostics. It is important to integrate research and education in the fields of genomics, personalized medicine, and bioinformatics, which will be possible with opening of the new Medical Faculty at Nazarbayev University. People in practice and training need to be educated about the key concepts of genomics and engaged so they can effectively apply their knowledge in a matter that will bring the era of genomic medicine to patient care. This requires the development of well

  10. Extreme genomes

    OpenAIRE

    DeLong, Edward F

    2000-01-01

    The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

  11. A Thousand Fly Genomes: An Expanded Drosophila Genome Nexus.

    Science.gov (United States)

    Lack, Justin B; Lange, Jeremy D; Tang, Alison D; Corbett-Detig, Russell B; Pool, John E

    2016-12-01

    The Drosophila Genome Nexus is a population genomic resource that provides D. melanogaster genomes from multiple sources. To facilitate comparisons across data sets, genomes are aligned using a common reference alignment pipeline which involves two rounds of mapping. Regions of residual heterozygosity, identity-by-descent, and recent population admixture are annotated to enable data filtering based on the user's needs. Here, we present a significant expansion of the Drosophila Genome Nexus, which brings the current data object to a total of 1,121 wild-derived genomes. New additions include 305 previously unpublished genomes from inbred lines representing six population samples in Egypt, Ethiopia, France, and South Africa, along with another 193 genomes added from recently-published data sets. We also provide an aligned D. simulans genome to facilitate divergence comparisons. This improved resource will broaden the range of population genomic questions that can addressed from multi-population allele frequencies and haplotypes in this model species. The larger set of genomes will also enhance the discovery of functionally relevant natural variation that exists within and between populations. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  12. Grass genomes

    OpenAIRE

    Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

    1998-01-01

    For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

  13. The UCSC Genome Browser Database: update 2006

    DEFF Research Database (Denmark)

    Hinrichs, A S; Karolchik, D; Baertsch, R

    2006-01-01

    The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, ...

  14. The UCSC genome browser database: update 2007

    DEFF Research Database (Denmark)

    Kuhn, R M; Karolchik, D; Zweig, A S

    2006-01-01

    The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up t...

  15. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  16. Evolution of small prokaryotic genomes

    Directory of Open Access Journals (Sweden)

    David José Martínez-Cano

    2015-01-01

    Full Text Available As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ~800 genes as well as endosymbiotic bacteria with as few as ~140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokaryotes have evolved diverse strategies for living with reduced gene sets inside a host-defined medium. These include utilization of host-encoded functions (some of them coded by genes acquired by gene transfer from the endosymbiont and/or other bacteria; metabolic complementation between co-symbionts; and forming consortiums with other bacteria within the host. Recent genome sequencing projects of intracellular mutualistic bacteria showed that previously believed universal evolutionary trends like reduced G+C content and conservation of genome synteny are not always present in highly reduced genomes. Finally, the simplified molecular machinery of some of these organisms with small genomes may be used to aid in the design of artificial minimal cells. Here we review recent genomic discoveries of the biology of prokaryotes endowed with small gene sets and discuss the evolutionary mechanisms that have been proposed to explain their peculiar nature.

  17. Better Jobs, Brighter Futures, a Stronger Washington. Washington's Community and Technical Colleges

    Science.gov (United States)

    Washington State Board for Community and Technical Colleges, 2015

    2015-01-01

    The world is changing rapidly. With changes in technology, demographics, and workforce trends, Washington needs colleges to not only keep pace, but lead the way. Washington's 34 community and technical colleges answer that call. The community and technical colleges have proven uniquely positioned to adapt to, embrace, and ignite change. Community…

  18. Emory University: MEDICI (Mining Essentiality Data to Identify Critical Interactions) for Cancer Drug Target Discovery and Development | Office of Cancer Genomics

    Science.gov (United States)

    The CTD2 Center at Emory University has developed a computational methodology to combine high-throughput knockdown data with known protein network topologies to infer the importance of protein-protein interactions (PPIs) for the survival of cancer cells.  Applying these data to the Achilles shRNA results, the CCLE cell line characterizations, and known and newly identified PPIs provides novel insights for potential new drug targets for cancer therapies and identifies important PPI hubs.

  19. RadGenomics project

    Energy Technology Data Exchange (ETDEWEB)

    Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu [National Inst. of Radiological Sciences, Chiba (Japan). Frontier Research Center] [and others

    2002-06-01

    Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

  20. RadGenomics project

    International Nuclear Information System (INIS)

    Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu

    2002-01-01

    Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

  1. Working Together: Wellness and Academic Achievement at Tribal Colleges and Universities

    Science.gov (United States)

    Duran, Bonnie; Magarati, Maya; Parker, Myra; Egashira, Leo; Kipp, Billie Jo

    2013-01-01

    This article describes the activities of the Indigenous Wellness Research Institute (IWRI) at the University of Washington, Washington State, in collaborating with tribal colleges and universities (TCUs) to examine alcohol, drug, and mental health issues among Native students. The authors provide first steps for the development of culturally…

  2. Family genome browser: visualizing genomes with pedigree information.

    Science.gov (United States)

    Juan, Liran; Liu, Yongzhuang; Wang, Yongtian; Teng, Mingxiang; Zang, Tianyi; Wang, Yadong

    2015-07-15

    Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically. The FGB is available at http://mlg.hit.edu.cn/FGB/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. MSeqDR mvTool: A mitochondrial DNA Web and API resource for comprehensive variant annotation, universal nomenclature collation, and reference genome conversion.

    Science.gov (United States)

    Shen, Lishuang; Attimonelli, Marcella; Bai, Renkui; Lott, Marie T; Wallace, Douglas C; Falk, Marni J; Gai, Xiaowu

    2018-06-01

    Accurate mitochondrial DNA (mtDNA) variant annotation is essential for the clinical diagnosis of diverse human diseases. Substantial challenges to this process include the inconsistency in mtDNA nomenclatures, the existence of multiple reference genomes, and a lack of reference population frequency data. Clinicians need a simple bioinformatics tool that is user-friendly, and bioinformaticians need a powerful informatics resource for programmatic usage. Here, we report the development and functionality of the MSeqDR mtDNA Variant Tool set (mvTool), a one-stop mtDNA variant annotation and analysis Web service. mvTool is built upon the MSeqDR infrastructure (https://mseqdr.org), with contributions of expert curated data from MITOMAP (https://www.mitomap.org) and HmtDB (https://www.hmtdb.uniba.it/hmdb). mvTool supports all mtDNA nomenclatures, converts variants to standard rCRS- and HGVS-based nomenclatures, and annotates novel mtDNA variants. Besides generic annotations from dbNSFP and Variant Effect Predictor (VEP), mvTool provides allele frequencies in more than 47,000 germline mitogenomes, and disease and pathogenicity classifications from MSeqDR, Mitomap, HmtDB and ClinVar (Landrum et al., 2013). mvTools also provides mtDNA somatic variants annotations. "mvTool API" is implemented for programmatic access using inputs in VCF, HGVS, or classical mtDNA variant nomenclatures. The results are reported as hyperlinked html tables, JSON, Excel, and VCF formats. MSeqDR mvTool is freely accessible at https://mseqdr.org/mvtool.php. © 2018 Wiley Periodicals, Inc.

  4. Washington Schools Learn from Value Engineering.

    Science.gov (United States)

    Doleae, Michael L.; Childs, Harvey C.

    1983-01-01

    Results of two value engineering studies have shown that a review early in the design process can help save costs in school construction, maintenance, operation, and replacement. The value engineering concepts and technical manual are being presented throughout the state of Washington. (MLF)

  5. Natural phenomena hazards, Hanford Site, Washington

    International Nuclear Information System (INIS)

    Conrads, T.J.

    1998-01-01

    This document presents the natural phenomena hazard loads for use in implementing DOE Order 5480.28, Natural Phenomena Hazards Mitigation, and supports development of double-shell tank systems specifications at the Hanford Site in south-central Washington State. The natural phenomena covered are seismic, flood, wind, volcanic ash, lightning, snow, temperature, solar radiation, suspended sediment, and relative humidity

  6. 40 CFR 81.348 - Washington.

    Science.gov (United States)

    2010-07-01

    ... 5/14/01 Attainment The City of Kent and a portion of the Green River valley bounded on the east and... Type Seattle-Tacoma Area: Seattle-Tacoma Urban Area (as defined by the Washington Department of Transportation urban area maps) King County (part) Attainment Pierce County (part) Attainment Snohomish County...

  7. Changing Housing Patterns in Metropolitan Washington

    Science.gov (United States)

    Grier, George; Grier, Eunice

    1975-01-01

    This testimony, before a public hearing of the New York City Commission on Human Rights in May 1974, summarizes extensive studies of changing minority residential patterns in metropolitan Washington and less extensive studies of other groups; the prospects for future desegregation and for using the growing economic potential of minority families…

  8. Washington Irving and the American Indian.

    Science.gov (United States)

    Littlefield, Daniel F., Jr.

    1979-01-01

    Some modern scholars feel that Washington Irving vacillated between romanticism and realism in his literary treatment of the American Indian. However, a study of all his works dealing with Indians, placed in context with his non-Indian works, reveals that his attitude towards Indians was intelligent and enlightened for his time. (CM)

  9. Doctors of Osteopathy Licensed in Washington.

    Science.gov (United States)

    Senters, Jo

    Based on information gathered by the Health Manpower Project through a survey cosponsored with the Washington Osteopathic Medical Association, this report begins with a statement of philosophy of osteopathic medicine and proceeds to comment on where such professional education is available. Remarks on the type of educational background of the…

  10. Washington Public Libraries Online: Collaborating in Cyberspace.

    Science.gov (United States)

    Wildin, Nancy

    1997-01-01

    Discussion of public libraries, the Internet, and the World Wide Web focuses on development of a Web site in Washington. Highlights include access to the Internet through online public access catalogs; partnerships between various types of libraries; hardware and software; HTML training; content design; graphics design; marketing; evaluation; and…

  11. Recidivism of Supermax Prisoners in Washington State

    Science.gov (United States)

    Lovell, David; Johnson, L. Clark; Cain, Kevin C.

    2007-01-01

    This study of recidivism among Washington supermax prisoners used a retrospective matched control design, matching supermax prisoners one-to-one with nonsupermax prisoners on mental illness status and up to eight recidivism predictors. Supermax prisoners committed new felonies at a higher rate than nonsupermax controls, but the difference was not…

  12. Timber resource statistics for eastern Washington, 1995.

    Science.gov (United States)

    Neil McKay; Patricia M. Bassett; Colin D. MacLean

    1995-01-01

    This report summarizes a 1990-91 timber resource inventory of Washington east of the crest of the Cascade Range. The inventory was conducted on all private and public lands except National Forests. Timber resource statistics from National Forest inventories also are presented. Detailed tables provide estimates of forest area, timber volume, growth, mortality, and...

  13. Timber resource statistics for western Washington.

    Science.gov (United States)

    Coffin D. MacLean; Patricia M. Bassett; Glenn. Yeary

    1992-01-01

    This report summarizes a 1988-90 timber resource inventory of 19 counties in western Washington: Clallam, Clark, Cowlitz, Grays Harbor, Island, Jefferson, King, Kitsap, Lewis, Mason, Pacific, Pierce, San Juan, Skagit, Skamania, Snohomish, Thurston, Wahkiakum, and Whatcom. Detailed tables of forest area, timber volume, growth, mortality, and harvest are presented.

  14. Washington (Wash) C. Winn: In Memoriam

    Centers for Disease Control (CDC) Podcasts

    2012-03-08

    Dr. Mike Miller and Dr. David Walker dicuss the career and life of noted clinical biologist, Dr. Washington C. Winn Jr.  Created: 3/8/2012 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 3/12/2012.

  15. Drivers' use of marijuana in Washington state : traffic tech.

    Science.gov (United States)

    2016-08-01

    In July 2014, Washington State allowed legal sales of : recreational marijuana. Working with the Washington : Traffic Safety Commission, NHTSA assisted the State in : conducting a roadside study to examine the prevalence : of marijuana use before and...

  16. An assessment of interstate safety investment properties in Washington state.

    Science.gov (United States)

    2014-12-01

    The Washington State Department of Transportation (WSDOT) commissioned the current study, targeting the entire interstate : mainline network in Washington State, to provide strategic direction to multi-biennial investment interstate locations that of...

  17. Trends and determinants of cycling in the Washington, DC region.

    Science.gov (United States)

    2011-01-01

    This report analyzes cycling trends, policies, and commuting in the Washington, DC area. The analysis is divided into two parts. : Part 1 focuses on cycling trends and policies in Washington (DC), Alexandria (VA), Arlington County (VA), Fairfax Count...

  18. Genome Imprinting

    Indian Academy of Sciences (India)

    the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

  19. Baculovirus Genomics

    NARCIS (Netherlands)

    Oers, van M.M.; Vlak, J.M.

    2007-01-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

  20. Genomic Testing

    Science.gov (United States)

    ... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

  1. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

  2. 76 FR 16323 - Irish Potatoes Grown in Washington; Continuance Referendum

    Science.gov (United States)

    2011-03-23

    ...; FV11-946-1 CR] Irish Potatoes Grown in Washington; Continuance Referendum AGENCY: Agricultural... conducted among eligible Washington potato growers to determine whether they favor continuance of the marketing order regulating the handling of Irish potatoes grown in Washington. DATES: The referendum will be...

  3. 76 FR 377 - Land Acquisitions; Cowlitz Indian Tribe of Washington

    Science.gov (United States)

    2011-01-04

    ... State of Washington by Auditor's File Nos. G 450664 and G 147358. Parcel II That portion of the... thereof acquired by the State of Washington by deed recorded under Auditor's File Nos. G 140380 and D... recorded under Auditor's File No. F 38759, records of Clark County, Washington, described as follows...

  4. 77 FR 25590 - Drawbridge Operation Regulation; Lake Washington Ship Canal, Seattle, WA

    Science.gov (United States)

    2012-05-01

    ...The Coast Guard has issued a temporary deviation from the operating schedule that governs University Bridge across the Lake Washington Ship Canal, mile 4.3, at Seattle, WA. This deviation is necessary to accommodate the Beat the Bridge charity foot race scheduled for Sunday, May 20, 2012. This deviation allows the bridge to remain in the closed position to allow safe movement of event participants.

  5. Insights into structural variations and genome rearrangements in prokaryotic genomes.

    Science.gov (United States)

    Periwal, Vinita; Scaria, Vinod

    2015-01-01

    Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversions, deletions and translocations have been largely studied in context of genetic diseases in eukaryotes. However, recent studies demonstrate that genome rearrangements can also have profound impact on prokaryotic genomes, leading to altered cell phenotype. In contrast to single-nucleotide variations, SVs provide a much deeper insight into organization of bacterial genomes at a much better resolution. SVs can confer change in gene copy number, creation of new genes, altered gene expression and many other functional consequences. High-throughput technologies have now made it possible to explore SVs at a much refined resolution in bacterial genomes. Through this review, we aim to highlight the importance of the less explored field of SVs in prokaryotic genomes and their impact. We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  6. Low-temperature geothermal resources of Washington

    Energy Technology Data Exchange (ETDEWEB)

    Schuster, J.E. [Washington State Dept. of Natural Resources, Olympia, WA (United States). Div. of Geology and Earth Resources; Bloomquist, R.G. [Washington State Energy Office, Olympia, WA (United States)

    1994-06-01

    This report presents information on the location, physical characteristics, and water chemistry of low-temperature geothermal resources in Washington. The database includes 941 thermal (>20C or 68F) wells, 34 thermal springs, lakes, and fumaroles, and 238 chemical analyses. Most thermal springs occur in the Cascade Range, and many are associated with stratovolcanoes. In contrast, 97 percent of thermal wells are located in the Columbia Basin of southeastern Washington. Some 83.5 percent are located in Adams, Benton, Franklin, Grant, Walla Walla, and Yakima Counties. Yakima County, with 259 thermal wells, has the most. Thermal wells do not seem to owe their origin to local sources of heat, such as cooling magma in the Earth`s upper crust, but to moderate to deep circulation of ground water in extensive aquifers of the Columbia River Basalt Group and interflow sedimentary deposits, under the influence of a moderately elevated (41C/km) average geothermal gradient.

  7. Fuel management at Washington State Ferries

    International Nuclear Information System (INIS)

    Brodeur, P.; Olds, J.

    2008-01-01

    This presentation discussed Washington State Ferry (WSF) operations and provided details of a biodiesel research and demonstration project. Washington has the largest ferry system in the United States, with a total of 28 vessels that operate on 10 routes through 20 terminals. Routes vary by transit times, navigational challenges, and the proximity to population centres. WSF fuel and emissions management initiatives include exhaust emission studies, clean fuel initiatives, machinery upgrades, fuel conservation initiatives, and biodiesel testing. The organization is also using waste heat recovery and a positive restraint system. The WSF biodiesel pilot program was conducted using soy-derived fuels with a purifier disk stack. The program is in agreement with recent legislation requiring that 2 per cent of annual diesel fuel sales are from biodiesel fuels, and state legislation requiring that state agencies use a minimum of 20 per cent biodiesel blends in diesel-powered vessels and vehicles. Details of project partnerships were included. tabs., figs

  8. Discordance in selected designee for return of genomic findings in the event of participant death and estate executor.

    Science.gov (United States)

    Goodman, Jessie L; Amendola, Laura M; Horike-Pyne, Martha; Trinidad, Susan B; Fullerton, Stephanie M; Burke, Wylie; Jarvik, Gail P

    2017-03-01

    Legal and ethical questions arise regarding disseminating genetic research results to family members in the event of a research participant's death; failure to return or return to legal next of kin or estate executor may not reflect participant desires. We sought to determine participant preferences for whether and to whom they would like their data released in the case of their death prior to receiving genomic results, focusing on whether the person selected was also their estate executor. The University of Washington NEXT Medicine Study of the Clinical Sequencing Exploratory Research program previously reported participant preferences regarding designating an individual to receive genomic results in the event of death, including whether they want results shared, and if so, with what person. Participants were also asked whether this designee is executor of their will or estate. To date, 61 individuals were asked about the concordance of their study designee and legal representative: 42 (69%) reported having a will or estate plan and of these, 14 (33%) chose someone other than their executor to receive their results. For the 14 who chose someone other than their estate executor to receive genetic results, 12 (86%) chose a family member, typically a biological relative, as their designee. Those with a different genomic designee than their executor were less likely to be partnered ( P  = 0.0024). For those partnered participants without an estate plan, spouses were not always chosen for return of genomic results. For one-third of our participants, the individual deemed most appropriate by the participant to receive their genomic results was not the executor. In the absence of an explicit designation, HIPAA may prohibit access to genomic results to persons other than the executor; hence asking for designation at the time of study enrollment (or initiation of clinical testing) is important.

  9. Snag Dynamics in Western Oregon and Washington

    OpenAIRE

    Ohmann, Janet L

    2002-01-01

    To achieve desired amounts and characteristics of snags and down wood, managers require analytical tools for projecting changes in dead wood over time, and for comparing those changes to management objectives such as providing dead wood for wildlife and ecosystem processes. The following information on rates of snag recruitment, decay, and fall across forests of western Oregon and Washington may be useful in planning for future levels of dead wood. Eventually the information will be incorpora...

  10. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  11. Theory of microbial genome evolution

    Science.gov (United States)

    Koonin, Eugene

    Bacteria and archaea have small genomes tightly packed with protein-coding genes. This compactness is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. By fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. Thus, the number of genes in prokaryotic genomes seems to reflect the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias. New genes acquired by microbial genomes, on average, appear to be adaptive. Evolution of bacterial and archaeal genomes involves extensive horizontal gene transfer and gene loss. Many microbes have open pangenomes, where each newly sequenced genome contains more than 10% `ORFans', genes without detectable homologues in other species. A simple, steady-state evolutionary model reveals two sharply distinct classes of microbial genes, one of which (ORFans) is characterized by effectively instantaneous gene replacement, whereas the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of at least a billion distinct genes in the prokaryotic genomic universe.

  12. Physical data collected from Seaglider SG030 during Cascadia September 2008 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2008-09-15 to 2008-09-19 (NCEI Accession 0156193)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  13. Physical data collected from Seaglider SG189 during Cuddy Survey in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2014-01-16 to 2014-04-27 (NCEI Accession 0162344)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  14. Physical data collected from Seaglider SG119 during WA Coast September 2008 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2008-09-15 to 2009-01-07 (NCEI Accession 0156194)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  15. Physical data collected from Seaglider SG194 during Cuddy Survey in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2013-10-25 to 2014-05-10 (NCEI Accession 0162349)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  16. Physical data collected from Seaglider SG005 during WA Coast June 2005 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2005-06-08 to 2005-11-16 (NCEI Accession 0155972)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  17. Physical data collected from Seaglider SG014 during WA Coast April 2006 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2006-04-24 to 2006-11-09 (NCEI Accession 0156076)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  18. Physical data collected from Seaglider SG012 during WA Coast November 2005 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2005-11-16 to 2006-03-04 (NCEI Accession 0156521)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  19. Physical data collected from Seaglider SG005 during WA Coast August 2004 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2004-08-30 to 2004-12-23 (NCEI Accession 0155941)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  20. Physical data collected from Seaglider SG101 during WA Coast, April 2008 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2008-04-01 to 2008-07-31 (NCEI Accession 0156172)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  1. Physical data collected from Seaglider SG195 during Cuddy Survey in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2013-10-25 to 2014-02-22 (NCEI Accession 0162357)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  2. Physical data collected from Seaglider SG030 during Cascadia 17 January 2008 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2008-01-17 to 2008-01-22 (NCEI Accession 0156178)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

  3. The Small Nuclear Genomes of Selaginella Are Associated with a Low Rate of Genome Size Evolution.

    Science.gov (United States)

    Baniaga, Anthony E; Arrigo, Nils; Barker, Michael S

    2016-06-03

    The haploid nuclear genome size (1C DNA) of vascular land plants varies over several orders of magnitude. Much of this observed diversity in genome size is due to the proliferation and deletion of transposable elements. To date, all vascular land plant lineages with extremely small nuclear genomes represent recently derived states, having ancestors with much larger genome sizes. The Selaginellaceae represent an ancient lineage with extremely small genomes. It is unclear how small nuclear genomes evolved in Selaginella We compared the rates of nuclear genome size evolution in Selaginella and major vascular plant clades in a comparative phylogenetic framework. For the analyses, we collected 29 new flow cytometry estimates of haploid genome size in Selaginella to augment publicly available data. Selaginella possess some of the smallest known haploid nuclear genome sizes, as well as the lowest rate of genome size evolution observed across all vascular land plants included in our analyses. Additionally, our analyses provide strong support for a history of haploid nuclear genome size stasis in Selaginella Our results indicate that Selaginella, similar to other early diverging lineages of vascular land plants, has relatively low rates of genome size evolution. Further, our analyses highlight that a rapid transition to a small genome size is only one route to an extremely small genome. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  4. The UCSC Genome Browser Database: 2008 update

    DEFF Research Database (Denmark)

    Karolchik, D; Kuhn, R M; Baertsch, R

    2007-01-01

    The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrat...

  5. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  6. Brief research report: sociodemographic factors associated with HIV status among African American women in Washington, DC

    Directory of Open Access Journals (Sweden)

    Perkins EL

    2013-09-01

    Full Text Available Emory L Perkins,1 Dexter R Voisin,2 Kesslyn A Brade Stennis1 1Department of Social Work, Bowie State University, Bowie, MD, USA; 2School of Social Service Administration, University of Chicago, Chicago, IL, USA Introduction: African American women living in Washington, DC have one of the highest Human immunodeficiency virus (HIV incidence rates in the US. However, this population has been understudied, especially as it relates to factors associated with HIV status. Methods: This cross-sectional study examined sociodemographic factors that were associated with having a negative or positive HIV status among a sample of 115 African American women between the ages of 24 and 44 years. We assessed such factors as age, education, sexual orientation, household income, sources of income, number of children, length of residency tenure in Washington, DC, and level of HIV-prevention knowledge. Results: Among the overall sample, 53 women self-identified as HIV-positive and 62 as HIV-negative. Compared to their HIV-negative counterparts, women who reported being HIV-positive were less educated, had lower household income, and had longer residency tenure in Washington, DC. There were no differences in HIV knowledge between HIV-positive and -negative study participants. Conclusion: These findings may provide important directions for targeting specific subpopulations of African Americans for HIV-prevention/intervention programs. Keywords: HIV status, African American women, sociodemographic factors

  7. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  8. Alternative Fuels for Washington's School Buses: A Report to the Washington State Legislature.

    Science.gov (United States)

    Lyons, John Kim; McCoy, Gilbert A.

    This document presents findings of a study that evaluated the use of both propane and compressed natural gas as alternative fuels for Washington State school buses. It discusses air quality improvement actions by state- and federal-level regulators and summarizes vehicle design, development, and commercialization activities by all major engine,…

  9. Comparative Genomics

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:

  10. Greenhouse gas mitigation options for Washington State

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, N.

    1996-04-01

    President Clinton, in 1993, established a goal for the United States to return emissions of greenhouse gases to 1990 levels by the year 2000. One effort established to help meet this goal was a three part Environmental Protection Agency state grant program. Washington State completed part one of this program with the release of the 1990 greenhouse gas emissions inventory and 2010 projected inventory. This document completes part two by detailing alternative greenhouse gas mitigation options. In part three of the program EPA, working in partnership with the States, may help fund innovative greenhouse gas reduction strategies. The greenhouse gas control options analyzed in this report have a wide range of greenhouse gas reductions, costs, and implementation requirements. In order to select and implement a prudent mix of control strategies, policy makers need to have some notion of the potential change in climate, the consequences of that change and the uncertainties contained therein. By understanding the risks of climate change, policy makers can better balance the use of scarce public resources for concerns that are immediate and present against those that affect future generations. Therefore, prior to analyzing alternative greenhouse gas control measures, this report briefly describes the phenomenon and uncertainties of global climate change, and then projects the likely consequences for Washington state.

  11. RPAN: rice pan-genome browser for ∼3000 rice genomes.

    Science.gov (United States)

    Sun, Chen; Hu, Zhiqiang; Zheng, Tianqing; Lu, Kuangchen; Zhao, Yue; Wang, Wensheng; Shi, Jianxin; Wang, Chunchao; Lu, Jinyuan; Zhang, Dabing; Li, Zhikang; Wei, Chaochun

    2017-01-25

    A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Personal genomics services: whose genomes?

    Science.gov (United States)

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

  13. 77 FR 37317 - Drawbridge Operation Regulation; Lake Washington, Seattle, WA

    Science.gov (United States)

    2012-06-21

    ..., 2012. The deviation allows the floating draw span of the SR 520 Lake Washington Bridge to remain in the... schedule that governs the State Route 520 (SR 520) Bridge across Lake Washington at Seattle, WA. This... allows the bridge to remain in the closed position to allow safe movement of event participants. DATES...

  14. To Be a Slave: The Boyhood of Booker T. Washington.

    Science.gov (United States)

    National Park Service (Dept. of Interior), Washington, DC.

    The Booker T. Washington National Monument preserves and protects the birth site and childhood home of Booker T. Washington, while interpreting his life experiences and significance in U.S. history as the most powerful African American between 1895 and 1915. The park provides a resource for public education and a focal point for continuing…

  15. Educator Supply and Demand in Washington State. 2004 Report

    Science.gov (United States)

    Lashway, Larry; Maloney, Rick; Hathaway, Randy; Bryant, B. J.

    2005-01-01

    This report describes the findings of the third Educator Supply and Demand Research study in the State of Washington. The intent of these Washington studies is to provide data to inform and shape decisions and activities in the following ways: (1) Provide useful information for educational policymakers, including the legislature, the State Board…

  16. Expanding Access and Opportunity: The Washington State Achievers Program

    Science.gov (United States)

    Ramsey, Jennifer; Gorgol, Laura

    2010-01-01

    In 2001, the Bill & Melinda Gates Foundation launched a 10-year, multi-million dollar initiative, the Washington State Achievers Program (WSA), to increase opportunities for low-income students to attend postsecondary institutions in Washington State. The Bill & Melinda Gates Foundation granted funds to the College Success Foundation…

  17. Expanding Access and Opportunity: The Washington State Achievers Scholarship

    Science.gov (United States)

    O'Brien, Colleen

    2011-01-01

    In 2001, the Bill & Melinda Gates Foundation launched the multi-year, multi-million dollar Washington State Achievers Scholarship program. Concerned about disparities in college participation for low-income students in the state of Washington versus their wealthier peers, the Gates Foundation partnered with the College Success Foundation…

  18. 75 FR 71139 - Land Acquisitions; Puyallup Tribe of Washington

    Science.gov (United States)

    2010-11-22

    ... Auditor, in Pierce County, Washington. Except that portion of Lot 3 conveyed to the State of Washington by Deeds recorded under Auditor's file number 689865 and 689858. Together with the East half of the... amendment of Short Plat Nos. 8502210395 and 8403080186, filed with the Pierce County Auditor, in Pierce...

  19. Are there laws of genome evolution?

    Directory of Open Access Journals (Sweden)

    Eugene V Koonin

    2011-08-01

    Full Text Available Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the evolutionary rates of orthologous genes; the power law-like distributions of paralogous family size and node degree in various biological networks; the negative correlation between a gene's sequence evolution rate and expression level; and differential scaling of functional classes of genes with genome size. The universals of genome evolution can be accounted for by simple mathematical models similar to those used in statistical physics, such as the birth-death-innovation model. These models do not explicitly incorporate selection; therefore, the observed universal regularities do not appear to be shaped by selection but rather are emergent properties of gene ensembles. Although a complete physical theory of evolutionary biology is inconceivable, the universals of genome evolution might qualify as "laws of evolutionary genomics" in the same sense "law" is understood in modern physics.

  20. The Saccharomyces Genome Database Variant Viewer.

    Science.gov (United States)

    Sheppard, Travis K; Hitz, Benjamin C; Engel, Stacia R; Song, Giltae; Balakrishnan, Rama; Binkley, Gail; Costanzo, Maria C; Dalusag, Kyla S; Demeter, Janos; Hellerstedt, Sage T; Karra, Kalpana; Nash, Robert S; Paskov, Kelley M; Skrzypek, Marek S; Weng, Shuai; Wong, Edith D; Cherry, J Michael

    2016-01-04

    The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. In recent years, we have moved toward increased representation of sequence variation and allelic differences within S. cerevisiae. The publication of numerous additional genomes has motivated the creation of new tools for their annotation and analysis. Here we present the Variant Viewer: a dynamic open-source web application for the visualization of genomic and proteomic differences. Multiple sequence alignments have been constructed across high quality genome sequences from 11 different S. cerevisiae strains and stored in the SGD. The alignments and summaries are encoded in JSON and used to create a two-tiered dynamic view of the budding yeast pan-genome, available at http://www.yeastgenome.org/variant-viewer. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

  2. Integrated solid waste management of Seattle, Washington

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-11-01

    The subject document reports the results of an in-depth investigation of the fiscal year 1992 cost of the City of Seattle, Washington, integrated municipal solid waste management (IMSWM) system, the energy consumed to operate the system, and the environmental performance requirements for each of the system`s waste-processing and disposal facilities. Actual data from records kept by participants is reported in this document. Every effort was made to minimize the use of assumptions, and no attempt is made to interpret the data reported. Analytical approaches are documented so that interested analysts may perform manipulation or further analysis of the data. As such, the report is a reference document for MSW management professionals who are interested in the actual costs and energy consumption for a one-year period, of an operating IMSWM systems.

  3. Nuclear terrorism: after the Washington summit

    International Nuclear Information System (INIS)

    Hautecouverture, Benjamin

    2016-01-01

    In this note, the author comments the issues addressed by the 2016 Nuclear Safety Summit (NSS) of Washington, and the content of its final statement. He notices that the scope of addressed topics has evolved since the first summits (issues related to highly enriched uranium and to plutonium), that not only technological but also political and diplomatic issues are taken into account, and that GNOs are always more involved. The author briefly comments some aspects of the content of the final statement: threat of nuclear terrorism, improvement of nuclear safety since 2010, recall of the three main pillars of the non proliferation Treaty (non proliferation, disarmament, specific uses of nuclear energy), implementation of nuclear safety under at the own responsibility and duty of countries possessing nuclear materials. Finally, the author discusses how the NSS process will go on, and evokes remaining questions regarding the existence of an actual international constraining regime, and financial and functional issues

  4. Water resources of King County, Washington

    Science.gov (United States)

    Richardson, Donald; Bingham, J.W.; Madison, R.J.; Williams, R.

    1968-01-01

    Although the total supply of water in King County is large, water problems are inevitable because of the large and rapidly expanding population. The county contains a third of the 3 million people in Washington, most of the population being concentrated in the Seattle metropolitan area. King County includes parts of two major physiographic features: the western area is part of the Puget Sound Lowland, and the eastern area is part of the Cascade Range. In these two areas, the terrain, weather, and natural resources (including water) contrast markedly. Average annual precipitation in the county is about 80 inches, ranging from about 30 inches near Puget Sound to more than 150 inches in parts of the Cascades. Annual evapotranspiration is estimated to range from 15 to 24 inches. Average annual runoff ranges from about 15 inches in the lowlands to more than 100 inches in the mountains. Most of the streamflow is in the major basins of the county--the Green-Duwamish, Lake Washington, and Snoqualmie basins. The largest of these is the Snoqualmie River basin (693 square miles), where average annual runoff during the period 1931-60 was about 79 inches. During the same period, annual runoff in the Lake Washington basin ( 607 square miles) averaged about 32 inches, and in the Green-Duwamish River basin (483 square miles), about 46 inches. Seasonal runoff is generally characterized by several high-flow periods in the winter, medium flows in the spring, and sustained low flows in the summer and fall. When floods occur in the county they come almost exclusively between October and March. The threat of flood damage is greatest on the flood plaits of the larger rivers, but in the Green-Duwamish Valley the threat was greatly reduced with the completion of Howard A. Hanson Dam in 1962. In the Snoqualmie River basin, where no such dam exists, the potential damage from a major flood increases each year as additional land is developed in the Snoqualmie Valley. 0nly moderate amounts of

  5. Space Radar Image of Wenatchee, Washington

    Science.gov (United States)

    1994-01-01

    This spaceborne radar image shows a segment of the Columbia River as it passes through the area of Wenatchee, Washington, about 220 kilometers (136 miles) east of Seattle. The Wenatchee Mountains, part of the Cascade Range, are shown in green at the lower left of the image. The Cascades create a 'rain shadow' for the region, limiting rainfall east of the range to less than 26 centimeters (10 inches) per year. The radar's ability to see different types of vegetation is highlighted in the contrast between the pine forests, that appear in green and the dry valley plain that shows up as dark purple. The cities of Wenatchee and East Wenatchee are the grid-like areas straddling the Columbia River in the left center of the image. With a population of about 60,000, the region produces about half of Washington state's lucrative apple crop. Several orchard areas appear as green rectangular patches to the right of the river in the lower right center. Radar images such as these can be used to monitor land use patterns in areas such as Wenatchee, that have diverse and rapidly changing urban, agricultural and wild land pressures. This image was acquired by Spaceborne Imaging Radar-C/X-Band Synthetic Aperture Radar (SIR-C/X-SAR) onboard the space shuttle Endeavour on October 10, 1994. The image is 38 kilometers by 45 kilometers (24 miles by 30 miles) and is centered at 47.3 degrees North latitude, 120.1 degrees West longitude. North is toward the upper left. The colors are assigned to different radar frequencies and polarizations of the radar as follows: red is L-band, horizontally transmitted and received; green is L-band, horizontally transmitted, vertically received; and blue is C-band, horizontally transmitted, vertically received. SIR-C/X-SAR, a joint mission of the German, Italian, and United States space agencies, is part of NASA's Mission to Planet Earth.

  6. Metro de Washington EE.UU.

    Directory of Open Access Journals (Sweden)

    Weese, Harry

    1979-09-01

    Full Text Available This article describes the works involved in the first stage of the Washington Underground (Subway system which was begun in 1969 and scheduled for completion in 1983 and is the most modern metropolitan railway in North America. Lines have double track and will carry three million passengers daily. Different construction methods have been used throughout: tunnel formed try digging a trench then roofed and covered, excavated tunnel and elevated structures. Stations features answer to the strictest demands, provided with closed circuit television, air conditioning, noise dampening Systems, special access ways, fire protection Systems and automatic traffic control. Special attention is given to the two bridges over the Pentagon and over the Anacostia, pointing out their differences and the elevated structure at the National Airport.

    Se describen en este articulo los trabajos de la primera fase del Metro de Washington que, iniciado en el año 1969 será, a su terminación en el año 1983, el más moderno sistema de ferrocarril metropolitano de Norte América. Es de doble carril y servirá para tres millones de usuarios. Se han empleado distintos sistemas de obra en su realización: túnel artificial realizado mediante una zanja que después se cubre; túnel perforado, y estructuras aéreas. Las características de las estaciones responden a las mayores exigencias, pues tienen circuito cerrado de televisión, aire acondicionado, sistemas para atenuar el ruido, accesos especiales, sistema de protección contra el fuego y control automático del Metro. Se estudian de un modo particular: los dos puentes sobre el Pentágono y el Anacostia, señalando sus diferencias y la estructura aérea del Aeropuerto Nacional.

  7. A web-based decision support system to enhance IPM programs in Washington tree fruit.

    Science.gov (United States)

    Jones, Vincent P; Brunner, Jay F; Grove, Gary G; Petit, Brad; Tangren, Gerald V; Jones, Wendy E

    2010-06-01

    Integrated pest management (IPM) decision-making has become more information intensive in Washington State tree crops in response to changes in pesticide availability, the development of new control tactics (such as mating disruption) and the development of new information on pest and natural enemy biology. The time-sensitive nature of the information means that growers must have constant access to a single source of verified information to guide management decisions. The authors developed a decision support system for Washington tree fruit growers that integrates environmental data [140 Washington State University (WSU) stations plus weather forecasts from NOAA], model predictions (ten insects, four diseases and a horticultural model), management recommendations triggered by model status and a pesticide database that provides information on non-target impacts on other pests and natural enemies. A user survey in 2008 found that the user base was providing recommendations for most of the orchards and acreage in the state, and that users estimated the value at $ 16 million per year. The design of the system facilitates education on a range of time-sensitive topics and will make it possible easily to incorporate other models, new management recommendations or information from new sensors as they are developed.

  8. LOW-ENERGY NUCLEAR PHYSICS NATIONAL HPC INITIATIVE: BUILDING A UNIVERSAL NUCLEAR ENERGY DENSITY FUNCTIONAL (UNEDF)

    Energy Technology Data Exchange (ETDEWEB)

    Bulgac, A

    2013-03-27

    This document is a summary of the physics research carried out by the University of Washington centered group. Attached are reports for the previous years as well as the full exit report of the entire UNEDF collaboration.

  9. Population Genomics of Paramecium Species.

    Science.gov (United States)

    Johri, Parul; Krenek, Sascha; Marinov, Georgi K; Doak, Thomas G; Berendonk, Thomas U; Lynch, Michael

    2017-05-01

    Population-genomic analyses are essential to understanding factors shaping genomic variation and lineage-specific sequence constraints. The dearth of such analyses for unicellular eukaryotes prompted us to assess genomic variation in Paramecium, one of the most well-studied ciliate genera. The Paramecium aurelia complex consists of ∼15 morphologically indistinguishable species that diverged subsequent to two rounds of whole-genome duplications (WGDs, as long as 320 MYA) and possess extremely streamlined genomes. We examine patterns of both nuclear and mitochondrial polymorphism, by sequencing whole genomes of 10-13 worldwide isolates of each of three species belonging to the P. aurelia complex: P. tetraurelia, P. biaurelia, P. sexaurelia, as well as two outgroup species that do not share the WGDs: P. caudatum and P. multimicronucleatum. An apparent absence of global geographic population structure suggests continuous or recent dispersal of Paramecium over long distances. Intergenic regions are highly constrained relative to coding sequences, especially in P. caudatum and P. multimicronucleatum that have shorter intergenic distances. Sequence diversity and divergence are reduced up to ∼100-150 bp both upstream and downstream of genes, suggesting strong constraints imposed by the presence of densely packed regulatory modules. In addition, comparison of sequence variation at non-synonymous and synonymous sites suggests similar recent selective pressures on paralogs within and orthologs across the deeply diverging species. This study presents the first genome-wide population-genomic analysis in ciliates and provides a valuable resource for future studies in evolutionary and functional genetics in Paramecium. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. Deep whole-genome sequencing of 90 Han Chinese genomes.

    Science.gov (United States)

    Lan, Tianming; Lin, Haoxiang; Zhu, Wenjuan; Laurent, Tellier Christian Asker Melchior; Yang, Mengcheng; Liu, Xin; Wang, Jun; Wang, Jian; Yang, Huanming; Xu, Xun; Guo, Xiaosen

    2017-09-01

    Genomes Project, as well as to other human genome projects. © The Authors 2017. Published by Oxford University Press.

  11. A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated Through Whole Genome Resequencing

    Directory of Open Access Journals (Sweden)

    Guangtu Gao

    2018-04-01

    Full Text Available Single-nucleotide polymorphisms (SNPs are highly abundant markers, which are broadly distributed in animal genomes. For rainbow trout (Oncorhynchus mykiss, SNP discovery has been previously done through sequencing of restriction-site associated DNA (RAD libraries, reduced representation libraries (RRL and RNA sequencing. Recently we have performed high coverage whole genome resequencing with 61 unrelated samples, representing a wide range of rainbow trout and steelhead populations, with 49 new samples added to 12 aquaculture samples from AquaGen (Norway that we previously used for SNP discovery. Of the 49 new samples, 11 were double-haploid lines from Washington State University (WSU and 38 represented wild and hatchery populations from a wide range of geographic distribution and with divergent migratory phenotypes. We then mapped the sequences to the new rainbow trout reference genome assembly (GCA_002163495.1 which is based on the Swanson YY doubled haploid line. Variant calling was conducted with FreeBayes and SAMtools mpileup, followed by filtering of SNPs based on quality score, sequence complexity, read depth on the locus, and number of genotyped samples. Results from the two variant calling programs were compared and genotypes of the double haploid samples were used for detecting and filtering putative paralogous sequence variants (PSVs and multi-sequence variants (MSVs. Overall, 30,302,087 SNPs were identified on the rainbow trout genome 29 chromosomes and 1,139,018 on unplaced scaffolds, with 4,042,723 SNPs having high minor allele frequency (MAF > 0.25. The average SNP density on the chromosomes was one SNP per 64 bp, or 15.6 SNPs per 1 kb. Results from the phylogenetic analysis that we conducted indicate that the SNP markers contain enough population-specific polymorphisms for recovering population relationships despite the small sample size used. Intra-Population polymorphism assessment revealed high level of polymorphism and

  12. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained...... by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans...

  13. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew David; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...

  14. HGVA: the Human Genome Variation Archive.

    Science.gov (United States)

    Lopez, Javier; Coll, Jacobo; Haimel, Matthias; Kandasamy, Swaathi; Tarraga, Joaquin; Furio-Tari, Pedro; Bari, Wasim; Bleda, Marta; Rueda, Antonio; Gräf, Stefan; Rendon, Augusto; Dopazo, Joaquin; Medina, Ignacio

    2017-07-03

    High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic data for key reference projects in a clean, fast and integrated fashion. HGVA provides an efficient and intuitive web-interface for easy data mining, a comprehensive RESTful API and client libraries in Python, Java and JavaScript for fast programmatic access to its knowledge base. HGVA calculates population frequencies for these projects and enriches their data with variant annotation provided by CellBase, a rich and fast annotation solution. HGVA serves as a proof-of-concept of the genome analysis developments being carried out by the University of Cambridge together with UK's 100 000 genomes project and the National Institute for Health Research BioResource Rare-Diseases, in particular, deploying open-source for Computational Biology (OpenCB) software platform for storing and analyzing massive genomic datasets. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Toward an Integrated BAC Library Resource for Genome Sequencing and Analysis; FINAL

    International Nuclear Information System (INIS)

    Simon, M. I.; Kim, U.-J.

    2002-01-01

    We developed a great deal of expertise in building large BAC libraries from a variety of DNA sources including humans, mice, corn, microorganisms, worms, and Arabidopsis. We greatly improved the technology for screening these libraries rapidly and for selecting appropriate BACs and mapping BACs to develop large overlapping contigs. We became involved in supplying BACs and BAC contigs to a variety of sequencing and mapping projects and we began to collaborate with Drs. Adams and Venter at TIGR and with Dr. Leroy Hood and his group at University of Washington to provide BACs for end sequencing and for mapping and sequencing of large fragments of chromosome 16. Together with Dr. Ian Dunham and his co-workers at the Sanger Center we completed the mapping and they completed the sequencing of the first human chromosome, chromosome 22. This was published in Nature in 1999 and our BAC contigs made a major contribution to this sequencing effort. Drs. Shizuya and Ding invented an automated highly accurate BAC mapping technique. We also developed long-term collaborations with Dr. Uli Weier at UCSF in the design of BAC probes for characterization of human tumors and specific chromosome deletions and breakpoints. Finally the contribution of our work to the human genome project has been recognized in the publication both by the international consortium and the NIH of a draft sequence of the human genome in Nature last year. Dr. Shizuya was acknowledged in the authorship of that landmark paper. Dr. Simon was also an author on the Venter/Adams Celera project sequencing the human genome that was published in Science last year

  16. A Genome-Wide Landscape of Retrocopies in Primate Genomes.

    Science.gov (United States)

    Navarro, Fábio C P; Galante, Pedro A F

    2015-07-29

    Gene duplication is a key factor contributing to phenotype diversity across and within species. Although the availability of complete genomes has led to the extensive study of genomic duplications, the dynamics and variability of gene duplications mediated by retrotransposition are not well understood. Here, we predict mRNA retrotransposition and use comparative genomics to investigate their origin and variability across primates. Analyzing seven anthropoid primate genomes, we found a similar number of mRNA retrotranspositions (∼7,500 retrocopies) in Catarrhini (Old Word Monkeys, including humans), but a surprising large number of retrocopies (∼10,000) in Platyrrhini (New World Monkeys), which may be a by-product of higher long interspersed nuclear element 1 activity in these genomes. By inferring retrocopy orthology, we dated most of the primate retrocopy origins, and estimated a decrease in the fixation rate in recent primate history, implying a smaller number of species-specific retrocopies. Moreover, using RNA-Seq data, we identified approximately 3,600 expressed retrocopies. As expected, most of these retrocopies are located near or within known genes, present tissue-specific and even species-specific expression patterns, and no expression correlation to their parental genes. Taken together, our results provide further evidence that mRNA retrotransposition is an active mechanism in primate evolution and suggest that retrocopies may not only introduce great genetic variability between lineages but also create a large reservoir of potentially functional new genomic loci in primate genomes. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  17. Natural phenomena analyses, Hanford Site, Washington

    International Nuclear Information System (INIS)

    Tallman, A.M.

    1989-01-01

    Probabilistic seismic hazard studies completed for the Washington Public Power Supply System's Nuclear Plant 2 and for the US Department of Energy's N Reactor sites, both on the Hanford Site, suggested that the Lawrence Livermore National Laboratory seismic exposure estimates were lower than appropriate, especially for sites near potential seismic sources. A probabilistic seismic hazard assessment was completed for those areas that contain process and/or waste management facilities. the lower bound magnitude of 5.0 is used in the hazard analysis and the characteristics of small-magnitude earthquakes relatively common to the Hanford Site are addressed. The recommended ground motion for high-hazard facilities is somewhat higher than the Lawrence Livermore National Laboratory model and the ground motion from small-magnitude earthquakes is addressed separately from the moderate- to large-magnitude earthquake ground motion. The severe wind and tornado hazards determined for the Hanford Siste are in agreement with work completed independently using 43 years of site data. The low-probability, high-hazard, design-basis flood at the Hanford Site is dominated by dam failure on the Columbia River. Further evaluation of the mechanisms and probabilities of such flooding is in progress. The Hanford Site is downwind from several active Cascade volcanoes. Geologic and historical data are used to estimate the ashfall hazard

  18. Spacelab ready for transport to Washington, DC

    Science.gov (United States)

    1998-01-01

    Spacelab is wrapped and ready for transport to the National Air and Space Museum in Washington, DC. Spacelab was designed by the European Space Agency (ESA) for the Space Shuttle program and first flew on STS-9 in November 1983. Its final flight was the STS-90 Neurolab mission in April 1998. A sister module will travel home and be placed on display in Europe. The Spacelab concept of modular experiment racks in a pressurized shirt-sleeve environment made it highly user-friendly and accessible. Numerous experiments conceived by hundreds of scientists on the ground were conducted by flight crews in orbit. Spacelab modules served as on-orbit homes for everything from squirrel monkeys to plant seeds. They supported astronomical as well as Earth observations, for servicing the Hubble Space Telescope and for research preparatory to the International Space Station. One of the greatest benefits afforded by the Spacelab missions was the opportunity to fly a mission more than once, with the second or third flight building on the experiences and data gathered from its predecessors.

  19. Washington in '97: Positive energy moves expected

    International Nuclear Information System (INIS)

    Matthews, C.D.

    1997-01-01

    After the stormy closing weeks of the 1996 electrons, when the fog finally lifted, a strong indication of the direction American politics is taking emerged. It is still moving clearly to the right. Donald Lambro, chief political correspondent of The Washington Times, put it this way, ''Contemporary liberalism may not be dead and buried yet, but it remains comatose and continues to wither away--without a clear and relevant agenda, without a credible champion, and without a majority party. Meanwhile, the Congress that will be sworn in next January will be one of the most conservative in decades.'' Why that will likely bode well for the US oil and gas industry is the theme of the following discussion. Outlined therein are: some thoughts on why Clinton won; a wrapup of key seats and committee members of the 105th Congress; news of a bipartisan forum for the oil/gas industry; improved outlook for movement on the Arctic National Wildlife Refuge (ANWR); progress on the national public education program; and a list of industry's challenges for the next few years

  20. THE ROLE OF HISTORICAL AERIAL PHOTOGRAPHS IN THE REMEDIATION OF WWI CHEMICAL CONTAMINATION IN THE SPRING VALLEY SUPERFUND SITE, WASHINGTON, DC

    Science.gov (United States)

    During World War 1, The American University in Washington D.C. was used by the U.S. Army as an experiment station for the development and testing of a variety of battlefield munitions including chemical weapons such as Mustard Gas, Phosgene, Ricin and Lewisite, among others. Afte...

  1. Facilities for Study and Research in the Offices of the United States Government at Washington. Bulletin, 1909, No. 1. Whole Number 398

    Science.gov (United States)

    Hadley, Arthur Twining

    1909-01-01

    This bulletin contains a report prepared by President Hadley of Yale University on the facilities for advanced study and research in the offices of the National Government at Washington. Especial interest attaches to this publication. It sets forth, in compact form, information which has frequently been sought by institutions and individuals…

  2. Microbial species delineation using whole genome sequences.

    Science.gov (United States)

    Varghese, Neha J; Mukherjee, Supratim; Ivanova, Natalia; Konstantinidis, Konstantinos T; Mavrommatis, Kostas; Kyrpides, Nikos C; Pati, Amrita

    2015-08-18

    Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI) metric, which is widely acknowledged as a robust measure of genomic relatedness. In this work, we demonstrate that the combination of gANI and the alignment fraction (AF) between two genomes accurately reflects their genomic relatedness. We introduce an efficient implementation of AF,gANI and discuss its successful application to 86.5M genome pairs between 13,151 prokaryotic genomes assigned to 3032 species. Subsequently, by comparing the genome clusters obtained from complete linkage clustering of these pairs to existing taxonomy, we observed that nearly 18% of all prokaryotic species suffer from anomalies in species definition. Our results can be used to explore central questions such as whether microorganisms form a continuum of genetic diversity or distinct species represented by distinct genetic signatures. We propose that this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment, supplemented by the traditional polyphasic approach, as required. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Evolution of the Largest Mammalian Genome.

    Science.gov (United States)

    Evans, Ben J; Upham, Nathan S; Golding, Goeffrey B; Ojeda, Ricardo A; Ojeda, Agustina A

    2017-06-01

    The genome of the red vizcacha rat (Rodentia, Octodontidae, Tympanoctomys barrerae) is the largest of all mammals, and about double the size of their close relative, the mountain vizcacha rat Octomys mimax, even though the lineages that gave rise to these species diverged from each other only about 5 Ma. The mechanism for this rapid genome expansion is controversial, and hypothesized to be a consequence of whole genome duplication or accumulation of repetitive elements. To test these alternative but nonexclusive hypotheses, we gathered and evaluated evidence from whole transcriptome and whole genome sequences of T. barrerae and O. mimax. We recovered support for genome expansion due to accumulation of a diverse assemblage of repetitive elements, which represent about one half and one fifth of the genomes of T. barrerae and O. mimax, respectively, but we found no strong signal of whole genome duplication. In both species, repetitive sequences were rare in transcribed regions as compared with the rest of the genome, and mostly had no close match to annotated repetitive sequences from other rodents. These findings raise new questions about the genomic dynamics of these repetitive elements, their connection to widespread chromosomal fissions that occurred in the T. barrerae ancestor, and their fitness effects-including during the evolution of hypersaline dietary tolerance in T. barrerae. ©The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  4. Deleterious mutation accumulation in organelle genomes.

    Science.gov (United States)

    Lynch, M; Blanchard, J L

    1998-01-01

    It is well established on theoretical grounds that the accumulation of mildly deleterious mutations in nonrecombining genomes is a major extinction risk in obligately asexual populations. Sexual populations can also incur mutational deterioration in genomic regions that experience little or no recombination, i.e., autosomal regions near centromeres, Y chromosomes, and organelle genomes. Our results suggest, for a wide array of genes (transfer RNAs, ribosomal RNAs, and proteins) in a diverse collection of species (animals, plants, and fungi), an almost universal increase in the fixation probabilities of mildly deleterious mutations arising in mitochondrial and chloroplast genomes relative to those arising in the recombining nuclear genome. This enhanced width of the selective sieve in organelle genomes does not appear to be a consequence of relaxed selection, but can be explained by the decline in the efficiency of selection that results from the reduction of effective population size induced by uniparental inheritance. Because of the very low mutation rates of organelle genomes (on the order of 10(-4) per genome per year), the reduction in fitness resulting from mutation accumulation in such genomes is a very long-term process, not likely to imperil many species on time scales of less than a million years, but perhaps playing some role in phylogenetic lineage sorting on time scales of 10 to 100 million years.

  5. Neah Bay, Washington Tsunami Forecast Grids for MOST Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Neah Bay, Washington Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST) model....

  6. Westport, Washington Tsunami Forecast Grids for MOST Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Westport, Washington Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST) model....

  7. Port Angeles, Washington Tsunami Forecast Grids for MOST Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Port Angeles, Washington Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST)...

  8. LiDAR (Terrain), THURSTON COUNTY, WASHINGTON, USA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Fugro EarthData Company furnished the collection, processing, and development of LiDAR for 825 square miles in Washington (805 square miles of Thurston County and 20...

  9. Southwestern Washington 1/3 arc-second DEM

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The 1/3-second Southwest Washington Elevation Grid provides bathymetric data in ASCII raster format of 1/3-second resolution in geographic coordinates. This grid is...

  10. Early Restoration Public Meeting, Washington, DC | NOAA Gulf Spill

    Science.gov (United States)

    benefit injured marshes, coastal dune and nearshore habitats, oysters, and human uses (on water recreation . Department of Commerce Herbert Hoover Building Auditorium 1401 Constitution Ave., NW Washington, D.C. 20230

  11. Final Report: Feasibility Study of Biomass in Snohomish County, Washington

    Energy Technology Data Exchange (ETDEWEB)

    Daryl Williams (Tulalip Tribes); Ray Clark (Clark Group)

    2005-01-31

    This report and its attachments summarizes the results of a unique tribal-farmer cooperative study to evaluate the feasibility of building one or more regional anaerobic digestion systems in Snohomish County, Washington.

  12. Toke Point, Washington Tsunami Forecast Grids for MOST Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Toke Point, Washington Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST) model....

  13. Endangered Species Case - Washington Toxics Coalition v. EPA

    Science.gov (United States)

    This Web page provides information on the Washington Toxics Coalition v. EPA case, related to protection of Pacific salmon and steelhead, and links to the biological opinions issued by the NMFS and EPA’s responses.

  14. La Push, Washington Tsunami Forecast Grids for MOST Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The La Push, Washington Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST) model....

  15. Timber resource statistics for the Olympic Peninsula, Washington.

    Science.gov (United States)

    Patricia M. Bassett; Daniel D. Oswald

    1961-01-01

    This report summarizes a 1978-79 timber resource inventory of five counties in the Olympic Peninsula of Washington: Clallam, Grays Harbor, Jefferson, Mason, and Thurston. Detailed tables of forest area, timber volume, growth, mortality, and harvest are presented.

  16. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

  17. Washington Windplant No. 1: Botanical resources field survey. Appendix B to Washington Windplant No. 1 EIS

    International Nuclear Information System (INIS)

    1994-12-01

    KENETECH Windpower, Inc., has applied to Klickitat County for a conditional use permit to construct and operate a 115 Megawatt windfarm on an approximately 5110 hectare (12,630 acre) site in the Columbia Hills near Goldendale, Washington. A transmission services agreement between the Bonneville Power Administration (BPA) and utilities purchasing the Project's output will also be required. Klickitat County and BPA initiated the preparation of a joint SEPA/NEPA Environmental Impact Statement, under the authority of the Washington State Environmental Policy Act and the National Environmental Policy Act. The EIS addresses, among other issues, the Project's potential impact on rare, threatened or endangered, and sensitive plant species and communities as well as plant species of potential cultural importance. A field survey along potential impact corridors (turbine strings, roadways, and the transmission line alignment) was conducted between April and June, 1994 in order to identify rare plant species, high-quality native plant communities, and plant species of potential cultural importance present in these corridors. In addition, habitat maps of the entire 5110-ha project area were field verified. This report contains the results of that survey and an assessment of the potential project impacts

  18. Uranium concentrations in groundwater, northeastern Washington

    Science.gov (United States)

    Kahle, Sue C.; Welch, Wendy B.; Tecca, Alison E.; Eliason, Devin M.

    2018-04-18

    A study of uranium in groundwater in northeastern Washington was conducted to make a preliminary assessment of naturally occurring uranium in groundwater relying on existing information and limited reconnaissance sampling. Naturally occurring uranium is associated with granitic and metasedimentary rocks, as well as younger sedimentary deposits, that occur in this region. The occurrence and distribution of uranium in groundwater is poorly understood. U.S. Environmental Protection Agency (EPA) regulates uranium in Group A community water systems at a maximum contaminant level (MCL) of 30 μg/L in order to reduce uranium exposure, protect from toxic kidney effects of uranium, and reduce the risk of cancer. However, most existing private wells in the study area, generally for single family use, have not been sampled for uranium. This document presents available uranium concentration data from throughout a multi-county region, identifies data gaps, and suggests further study aimed at understanding the occurrence of uranium in groundwater.The study encompasses about 13,000 square miles (mi2) in the northeastern part of Washington with a 2010 population of about 563,000. Other than the City of Spokane, most of the study area is rural with small towns interspersed throughout the region. The study area also includes three Indian Reservations with small towns and scattered population. The area has a history of uranium exploration and mining, with two inactive uranium mines on the Spokane Indian Reservation and one smaller inactive mine on the outskirts of Spokane. Historical (1977–2016) uranium in groundwater concentration data were used to describe and illustrate the general occurrence and distribution of uranium in groundwater, as well as to identify data deficiencies. Uranium concentrations were detected at greater than 1 microgram per liter (μg/L) in 60 percent of the 2,382 historical samples (from wells and springs). Uranium concentrations ranged from less than 1 to

  19. National Uranium Resource Evaluation: Okanogan Quadrangle, Washington

    International Nuclear Information System (INIS)

    Bernardi, M.L.; Powell, L.K.; Wicklund, M.A.

    1982-06-01

    The Okanogan Quadrangle, Washington, was evaluated to identify and delineate areas containing environments favorable for the occurrence of uranium deposits using criteria developed for the National Uranium Resource Evaluation program. Reconnaissance and detailed surface studies were augmented by aerial radiometric surveys and hydrogeochemical and stream-sediment reconnaissance studies. The results of the investigations indicate six environments favorable for uranium deposits. They are unclassified, anatectic, allogenic, and contact-metasomatic deposits in Late Precambrian and (or) Early Paleozoic mantling metamorphic core-complex rocks of the Kettle gneiss dome; magmatic-hydrothermal deposits in the Gold Creek pluton, the Magee Creek pluton, the Wellington Peak pluton, and the Midnite Mine pluton, all located in the southeast quadrant of the quadrangle; magmatic-hydrothermal allogenic deposits in Late Paleozoic and (or) Early Mesozoic black shales in the Castle Mountain area; allogenic deposits in Early Paleozoic metasedimentary rocks in the Harvey Creek area and in Late Precambrian metasedimentary rocks in the Blue Mountain area; and sandstone deposits in Eocene sedimentary rocks possibly present in the Enterprise Valley. Seven geologic units are considered unfavorable for uranium deposits. They are all the remaining metamorphic core-complex rocks, Precambrian metasedimentary rocks,Tertiary sedimentary and volcanic rocks, and all Pleistocene and Recent deposits; and, excluding those rocks in the unevaluated areas, include all the remaining plutonic rocks, Paleozoic miogeoclinical rocks, and Upper Paleozoic and Mesozoic eugeosynclinal rocks. Three areas, the Cobey Creek-Frosty Creek area, the Oregon City Ridge-Wilmont Creek area, and the area underlain by the Middle Cambrian Metaline Formation and its stratigraphic equivalents may possibly be favorable but are unevaluated due to lack of data

  20. Modeling landslide recurrence in Seattle, Washington, USA

    Science.gov (United States)

    Salciarini, Diana; Godt, Jonathan W.; Savage, William Z.; Baum, Rex L.; Conversini, Pietro

    2008-01-01

    To manage the hazard associated with shallow landslides, decision makers need an understanding of where and when landslides may occur. A variety of approaches have been used to estimate the hazard from shallow, rainfall-triggered landslides, such as empirical rainfall threshold methods or probabilistic methods based on historical records. The wide availability of Geographic Information Systems (GIS) and digital topographic data has led to the development of analytic methods for landslide hazard estimation that couple steady-state hydrological models with slope stability calculations. Because these methods typically neglect the transient effects of infiltration on slope stability, results cannot be linked with historical or forecasted rainfall sequences. Estimates of the frequency of conditions likely to cause landslides are critical for quantitative risk and hazard assessments. We present results to demonstrate how a transient infiltration model coupled with an infinite slope stability calculation may be used to assess shallow landslide frequency in the City of Seattle, Washington, USA. A module called CRF (Critical RainFall) for estimating deterministic rainfall thresholds has been integrated in the TRIGRS (Transient Rainfall Infiltration and Grid-based Slope-Stability) model that combines a transient, one-dimensional analytic solution for pore-pressure response to rainfall infiltration with an infinite slope stability calculation. Input data for the extended model include topographic slope, colluvial thickness, initial water-table depth, material properties, and rainfall durations. This approach is combined with a statistical treatment of rainfall using a GEV (General Extreme Value) probabilistic distribution to produce maps showing the shallow landslide recurrence induced, on a spatially distributed basis, as a function of rainfall duration and hillslope characteristics.

  1. Natural gas pipeline leaks across Washington, DC.

    Science.gov (United States)

    Jackson, Robert B; Down, Adrian; Phillips, Nathan G; Ackley, Robert C; Cook, Charles W; Plata, Desiree L; Zhao, Kaiguang

    2014-01-01

    Pipeline safety in the United States has increased in recent decades, but incidents involving natural gas pipelines still cause an average of 17 fatalities and $133 M in property damage annually. Natural gas leaks are also the largest anthropogenic source of the greenhouse gas methane (CH4) in the U.S. To reduce pipeline leakage and increase consumer safety, we deployed a Picarro G2301 Cavity Ring-Down Spectrometer in a car, mapping 5893 natural gas leaks (2.5 to 88.6 ppm CH4) across 1500 road miles of Washington, DC. The δ(13)C-isotopic signatures of the methane (-38.2‰ ± 3.9‰ s.d.) and ethane (-36.5 ± 1.1 s.d.) and the CH4:C2H6 ratios (25.5 ± 8.9 s.d.) closely matched the pipeline gas (-39.0‰ and -36.2‰ for methane and ethane; 19.0 for CH4/C2H6). Emissions from four street leaks ranged from 9200 to 38,200 L CH4 day(-1) each, comparable to natural gas used by 1.7 to 7.0 homes, respectively. At 19 tested locations, 12 potentially explosive (Grade 1) methane concentrations of 50,000 to 500,000 ppm were detected in manholes. Financial incentives and targeted programs among companies, public utility commissions, and scientists to reduce leaks and replace old cast-iron pipes will improve consumer safety and air quality, save money, and lower greenhouse gas emissions.

  2. Nuclear waste - A view from Washington, DC

    International Nuclear Information System (INIS)

    Mc Cormack, M.

    1984-01-01

    The view from Washington is an optimistic one. With support of the vast amount of research, development and engineering that scientists and engineers have completed and will do in the future, this country certainly is now headed towards a successful and orderly program for handling all radioactive wastes safely and inexpensively. The high-level waste program, for instance, will require only about 2% of the cost of electricity produced from nuclear power. It is the need for the federal government to create, by law, a public corporation for handling the fuel cycle for commercial nuclear fuel. Such a Federal Nuclear Fuel Cycle Corporation (FNFCC) would handle almost all of the nuclear power fuel cycle in a manner similar to the DOE management of the fuel cycle for the weapons program. Except for the mining and milling of uranium and the fabrication of uranium (only) fuel elements, the federal government would pre-empt ownership of all facilities used in the fuel cycle and operate them by contract with private industry (as with the weapons fuel cycle). Ownership of all fissile and fertile material (and all existing and future fuel elements) would be preempted by law and vested in the FNFCC. Reprocessing fuel to extract and glassify waste for permanent geologic disposal is the most attractive method for handling spent fuel from a safety and environmental perspective. Also recycling fuel is probably more environmentally attractive than mining more uranium, especially from lower grade ores. This concept of an FNFCC has been suggested to the Administration and to some Congressional leaders. There has been no known opposition expressed, but there is some indication of a reluctance to undertake such a major problem-solving initiative in one step

  3. THE PROPOSED NATIONAL ARBORETUM AT WASHINGTON.

    Science.gov (United States)

    Coville, F V

    1925-12-25

    Nature. The proposed national arboretum at Washington would contain a permanent living collection of trees and other outdoor plants for purposes of scientific research and education. It would include the trees, shrubs, and perennials used in forestry and horticulture, and the wild relatives of these plants. It would be a bureau of standards for horticulture. It would contain a water garden and a wildrice preserve, and it would serve incidentally as a bird sanctuary. Economic value. The arboretum would make the work of the Department of Agriculture more valuable to the country in many ways, but especially through plant breeding. The development of faster-growing timber trees, improved fruits, and disease-resistant plants generally, through the facilities afforded by the arboretum, would increase profoundly the agricultural wealth and welfare of the United States. Location. The Mount Hamilton and Hickey Hill tracts in the District of Columbia, together with the Anacostia River flats above Benning Bridge, constitute an admirable site for the arboretum, convenient in location and with a great variety of soils. Cost. About 400 acres of the proposed site is already owned by the government. It consists of marsh land, about to be drained by army engineers. The Mount Hamilton and Hickey Hill area, 408 acres, privately owned, was reported by the assessor in January, 1925, to be valued at $343,048, distributed among thirty owners. Maintenance. If the purchase of the Mount Hamilton and Hickey Hill tracts in the fiscal year 1927 is authorized, it is estimated that the cost of maintenance of the arboretum for the first three years would be as follows: 1927. Nothing 1928. $25,000 1929. $50,000.

  4. Materials Genome Initiative

    Science.gov (United States)

    Vickers, John

    2015-01-01

    The Materials Genome Initiative (MGI) project element is a cross-Center effort that is focused on the integration of computational tools to simulate manufacturing processes and materials behavior. These computational simulations will be utilized to gain understanding of processes and materials behavior to accelerate process development and certification to more efficiently integrate new materials in existing NASA projects and to lead to the design of new materials for improved performance. This NASA effort looks to collaborate with efforts at other government agencies and universities working under the national MGI. MGI plans to develop integrated computational/experimental/ processing methodologies for accelerating discovery and insertion of materials to satisfy NASA's unique mission demands. The challenges include validated design tools that incorporate materials properties, processes, and design requirements; and materials process control to rapidly mature emerging manufacturing methods and develop certified manufacturing processes

  5. Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database.

    Science.gov (United States)

    Winsor, Geoffrey L; Griffiths, Emma J; Lo, Raymond; Dhillon, Bhavjinder K; Shay, Julie A; Brinkman, Fiona S L

    2016-01-04

    The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Funding Opportunity: Genomic Data Centers

    Science.gov (United States)

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  7. Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science.

    Science.gov (United States)

    Smith, David Roy

    2017-05-01

    Next-generation sequencing technologies have revolutionized genomics and altered the scientific publication landscape. Life-science journals abound with genome papers-peer-reviewed descriptions of newly sequenced chromosomes. Although they once filled the pages of Nature and Science, genome papers are now mostly relegated to journals with low-impact factors. Some have forecast the death of the genome paper and argued that they are using up valuable resources and not advancing science. However, the publication rate of genome papers is on the rise. This increase is largely because some journals have created a new category of manuscript called genome reports, which are short, fast-tracked papers describing a chromosome sequence(s), its GenBank accession number and little else. In 2015, for example, more than 2000 genome reports were published, and 2016 is poised to bring even more. Here, I highlight the growing popularity of genome reports and discuss their merits, drawbacks and impact on science and the academic publication infrastructure. Genome reports can be excellent assets for the research community, but they are also being used as quick and easy routes to a publication, and in some instances they are not peer reviewed. One of the best arguments for genome reports is that they are a citable, user-generated genomic resource providing essential methodological and biological information, which may not be present in the sequence database. But they are expensive and time-consuming avenues for achieving such a goal. © The Author 2016. Published by Oxford University Press.

  8. A Symposium Associated with the Opening of the Play Copenhagen in Washington

    Energy Technology Data Exchange (ETDEWEB)

    Schwartz, Brian

    2002-12-31

    On March 2, 2002 a special all day symposium was held in conjunction with the opening of the play Copenhagen in Washington. The play Copenhagen reenacts the 1941 visit of Werner Heisenberg, who was then in charge of the Nazi nuclear power program, to Niels Bohr, his mentor, and collaborator in creating quantum mechanics, complementarity, and the uncertainty principle, in German-occupied Denmark. The symposium entitled: THE COPENHAGEN INTERPRETATION: SCIENCE AND HISTORY ON STAGE was presented at the Baird Auditorium, in the National Museum of Natural History of the Smithsonian Institution. The program consisted of three two-hour sessions: (1) The Science of Copenhagen and its Influence of the 20th Century. (2) Bohr and Heisenberg: A strong Interaction. (3) Theater as Science ??? Science as Theater. The speakers included: Robert C. Card, Under Secretary of Energy; Ulrik Federspiel, Danish Ambassador to the US; John Marburger, III, Science Advisor President Bush; Jerome I. Friedman, MIT; Lene Vestergaard Hau, Harvard University; Richard Rhodes, Author; Rita Colwell, Director, NSF; Jeremy Bernstein, Author; Jochen H. Heisenberg, University of New Hampshire; Finn Aaserud, Director of the Niels Bohr Archive; Vilhelm A. Bohr, NIH; Thomas Powers, Author; Paul Lawrence Rose, Penn State University; Steven Barfield, University of Westminster, Jennifer Uphoff Gray, Associate Director, Copenhagen; Elizabeth Ireland McCann, Producer, Copenhagen; Lloyd Rose, Washington Post. Details of he program and useful information on the play Copenhagen are available on the web site http://web.gc.cuny.edu/ashp/nml/artsci/copenhagen.shtml . The complete symposium was video recorded and the set of 3 two-hour tapes can be obtained through the web site. The symposium was organized by Brian Schwartz, The Graduate Center, CUNY, Harry Lustig, Provost Emeritus at the City College of New York and Arthur Molella, Director, Lemelson Center, Smithsonian Institution. For further information contact Brian

  9. A Symposium Associated with the Opening of the Play Copenhagen in Washington

    International Nuclear Information System (INIS)

    Schwartz, Brian

    2002-01-01

    On March 2, 2002 a special all day symposium was held in conjunction with the opening of the play Copenhagen in Washington. The play Copenhagen reenacts the 1941 visit of Werner Heisenberg, who was then in charge of the Nazi nuclear power program, to Niels Bohr, his mentor, and collaborator in creating quantum mechanics, complementarity, and the uncertainty principle, in German-occupied Denmark. The symposium entitled: THE COPENHAGEN INTERPRETATION: SCIENCE AND HISTORY ON STAGE was presented at the Baird Auditorium, in the National Museum of Natural History of the Smithsonian Institution. The program consisted of three two-hour sessions: (1) The Science of Copenhagen and its Influence of the 20th Century. (2) Bohr and Heisenberg: A strong Interaction. (3) Theater as Science ??? Science as Theater. The speakers included: Robert C. Card, Under Secretary of Energy; Ulrik Federspiel, Danish Ambassador to the US; John Marburger, III, Science Advisor President Bush; Jerome I. Friedman, MIT; Lene Vestergaard Hau, Harvard University; Richard Rhodes, Author; Rita Colwell, Director, NSF; Jeremy Bernstein, Author; Jochen H. Heisenberg, University of New Hampshire; Finn Aaserud, Director of the Niels Bohr Archive; Vilhelm A. Bohr, NIH; Thomas Powers, Author; Paul Lawrence Rose, Penn State University; Steven Barfield, University of Westminster, Jennifer Uphoff Gray, Associate Director, Copenhagen; Elizabeth Ireland McCann, Producer, Copenhagen; Lloyd Rose, Washington Post. Details of he program and useful information on the play Copenhagen are available on the web site http://web.gc.cuny.edu/ashp/nml/artsci/copenhagen.shtml . The complete symposium was video recorded and the set of 3 two-hour tapes can be obtained through the web site. The symposium was organized by Brian Schwartz, The Graduate Center, CUNY, Harry Lustig, Provost Emeritus at the City College of New York and Arthur Molella, Director, Lemelson Center, Smithsonian Institution. For further information contact Brian

  10. Exploring Other Genomes: Bacteria.

    Science.gov (United States)

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  11. Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    Energy Technology Data Exchange (ETDEWEB)

    Reeve, Wayne [Murdoch University

    2013-03-01

    Wayne Reeve of Murdoch University on "Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  12. Simultaneous gene finding in multiple genomes.

    Science.gov (United States)

    König, Stefanie; Romoth, Lars W; Gerischer, Lizzy; Stanke, Mario

    2016-11-15

    As the tree of life is populated with sequenced genomes ever more densely, the new challenge is the accurate and consistent annotation of entire clades of genomes. We address this problem with a new approach to comparative gene finding that takes a multiple genome alignment of closely related species and simultaneously predicts the location and structure of protein-coding genes in all input genomes, thereby exploiting negative selection and sequence conservation. The model prefers potential gene structures in the different genomes that are in agreement with each other, or-if not-where the exon gains and losses are plausible given the species tree. We formulate the multi-species gene finding problem as a binary labeling problem on a graph. The resulting optimization problem is NP hard, but can be efficiently approximated using a subgradient-based dual decomposition approach. The proposed method was tested on whole-genome alignments of 12 vertebrate and 12 Drosophila species. The accuracy was evaluated for human, mouse and Drosophila melanogaster and compared to competing methods. Results suggest that our method is well-suited for annotation of (a large number of) genomes of closely related species within a clade, in particular, when RNA-Seq data are available for many of the genomes. The transfer of existing annotations from one genome to another via the genome alignment is more accurate than previous approaches that are based on protein-spliced alignments, when the genomes are at close to medium distances. The method is implemented in C ++ as part of Augustus and available open source at http://bioinf.uni-greifswald.de/augustus/ CONTACT: stefaniekoenig@ymail.com or mario.stanke@uni-greifswald.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  13. University Internationalization and University Autonomy

    DEFF Research Database (Denmark)

    Turcan, Romeo V.; Gulieva, Valeria

    2016-01-01

    Turcan and Gulieva deepen our theoretical understanding of the process of university internationalisation by exploring the relationship between university internationalisation and university autonomy. They conjecture that the process of university internationalisation and its sustainability are d......, dissimilar, and sometimes conflicting dimensions of the financial, legal, organisational, staffing, and academic autonomy of the host country, are compromising key aspects of their own autonomy and core mission?......Turcan and Gulieva deepen our theoretical understanding of the process of university internationalisation by exploring the relationship between university internationalisation and university autonomy. They conjecture that the process of university internationalisation and its sustainability...... are determined by the structure and exercise of university autonomy settings at home and in the host countries, and that the process itself cannot be successfully achieved and maintained without changes in the autonomy settings. The key question the authors ask is to what degree universities, in embracing new...

  14. Genomics With Cloud Computing

    OpenAIRE

    Sukhamrit Kaur; Sandeep Kaur

    2015-01-01

    Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computin...

  15. Journal of Genetics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Department of Biological Sciences, George Washington University, 333 Lisner Hall, 2023 G St. NW, Washington, DC 20052, USA; Institute for Neuroscience, George Washington University, 636 Ross Hall, 2300 I St. NW, Washington DC 20037, USA; Department of Biology, Genome Evolution Laboratory, National University ...

  16. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  17. Refining aging criteria for northern sea otters in Washington State

    Science.gov (United States)

    Schuler, Krysten L.; Baker, Bridget B.; Mayer, Karl A.; Perez-Heydrich, Carolina; Holahan, Paula M.; Thomas, Nancy J.; White, C. LeAnn

    2018-01-01

    Measurement of skull ossification patterns is a standard method for aging various mammalian species and has been used to age Russian, Californian, and Alaskan sea otter populations. Cementum annuli counts have also been verified as an accurate aging method for the Alaskan sea otter population. In this study, cementum annuli count results and skull ossification patterns were compared as methods for aging the northern sea otter (Enhydra lutris kenyoni) population in Washington State. Significant agreement was found between the two methods suggesting that either method could be used to age the Washington population of otters. This study also found that ossification of the squamosal-jugal suture at the ventral glenoid fossa can be used to differentiate male subadults from adults. To assist field biologists or others without access to cementum annuli or skull ossification analysis techniques, a suite of morphologic, physiologic, and developmental characteristics were analyzed to assess whether a set of these more easily accessible parameters could also predict age class for the Washington population of otters. Tooth condition score, evidence of reproductive activity in females, and tooth eruption pattern were identified as the most useful criteria for classifying Washington sea otters as pups, juveniles, subadults, or adults/aged adults. A simple decision tree based on characteristics accessible in the field or at necropsy was created that can be used to reliably predict age class of Washington sea otters as determined by cementum annuli.

  18. The Modern Synthesis in the Light of Microbial Genomics.

    Science.gov (United States)

    Booth, Austin; Mariscal, Carlos; Doolittle, W Ford

    2016-09-08

    We review the theoretical implications of findings in genomics for evolutionary biology since the Modern Synthesis. We examine the ways in which microbial genomics has influenced our understanding of the last universal common ancestor, the tree of life, species, lineages, and evolutionary transitions. We conclude by advocating a piecemeal toolkit approach to evolutionary biology, in lieu of any grand unified theory updated to include microbial genomics.

  19. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  20. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  1. Genomic and Functional Approaches to Understanding Cancer Aneuploidy

    NARCIS (Netherlands)

    Taylor, Alison M.; Shih, Juliann; Ha, Gavin; Gao, Galen F.; Zhang, Xiaoyang; Berger, Ashton C.; Schumacher, Steven E.; Wang, Chen; Hu, Hai; Liu, Jianfang; Lazar, Alexander J.; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean C.; Zhang, Jiashan (Julia); Chudamani, Sudha; Liu, Jia; Lolla, Laxmi; Naresh, Rashi; Pihl, Todd; Sun, Qiang; Wan, Yunhu; Wu, Ye; Cho, Juok; DeFreitas, Timothy; Frazer, Scott; Gehlenborg, Nils; Getz, Gad; Heiman, David I.; Kim, Jaegil; Lawrence, Michael S.; Lin, Pei; Meier, Sam; Noble, Michael S.; Saksena, Gordon; Voet, Doug; Zhang, Hailei; Bernard, Brady; Chambwe, Nyasha; Dhankani, Varsha; Knijnenburg, Theo; Kramer, Roger; Leinonen, Kalle; Liu, Yuexin; Miller, Michael; Reynolds, Sheila; Shmulevich, Ilya; Thorsson, Vesteinn; Zhang, Wei; Akbani, Rehan; Broom, Bradley M.; Hegde, Apurva M.; Ju, Zhenlin; Kanchi, Rupa S.; Korkut, Anil; Li, Jun; Liang, Han; Ling, Shiyun; Liu, Wenbin; Lu, Yiling; Mills, Gordon B.; Ng, Kwok Shing; Rao, Arvind; Ryan, Michael; Wang, Jing; Weinstein, John N.; Zhang, Jiexin; Abeshouse, Adam; Armenia, Joshua; Chakravarty, Debyani; Chatila, Walid K.; de Bruijn, Ino; Gao, Jianjiong; Gross, Benjamin E.; Heins, Zachary J.; Kundra, Ritika; La, Konnor; Ladanyi, Marc; Luna, Augustin; Nissan, Moriah G.; Ochoa, Angelica; Phillips, Sarah M.; Reznik, Ed; Sanchez-Vega, Francisco; Sander, Chris; Schultz, Nikolaus; Sheridan, Robert; Sumer, S. Onur; Sun, Yichao; Taylor, Barry S.; Wang, Jioajiao; Zhang, Hongxin; Anur, Pavana; Peto, Myron; Spellman, Paul; Benz, Christopher; Stuart, Joshua M.; Wong, Christopher K.; Yau, Christina; Hayes, D. Neil; Parker, Joel S.; Wilkerson, Matthew D.; Ally, Adrian; Balasundaram, Miruna; Bowlby, Reanne; Brooks, Denise; Carlsen, Rebecca; Chuah, Eric; Dhalla, Noreen; Holt, Robert; Jones, Steven J.M.; Kasaian, Katayoon; Lee, Darlene; Ma, Yussanne; Marra, Marco A.; Mayo, Michael; Moore, Richard A.; Mungall, Andrew J.; Mungall, Karen; Robertson, A. Gordon; Sadeghi, Sara; Schein, Jacqueline E.; Sipahimalani, Payal; Tam, Angela; Thiessen, Nina; Tse, Kane; Wong, Tina; Berger, Ashton C.; Beroukhim, Rameen; Cherniack, Andrew D.; Cibulskis, Carrie; Gabriel, Stacey B.; Gao, Galen F.; Ha, Gavin; Meyerson, Matthew; Schumacher, Steven E.; Shih, Juliann; Kucherlapati, Melanie H.; Kucherlapati, Raju S.; Baylin, Stephen; Cope, Leslie; Danilova, Ludmila; Bootwalla, Moiz S.; Lai, Phillip H.; Maglinte, Dennis T.; Van Den Berg, David J.; Weisenberger, Daniel J.; Auman, J. Todd; Balu, Saianand; Bodenheimer, Tom; Fan, Cheng; Hoadley, Katherine A.; Hoyle, Alan P.; Jefferys, Stuart R.; Jones, Corbin D.; Meng, Shaowu; Mieczkowski, Piotr A.; Mose, Lisle E.; Perou, Amy H.; Perou, Charles M.; Roach, Jeffrey; Shi, Yan; Simons, Janae V.; Skelly, Tara; Soloway, Matthew G.; Tan, Donghui; Veluvolu, Umadevi; Fan, Huihui; Hinoue, Toshinori; Laird, Peter W.; Shen, Hui; Zhou, Wanding; Bellair, Michelle; Chang, Kyle; Covington, Kyle; Creighton, Chad J.; Dinh, Huyen; Doddapaneni, Harsha Vardhan; Donehower, Lawrence A.; Drummond, Jennifer; Gibbs, Richard A.; Glenn, Robert; Hale, Walker; Han, Yi; Hu, Jianhong; Korchina, Viktoriya; Lee, Sandra; Lewis, Lora; Li, Wei; Liu, Xiuping; Morgan, Margaret; Morton, Donna; Muzny, Donna; Santibanez, Jireh; Sheth, Margi; Shinbrot, Eve; Wang, Linghua; Wang, Min; Wheeler, David A.; Xi, Liu; Zhao, Fengmei; Hess, Julian; Appelbaum, Elizabeth L.; Bailey, Matthew; Cordes, Matthew G.; Ding, Li; Fronick, Catrina C.; Fulton, Lucinda A.; Fulton, Robert S.; Kandoth, Cyriac; Mardis, Elaine R.; McLellan, Michael D.; Miller, Christopher A.; Schmidt, Heather K.; Wilson, Richard K.; Crain, Daniel; Curley, Erin; Gardner, Johanna; Lau, Kevin; Mallery, David; Morris, Scott; Paulauskis, Joseph; Penny, Robert; Shelton, Candace; Shelton, Troy; Sherman, Mark; Thompson, Eric; Yena, Peggy; Bowen, Jay; Gastier-Foster, Julie M.; Gerken, Mark; Leraas, Kristen M.; Lichtenberg, Tara M.; Ramirez, Nilsa C.; Wise, Lisa; Zmuda, Erik; Corcoran, Niall; Costello, Tony; Hovens, Christopher; Carvalho, Andre L.; de Carvalho, Ana C.; Fregnani, José H.; Longatto-Filho, Adhemar; Reis, Rui M.; Scapulatempo-Neto, Cristovam; Silveira, Henrique C.S.; Vidal, Daniel O.; Burnette, Andrew; Eschbacher, Jennifer; Hermes, Beth; Noss, Ardene; Singh, Rosy; Anderson, Matthew L.; Castro, Patricia D.; Ittmann, Michael; Huntsman, David; Kohl, Bernard; Le, Xuan; Thorp, Richard; Andry, Chris; Duffy, Elizabeth R.; Lyadov, Vladimir; Paklina, Oxana; Setdikova, Galiya; Shabunin, Alexey; Tavobilov, Mikhail; McPherson, Christopher; Warnick, Ronald; Berkowitz, Ross; Cramer, Daniel; Feltmate, Colleen; Horowitz, Neil; Kibel, Adam; Muto, Michael; Raut, Chandrajit P.; Malykh, Andrei; Barnholtz-Sloan, Jill S.; Barrett, Wendi; Devine, Karen; Fulop, Jordonna; Ostrom, Quinn T.; Shimmel, Kristen; Wolinsky, Yingli; Sloan, Andrew E.; De Rose, Agostino; Giuliante, Felice; Goodman, Marc; Karlan, Beth Y.; Hagedorn, Curt H.; Eckman, John; Harr, Jodi; Myers, Jerome; Tucker, Kelinda; Zach, Leigh Anne; Deyarmin, Brenda; Hu, Hai; Kvecher, Leonid; Larson, Caroline; Mural, Richard J.; Somiari, Stella; Vicha, Ales; Zelinka, Tomas; Bennett, Joseph; Iacocca, Mary; Rabeno, Brenda; Swanson, Patricia; Latour, Mathieu; Lacombe, Louis; Têtu, Bernard; Bergeron, Alain; McGraw, Mary; Staugaitis, Susan M.; Chabot, John; Hibshoosh, Hanina; Sepulveda, Antonia; Su, Tao; Wang, Timothy; Potapova, Olga; Voronina, Olga; Desjardins, Laurence; Mariani, Odette; Roman-Roman, Sergio; Sastre, Xavier; Stern, Marc Henri; Cheng, Feixiong; Signoretti, Sabina; Berchuck, Andrew; Bigner, Darell; Lipp, Eric; Marks, Jeffrey; McCall, Shannon; McLendon, Roger; Secord, Angeles; Sharp, Alexis; Behera, Madhusmita; Brat, Daniel J.; Chen, Amy; Delman, Keith; Force, Seth; Khuri, Fadlo; Magliocca, Kelly; Maithel, Shishir; Olson, Jeffrey J.; Owonikoko, Taofeek; Pickens, Alan; Ramalingam, Suresh; Shin, Dong M.; Sica, Gabriel; Van Meir, Erwin G.; Zhang, Hongzheng; Eijckenboom, Wil; Gillis, Ad; Korpershoek, Esther; Looijenga, Leendert; Oosterhuis, Wolter; Stoop, Hans; van Kessel, Kim E.; Zwarthoff, Ellen C.; Calatozzolo, Chiara; Cuppini, Lucia; Cuzzubbo, Stefania; DiMeco, Francesco; Finocchiaro, Gaetano; Mattei, Luca; Perin, Alessandro; Pollo, Bianca; Chen, Chu; Houck, John; Lohavanichbutr, Pawadee; Hartmann, Arndt; Stoehr, Christine; Stoehr, Robert; Taubert, Helge; Wach, Sven; Wullich, Bernd; Kycler, Witold; Murawa, Dawid; Wiznerowicz, Maciej; Chung, Ki; Edenfield, W. Jeffrey; Martin, Julie; Baudin, Eric; Bubley, Glenn; Bueno, Raphael; De Rienzo, Assunta; Richards, William G.; Kalkanis, Steven; Mikkelsen, Tom; Noushmehr, Houtan; Scarpace, Lisa; Girard, Nicolas; Aymerich, Marta; Campo, Elias; Giné, Eva; Guillermo, Armando López; Van Bang, Nguyen; Hanh, Phan Thi; Phu, Bui Duc; Tang, Yufang; Colman, Howard; Evason, Kimberley; Dottino, Peter R.; Martignetti, John A.; Gabra, Hani; Juhl, Hartmut; Akeredolu, Teniola; Stepa, Serghei; Hoon, Dave; Ahn, Keunsoo; Kang, Koo Jeong; Beuschlein, Felix; Breggia, Anne; Birrer, Michael; Bell, Debra; Borad, Mitesh; Bryce, Alan H.; Castle, Erik; Chandan, Vishal; Cheville, John; Copland, John A.; Farnell, Michael; Flotte, Thomas; Giama, Nasra; Ho, Thai; Kendrick, Michael; Kocher, Jean Pierre; Kopp, Karla; Moser, Catherine; Nagorney, David; O'Brien, Daniel; O'Neill, Brian Patrick; Patel, Tushar; Petersen, Gloria; Que, Florencia; Rivera, Michael; Roberts, Lewis; Smallridge, Robert; Smyrk, Thomas; Stanton, Melissa; Thompson, R. Houston; Torbenson, Michael; Yang, Ju Dong; Zhang, Lizhi; Brimo, Fadi; Ajani, Jaffer A.; Angulo Gonzalez, Ana Maria; Behrens, Carmen; Bondaruk, Jolanta; Broaddus, Russell; Czerniak, Bogdan; Esmaeli, Bita; Fujimoto, Junya; Gershenwald, Jeffrey; Guo, Charles; Lazar, Alexander J.; Logothetis, Christopher; Meric-Bernstam, Funda; Moran, Cesar; Ramondetta, Lois; Rice, David; Sood, Anil; Tamboli, Pheroze; Thompson, Timothy; Troncoso, Patricia; Tsao, Anne; Wistuba, Ignacio; Carter, Candace; Haydu, Lauren; Hersey, Peter; Jakrot, Valerie; Kakavand, Hojabr; Kefford, Richard; Lee, Kenneth; Long, Georgina; Mann, Graham; Quinn, Michael; Saw, Robyn; Scolyer, Richard; Shannon, Kerwin; Spillane, Andrew; Stretch, Jonathan; Synott, Maria; Thompson, John; Wilmott, James; Al-Ahmadie, Hikmat; Chan, Timothy A.; Ghossein, Ronald; Gopalan, Anuradha; Levine, Douglas A.; Reuter, Victor; Singer, Samuel; Singh, Bhuvanesh; Tien, Nguyen Viet; Broudy, Thomas; Mirsaidi, Cyrus; Nair, Praveen; Drwiega, Paul; Miller, Judy; Smith, Jennifer; Zaren, Howard; Park, Joong Won; Hung, Nguyen Phi; Kebebew, Electron; Linehan, W. Marston; Metwalli, Adam R.; Pacak, Karel; Pinto, Peter A.; Schiffman, Mark; Schmidt, Laura S.; Vocke, Cathy D.; Wentzensen, Nicolas; Worrell, Robert; Yang, Hannah; Moncrieff, Marc; Goparaju, Chandra; Melamed, Jonathan; Pass, Harvey; Botnariuc, Natalia; Caraman, Irina; Cernat, Mircea; Chemencedji, Inga; Clipca, Adrian; Doruc, Serghei; Gorincioi, Ghenadie; Mura, Sergiu; Pirtac, Maria; Stancul, Irina; Tcaciuc, Diana; Albert, Monique; Alexopoulou, Iakovina; Arnaout, Angel; Bartlett, John; Engel, Jay; Gilbert, Sebastien; Parfitt, Jeremy; Sekhon, Harman; Thomas, George; Rassl, Doris M.; Rintoul, Robert C.; Bifulco, Carlo; Tamakawa, Raina; Urba, Walter; Hayward, Nicholas; Timmers, Henri; Antenucci, Anna; Facciolo, Francesco; Grazi, Gianluca; Marino, Mirella; Merola, Roberta; de Krijger, Ronald; Gimenez-Roqueplo, Anne Paule; Piché, Alain; Chevalier, Simone; McKercher, Ginette; Birsoy, Kivanc; Barnett, Gene; Brewer, Cathy; Farver, Carol; Naska, Theresa; Pennell, Nathan A.; Raymond, Daniel; Schilero, Cathy; Smolenski, Kathy; Williams, Felicia; Morrison, Carl; Borgia, Jeffrey A.; Liptay, Michael J.; Pool, Mark; Seder, Christopher W.; Junker, Kerstin; Omberg, Larsson; Dinkin, Mikhail; Manikhas, George; Alvaro, Domenico; Bragazzi, Maria Consiglia; Cardinale, Vincenzo; Carpino, Guido; Gaudio, Eugenio; Chesla, David; Cottingham, Sandra; Dubina, Michael; Moiseenko, Fedor; Dhanasekaran, Renumathy; Becker, Karl Friedrich; Janssen, Klaus Peter; Slotta-Huspenina, Julia; Abdel-Rahman, Mohamed H.; Aziz, Dina; Bell, Sue; Cebulla, Colleen M.; Davis, Amy; Duell, Rebecca; Elder, J. Bradley; Hilty, Joe; Kumar, Bahavna; Lang, James; Lehman, Norman L.; Mandt, Randy; Nguyen, Phuong; Pilarski, Robert; Rai, Karan; Schoenfield, Lynn; Senecal, Kelly; Wakely, Paul; Hansen, Paul; Lechan, Ronald; Powers, James; Tischler, Arthur; Grizzle, William E.; Sexton, Katherine C.; Kastl, Alison; Henderson, Joel; Porten, Sima; Waldmann, Jens; Fassnacht, Martin; Asa, Sylvia L.; Schadendorf, Dirk; Couce, Marta; Graefen, Markus; Huland, Hartwig; Sauter, Guido; Schlomm, Thorsten; Simon, Ronald; Tennstedt, Pierre; Olabode, Oluwole; Nelson, Mark; Bathe, Oliver; Carroll, Peter R.; Chan, June M.; Disaia, Philip; Glenn, Pat; Kelley, Robin K.; Landen, Charles N.; Phillips, Joanna; Prados, Michael; Simko, Jeffry; Smith-McCune, Karen; VandenBerg, Scott; Roggin, Kevin; Fehrenbach, Ashley; Kendler, Ady; Sifri, Suzanne; Steele, Ruth; Jimeno, Antonio; Carey, Francis; Forgie, Ian; Mannelli, Massimo; Carney, Michael; Hernandez, Brenda; Campos, Benito; Herold-Mende, Christel; Jungk, Christin; Unterberg, Andreas; von Deimling, Andreas; Bossler, Aaron; Galbraith, Joseph; Jacobus, Laura; Knudson, Michael; Knutson, Tina; Ma, Deqin; Milhem, Mohammed; Sigmund, Rita; Godwin, Andrew K.; Madan, Rashna; Rosenthal, Howard G.; Adebamowo, Clement; Adebamowo, Sally N.; Boussioutas, Alex; Beer, David; Giordano, Thomas; Mes-Masson, Anne Marie; Saad, Fred; Bocklage, Therese; Landrum, Lisa; Mannel, Robert; Moore, Kathleen; Moxley, Katherine; Postier, Russel; Walker, Joan; Zuna, Rosemary; Feldman, Michael; Valdivieso, Federico; Dhir, Rajiv; Luketich, James; Mora Pinero, Edna M.; Quintero-Aguilo, Mario; Carlotti, Carlos Gilberto; Dos Santos, Jose Sebastião; Kemp, Rafael; Sankarankuty, Ajith; Tirapelli, Daniela; Catto, James; Agnew, Kathy; Swisher, Elizabeth; Creaney, Jenette; Robinson, Bruce; Shelley, Carl Simon; Godwin, Eryn M.; Kendall, Sara; Shipman, Cassaundra; Bradford, Carol; Carey, Thomas; Haddad, Andrea; Moyer, Jeffey; Peterson, Lisa; Prince, Mark; Rozek, Laura; Wolf, Gregory; Bowman, Rayleen; Fong, Kwun M.; Yang, Ian; Korst, Robert; Rathmell, W. Kimryn; Fantacone-Campbell, J. Leigh; Hooke, Jeffrey A.; Kovatich, Albert J.; Shriver, Craig D.; DiPersio, John; Drake, Bettina; Govindan, Ramaswamy; Heath, Sharon; Ley, Timothy; Van Tine, Brian; Westervelt, Peter; Rubin, Mark A.; Lee, Jung Il; Aredes, Natália D.; Mariamidze, Armaz; Cherniack, Andrew D.; Beroukhim, Rameen; Meyerson, Matthew

    2018-01-01

    Aneuploidy, whole chromosome or chromosome arm imbalance, is a near-universal characteristic of human cancers. In 10,522 cancer genomes from The Cancer Genome Atlas, aneuploidy was correlated with TP53 mutation, somatic mutation rate, and expression of proliferation genes. Aneuploidy was

  2. Genome Island: A Virtual Science Environment in Second Life

    Science.gov (United States)

    Clark, Mary Anne

    2009-01-01

    Mary Anne CLark describes the organization and uses of Genome Island, a virtual laboratory complex constructed in Second Life. Genome Island was created for teaching genetics to university undergraduates but also provides a public space where anyone interested in genetics can spend a few minutes, or a few hours, interacting with genetic…

  3. Rapid Crustal Uplift at Birch Bay, Washington

    Science.gov (United States)

    Sherrod, B. L.; Kelsey, H. M.; Blakely, R. J.

    2010-12-01

    Geomorphology and coastal marsh stratigraphy suggest late Holocene uplift of the shoreline at Birch Bay, located northwest of Bellingham, Washington, during an earthquake on a shallow fault. LiDAR images show a raised, late Holocene shoreline along Birch Bay, with ~1 m of elevation difference between the modern shoreline and the inferred paleoshoreline. Commercial seismic reflection images reveal an anticline in Tertiary and possibly Quaternary deposits underlying Birch Bay. NW-trending magnetic anomalies are likely associated with the Birch Bay anticline and other nearby structures. Taken together, the geophysical data and lidar images suggest uplift of young deposits along a NW-trending blind reverse fault. Stratigraphy from Terrell Creek marsh, located just south of Birch Bay, shows freshwater peat buried by lower intertidal muds, indicating local submergence ~1300 yr BP. Stratigraphy of a 70-cm sediment core from Birch Bay marsh, sitting astride the anticline imaged with seismic reflection data, shows mud buried by detrital peat. One radiocarbon age from the core places the abrupt change from mud to peat prior to 1520-1700 yr BP. We divide fossil diatom assemblages straddling the mud-peat contact at Birch Bay into three zones. The oldest zone consists primarily of intertidal and marine diatoms, dominated by Paralia sulcata, Scoleoneis tumida, Grammataphora oceanica, and Gyrosigma balticum. An intermediate zone, beginning at the sharp contact between mud and overlying peat, consists of a mixture of brackish marsh and freshwater species, dominated by Diploneis interrupta, with lesser amounts of Aulacoseira sp., Pinnularia viridis, Eunotia pectinalis, and Paralia sulcata. A third and youngest zone lies in the upper half of the peat and is dominated by poorly preserved freshwater diatoms, mostly Aulacoseira cf. crassapuntata, Pinnularia viridis, P. maior, Eunotia pectinalis, and E. praerupta. Paleoecological inferences, based on distributions of modern diatoms

  4. Thatcher Bay, Washington, Nearshore Restoration Assessment

    Science.gov (United States)

    Breems, Joel; Wyllie-Echeverria, Sandy; Grossman, Eric E.; Elliott, Joel

    2009-01-01

    The San Juan Archipelago, located at the confluence of the Puget Sound, the Straits of Juan de Fuca in Washington State, and the Straits of Georgia, British Columbia, Canada, provides essential nearshore habitat for diverse salmonid, forage fish, and bird populations. With 408 miles of coastline, the San Juan Islands provide a significant portion of the available nearshore habitat for the greater Puget Sound and are an essential part of the regional efforts to restore Puget Sound (Puget Sound Shared Strategy 2005). The nearshore areas of the San Juan Islands provide a critical link between the terrestrial and marine environments. For this reason the focus on restoration and conservation of nearshore habitat in the San Juan Islands is of paramount importance. Wood-waste was a common by-product of historical lumber-milling operations. To date, relatively little attention has been given to the impact of historical lumber-milling operations in the San Juan Archipelago. Thatcher Bay, on Blakely Island, located near the east edge of the archipelago, is presented here as a case study on the restoration potential for a wood-waste contaminated nearshore area. Case study components include (1) a brief discussion of the history of milling operations. (2) an estimate of the location and amount of the current distribution of wood-waste at the site, (3) a preliminary examination of the impacts of wood-waste on benthic flora and fauna at the site, and (4) the presentation of several restoration alternatives for the site. The history of milling activity in Thatcher Bay began in 1879 with the construction of a mill in the southeastern part of the bay. Milling activity continued for more than 60 years, until the mill closed in 1942. Currently, the primary evidence of the historical milling operations is the presence of approximately 5,000 yd3 of wood-waste contaminated sediments. The distribution and thickness of residual wood-waste at the site was determined by using sediment

  5. Organelles genome stability of wheat plantlets produced by anther ...

    African Journals Online (AJOL)

    Yomi

    2012-03-15

    Mar 15, 2012 ... 1Department of Biotechnology, Faculty of Agricultural Technology, Al-Balqa' Applied University, ... genetic stability of wheat organelles genomes for plantlets produced by anther culture using restriction ..... of transgenic plants.

  6. Similar Ratios of Introns to Intergenic Sequence across Animal Genomes.

    Science.gov (United States)

    Francis, Warren R; Wörheide, Gert

    2017-06-01

    One central goal of genome biology is to understand how the usage of the genome differs between organisms. Our knowledge of genome composition, needed for downstream inferences, is critically dependent on gene annotations, yet problems associated with gene annotation and assembly errors are usually ignored in comparative genomics. Here, we analyze the genomes of 68 species across 12 animal phyla and some single-cell eukaryotes for general trends in genome composition and transcription, taking into account problems of gene annotation. We show that, regardless of genome size, the ratio of introns to intergenic sequence is comparable across essentially all animals, with nearly all deviations dominated by increased intergenic sequence. Genomes of model organisms have ratios much closer to 1:1, suggesting that the majority of published genomes of nonmodel organisms are underannotated and consequently omit substantial numbers of genes, with likely negative impact on evolutionary interpretations. Finally, our results also indicate that most animals transcribe half or more of their genomes arguing against differences in genome usage between animal groups, and also suggesting that the transcribed portion is more dependent on genome size than previously thought. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  7. Results of the Washington Passive Solar Design/Build Competition

    Energy Technology Data Exchange (ETDEWEB)

    Nylen, N.

    1981-01-01

    In an effort to encourage the design, construction, and marketing of moderately priced passive solar homes in Washington state, the Western Solar Utilization Network (Western SUN) recently sponsored the Washington Passive Solar Design/Build Competition. The competition drew an overwhelming response from designers and builders throughout Washington. Thermal performance of the designs was evaluated by a technical review committee, and final selections were made by the Competition Jury in accordance with the following criteria: perceived market acceptance, thermal performance, cost effectiveness, simplicity of design and operation, and completeness of the passive concept. Design contract awards totaling $50,000 were made available to winners in four categories, including single and multi-family, new and remodeled residences. In order to receive the award in its entirety, winning design/build teams are required to construct their design by April, 1983. As a result of the competition, a great deal was learned about the attitudes and knowledge of professionals and the general public regarding the use of solar energy in Washington state. Among the points that will be highlighted in this paper are the following: (1) a design/build competition is an effective vehicle for promoting solar energy among professionals in the housing community as well as the general public; (2) passive solar techniques can contribute significantly to the heating and cooling needs of residential housing throughout the state of Washington; (3) there is a great deal of interest and talent among the designers and builders of solar residences in Washington; and (4) follow-up activities, including the promotion of winning designs, the systematic collection of performance data, and identification of the major obstacles confronting designers and builders of solar homes, are critical to the success of the program in achieving both its short-term and long-term goals.

  8. Genomics With Cloud Computing

    Directory of Open Access Journals (Sweden)

    Sukhamrit Kaur

    2015-04-01

    Full Text Available Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computing to genomics are like easy access and sharing of data security of data less cost to pay for resources but still there are some demerits like large time needed to transfer data less network bandwidth.

  9. Genome Assembly Forensics: Metrics for Assessing Assembly Correctness (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    Energy Technology Data Exchange (ETDEWEB)

    Pop, Mihai

    2011-10-13

    University of Maryland's Mihai Pop on Genome Assembly Forensics: Metrics for Assessing Assembly Correctness at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  10. Sequencing Single Cell Microbial Genomes with Microfluidic Amplifications Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    Energy Technology Data Exchange (ETDEWEB)

    Quake, Steve

    2011-10-12

    Stanford University's Steve Quake on "Sequencing Single Cell Microbial Genomes with Microfluidic Amplification Tools" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  11. MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data.

    Science.gov (United States)

    Uchiyama, Ikuo; Mihara, Motohiro; Nishide, Hiroyo; Chiba, Hirokazu

    2015-01-01

    The microbial genome database for comparative analysis (MBGD) (available at http://mbgd.genome.ad.jp/) is a comprehensive ortholog database for flexible comparative analysis of microbial genomes, where the users are allowed to create an ortholog table among any specified set of organisms. Because of the rapid increase in microbial genome data owing to the next-generation sequencing technology, it becomes increasingly challenging to maintain high-quality orthology relationships while allowing the users to incorporate the latest genomic data available into an analysis. Because many of the recently accumulating genomic data are draft genome sequences for which some complete genome sequences of the same or closely related species are available, MBGD now stores draft genome data and allows the users to incorporate them into a user-specific ortholog database using the MyMBGD functionality. In this function, draft genome data are incorporated into an existing ortholog table created only from the complete genome data in an incremental manner to prevent low-quality draft data from affecting clustering results. In addition, to provide high-quality orthology relationships, the standard ortholog table containing all the representative genomes, which is first created by the rapid classification program DomClust, is now refined using DomRefine, a recently developed program for improving domain-level clustering using multiple sequence alignment information. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Coordinated Collection Development via CD-ROM. A Pilot Project Granted by LSCA Title III Funds to Crosby Library, Gonzaga University. Final Narrative Report.

    Science.gov (United States)

    Peterson, Elaine; Carr, Mary M.

    Three colleges in the state of Washington--Gonzaga College (Crosby Library), Whitworth College, and Eastern Washington University--received grants from the Fred Meyer Charitable Trust and the Library Services and Construction Act to facilitate coordinated collection development in the areas of education and business/economics, so that their…

  13. Locating inputs of freshwater to Lynch Cove, Hood Canal, Washington, using aerial infrared photography

    Science.gov (United States)

    Sheibley, Rich W.; Josberger, Edward G.; Chickadel, Chris

    2010-01-01

    The input of freshwater and associated nutrients into Lynch Cove and lower Hood Canal (fig. 1) from sources such as groundwater seeps, small streams, and ephemeral creeks may play a major role in the nutrient loading and hydrodynamics of this low dissolved-oxygen (hypoxic) system. These disbursed sources exhibit a high degree of spatial variability. However, few in-situ measurements of groundwater seepage rates and nutrient concentrations are available and thus may not represent adequately the large spatial variability of groundwater discharge in the area. As a result, our understanding of these processes and their effect on hypoxic conditions in Hood Canal is limited. To determine the spatial variability and relative intensity of these sources, the U.S. Geological Survey Washington Water Science Center collaborated with the University of Washington Applied Physics Laboratory to obtain thermal infrared (TIR) images of the nearshore and intertidal regions of Lynch Cove at or near low tide. In the summer, cool freshwater discharges from seeps and streams, flows across the exposed, sun-warmed beach, and out on the warm surface of the marine water. These temperature differences are readily apparent in aerial thermal infrared imagery that we acquired during the summers of 2008 and 2009. When combined with co-incident video camera images, these temperature differences allow identification of the location, the type, and the relative intensity of the sources.

  14. WashingtonOnline Virtual Campus: Infusing Culture in Dispersed Web-Based Higher Education

    Directory of Open Access Journals (Sweden)

    Shalin Hai-Jew

    2004-08-01

    Full Text Available Started in 1997, WashingtonOnline Virtual Campus (WAOL consists of a consortium of 34 community colleges around Washington State to provide asynchronous online learning. WAOL bears many of the features of a loosely coupled organization with its geographically dispersed frontline instructors, fragmented external environment, modularity of courses and supervision, and its use of enhanced leadership and technology to communicate a culture. Recent surveys of its administration, instructors, and staff found disparities in various constituencies’ perspectives on the organization’s culture, decision-making, values, brand or reputation, communications, and WAOL’s authorizing environment. Research suggests that WAOL benefits from some aspects of loose coupling: greater adaptive abilities and responsiveness to the State’s college system; “fast” course development and launching; and isolated breakdowns. There is, however, a persistent difficulty in conveying a cohesive culture. There is a perception of WAOL’s invisibility among its varied constituencies. This organization is at a crossroads, with the threat of colleges disconnecting from this consortium. WAOL should redefine its direction and purpose, such as coupling with local universities to provide not only associates degrees but full Baccalaureate and/ or Masters degrees. It may strengthen its position by improving learner supports, publicizing its decisions, creating a stronger sense of virtual community among the instructors (as in its recent creation of an online community for instructors, increased participative decision-making and use of line faculty and staff insights, and greater course varieties.

  15. 10KP: A phylodiverse genome sequencing plan

    Science.gov (United States)

    Cheng, Shifeng; Melkonian, Michael; Brockington, Samuel; Archibald, John M; Delaux, Pierre-Marc; Melkonian, Barbara; Mavrodiev, Evgeny V; Sun, Wenjing; Fu, Yuan; Yang, Huanming; Soltis, Douglas E; Graham, Sean W; Soltis, Pamela S; Liu, Xin; Xu, Xun

    2018-01-01

    Abstract Understanding plant evolution and diversity in a phylogenomic context is an enormous challenge due, in part, to limited availability of genome-scale data across phylodiverse species. The 10KP (10,000 Plants) Genome Sequencing Project will sequence and characterize representative genomes from every major clade of embryophytes, green algae, and protists (excluding fungi) within the next 5 years. By implementing and continuously improving leading-edge sequencing technologies and bioinformatics tools, 10KP will catalogue the genome content of plant and protist diversity and make these data freely available as an enduring foundation for future scientific discoveries and applications. 10KP is structured as an international consortium, open to the global community, including botanical gardens, plant research institutes, universities, and private industry. Our immediate goal is to establish a policy framework for this endeavor, the principles of which are outlined here. PMID:29618049

  16. 10KP: A phylodiverse genome sequencing plan.

    Science.gov (United States)

    Cheng, Shifeng; Melkonian, Michael; Smith, Stephen A; Brockington, Samuel; Archibald, John M; Delaux, Pierre-Marc; Li, Fay-Wei; Melkonian, Barbara; Mavrodiev, Evgeny V; Sun, Wenjing; Fu, Yuan; Yang, Huanming; Soltis, Douglas E; Graham, Sean W; Soltis, Pamela S; Liu, Xin; Xu, Xun; Wong, Gane Ka-Shu

    2018-03-01

    Understanding plant evolution and diversity in a phylogenomic context is an enormous challenge due, in part, to limited availability of genome-scale data across phylodiverse species. The 10KP (10,000 Plants) Genome Sequencing Project will sequence and characterize representative genomes from every major clade of embryophytes, green algae, and protists (excluding fungi) within the next 5 years. By implementing and continuously improving leading-edge sequencing technologies and bioinformatics tools, 10KP will catalogue the genome content of plant and protist diversity and make these data freely available as an enduring foundation for future scientific discoveries and applications. 10KP is structured as an international consortium, open to the global community, including botanical gardens, plant research institutes, universities, and private industry. Our immediate goal is to establish a policy framework for this endeavor, the principles of which are outlined here.

  17. Microbial genome analysis: the COG approach.

    Science.gov (United States)

    Galperin, Michael Y; Kristensen, David M; Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

    2017-09-14

    For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a popular tool for microbial genome annotation and comparative genomics. Initially created for the purpose of evolutionary classification of protein families, the COG have been used, apart from straightforward functional annotation of sequenced genomes, for such tasks as (i) unification of genome annotation in groups of related organisms; (ii) identification of missing and/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighborhoods, in many cases allowing prediction of novel functional systems; (iv) analysis of metabolic pathways and prediction of alternative forms of enzymes; (v) comparison of organisms by COG functional categories; and (vi) prioritization of targets for structural and functional characterization. Here we review the principles of the COG approach and discuss its key advantages and drawbacks in microbial genome analysis. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

  18. Economic Impact of Pacific Northwest National Laboratory on the State of Washington in Fiscal Year 2013

    Energy Technology Data Exchange (ETDEWEB)

    Scott, Michael J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Niemeyer, Jackie M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2014-12-01

    Pacific Northwest National Laboratory (PNNL) is a large economic entity, with $1.06 billion in annual funding, $936 million in total spending, and 4,344 employees in fiscal year (FY) 2013. Four thousand, one hundred and one (4,101) employees live in Washington State. The Laboratory directly and indirectly supports almost $1.31 billion in economic output, 6,802 jobs, and $514 million in Washington State wage income from current operations. The state also gains more than $1.21 billion in output, more than 6,400 jobs, and $459 million in income through closely related economic activities, such as visitors, health care spending, spending by resident retirees, and spinoff companies. PNNL affects Washington’s economy through commonly recognized economic channels, including spending on payrolls and other goods and services that support Laboratory operations. Less-commonly recognized channels also have their own impacts and include company-supported spending on health care for its staff members and retirees, spending of its resident retirees, Laboratory visitor spending, and the economic activities in a growing constellation of “spinoff” companies founded on PNNL research, technology, and managerial expertise. PNNL also has a significant impact on science and technology education and community nonprofit organizations. PNNL is an active participant in the future scientific enterprise in Washington with the state’s K-12 schools, colleges, and universities. The Laboratory sends staff members to the classroom and brings hundreds of students to the PNNL campus to help train the next generation of scientists, engineers, mathematicians, and technicians. This investment in human capital, though difficult to measure in terms of current dollars of economic output, is among the important lasting legacies of the Laboratory. Finally, PNNL contributes to the local community with millions of dollars’ worth of cash and in-kind corporate and staff contributions, all of which

  19. Economic Impact of Pacific Northwest National Laboratory on the State of Washington in Fiscal Year 2014

    Energy Technology Data Exchange (ETDEWEB)

    Scott, Michael J.; Niemeyer, Jackie M.

    2015-11-09

    PNNL is a large economic entity with a total of 4,308 employees, $939 million (M) in total funding, and $1.02 billion (B) in total spending during FY 2014. The number of employees that live in Washington State is 4,026 or 93 percent of the Laboratory staff. he Laboratory directly and indirectly supported $1.45 billion in economic output, 6,832 jobs, and $517 million in Washington State wage income from current operations. The state also gained more than $1.19 billion in output, over 6,200 jobs, and $444 million in income through closely related economic activities such as visitors, health care spending, spending by resident retirees, and spinoff companies. PNNL affects Washington’s economy through commonly recognized economic channels, including spending on payrolls and other goods and services that support Laboratory operations. Less commonly recognized channels also have their own impacts and include company-supported spending on health care for its staff members and retirees, spending of its resident retirees, Laboratory visitor spending, and the economic activities in a growing constellation of “spinoff” companies founded on PNNL research, technology, and managerial expertise. PNNL also has a significant impact on science and technology education and community not-for-profit organizations. PNNL is an active participant in the future scientific enterprise in Washington with the state’s K-12 schools, colleges, and universities. The Laboratory sends staff members to the classroom and brings hundreds of students to the PNNL campus to help train the next generation of scientists, engineers, mathematicians, and technicians. This investment in human capital, though difficult to measure in terms of current dollars of economic output, is among the important lasting legacies of the Laboratory. Finally, PNNL contributes to the local community with millions of dollars’ worth of cash and in-kind corporate and staff contributions, all of which strengthen the

  20. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend

    2002-01-01

    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies.

  1. Excellence Initiatives to Establish World-Class Universities: Evaluation of Recent Experiences

    OpenAIRE

    Jamil Salmi; Isak Froumin

    2013-01-01

    Jamil Salmi, Ph. D., coordinator of the World Banks tertiary education program (NW, Washington, D.C., United States), member of the International Advisory Panel, National Research University -Higher School of Economics, Moscow, Russian Federation. Email: Address: The World Bank Institute, 1818 H Street, NW, Washington, D.C. 20433, United States.Isak Froumin, Ped.D., Professor, Director of Research and Development at the Education Institute, National Research Unive...

  2. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  3. Visualization for genomics: the Microbial Genome Viewer.

    Science.gov (United States)

    Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

    2004-07-22

    A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

  4. Genomic prediction using subsampling

    OpenAIRE

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-01-01

    Background Genome-wide assisted selection is a critical tool for the?genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each rou...

  5. Universe symmetries

    International Nuclear Information System (INIS)

    Souriau, J.M.

    1984-01-01

    The sky uniformity can be noticed in studying the repartition of objects far enough. The sky isotropy description uses space rotations. The group theory elements will allow to give a meaning at the same time precise and general to the word a ''symmetry''. Universe models are reviewed, which must have both of the following qualities: - conformity with the physic known laws; - rigorous symmetry following one of the permitted groups. Each of the models foresees that universe evolution obeys an evolution equation. Expansion and big-bang theory are recalled. Is universe an open or closed space. Universe is also electrically neutral. That leads to a work hypothesis: the existing matter is not given data of universe but it appeared by evolution from nothing. Problem of matter and antimatter is then raised up together with its place in universe [fr

  6. Ebolavirus comparative genomics

    DEFF Research Database (Denmark)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms...

  7. Hello Mr. President! Rollenspiele zwischen Hollywood und Washington

    NARCIS (Netherlands)

    Mehring, F.

    2016-01-01

    Hello Mr. President Rollenspiele zwischen Hollywood und Washington Am 8. November 2016 entscheidet sich, wer zum 58. Präsidenten der USA gewählt wird: Die ehemalige Außenministerin Hillary Clinton oder der republikanische Kandidat Donald Trump. In der heißen Phase des Wahlkampfs fällt besonders

  8. Experience with Honeycrisp apple storage management in Washington

    Science.gov (United States)

    High demand and premium pricing have led to rapid increases in Honeycrisp plantings and fruit volume in Washington State, USA since introduction of the cultivar in 1999. Most fruit is packed and sold by January because of strong demand coupled with difficulties associated with extended storage. Howe...

  9. The State of Washington's Children, Summer 2002. [Tenth Annual Report].

    Science.gov (United States)

    Connell, Frederick A.; Brandon, Richard; Hill, Sheri L.; Carter, S. Louise; Garrison, Michelle M.; DeWys, Shelley; Mandell, Dorothy J.

    This Kids Count report is the tenth to examine annually statewide trends in the well-being of Washington's children and focuses on child poverty and the needs of the working poor. The statistical portrait is based on indicators of child well-being in five areas: (1) family and community, including teen birth rate, teen pregnancy rate, births to…

  10. Booker T. Washington's Audacious Vocationalist Philosophy

    Science.gov (United States)

    Lewis, Theodore

    2014-01-01

    Booker T. Washington was born a slave in the American South, rising remarkably in the period after slavery to become a leader of his race. His advocacy of appeasement with the Southern white establishment incurred the ire of his black peers, given the withdrawal of the franchise from ex-slaves in southern states after a brief period of positive…

  11. Digital Learning Compass: Distance Education State Almanac 2017. Washington

    Science.gov (United States)

    Seaman, Julia E.; Seaman, Jeff

    2017-01-01

    This brief report uses data collected under the U.S. Department of Education's National Center for Educational Statistics (NCES) Integrated Postsecondary Education Data System (IPEDS) Fall Enrollment survey to highlight distance education data in the state of Washington. The sample for this analysis is comprised of all active, degree-granting…

  12. 78 FR 46258 - Drawbridge Operation Regulation Lake Washington, Seattle, WA

    Science.gov (United States)

    2013-07-31

    ... that governs the Evergreen Point Floating Bridge (State Route 520 across Lake Washington) at Seattle... Department of Transportation has requested that the draw span of the Evergreen Point Floating Bridge (State... this time, which would divert road traffic onto the Evergreen Point Floating Bridge. The closure of the...

  13. Managing the Development of the Public Telecommunications Center, Spokane, Washington.

    Science.gov (United States)

    Schaar, Walter

    When the city council of Spokane (Washington) decided in 1971 to establish a cable franchise, it created a citizens' committee to set cable specifications. Representing Spokane School District 81 and KSPS-TV (a public television station licensed to the public schools of Spokane), the author of this document served on the committee that set five…

  14. The State of Washington's Children, Fall 2001. [Ninth Annual Report].

    Science.gov (United States)

    Washington Univ., Seattle. School of Public Health and Community Medicine.

    This Kids Count report is the ninth to examine annually statewide trends in the well-being of Washington's children. The statistical portrait is based on indicators of child well-being in five areas: (1) family and community, including teen birth rate, teen pregnancy rate, divorces involving children, and births to unmarried mothers; (2) economic…

  15. The State of Washington's Children. [Seventh Annual Report].

    Science.gov (United States)

    Marvinney, Sandy, Ed.

    This KIDS COUNT seventh annual report examines statewide trends in the well-being of Washington's children. The statistical portrait is based 24 key indicators of well-being: (1) teen birth rate; (2) teen pregnancy rate; (3) births to unmarried mothers; (4) divorces involving children; (5) family foster caseload; (6) average real wages; (7) per…

  16. Productivity of nonindustrial private forests in western Washington: alternative futures.

    Science.gov (United States)

    Ralph J. Alig; Darius M. Adams

    1995-01-01

    Nonindustrial private timberlands in western Washington have high productive potential and contribute harvest amounts somewhat more than proportional to their area. Of all private ownerships they are influenced the most by land use shifts and are affected in important ways by forest practice regulations. About 1 million acres of nonindustrial private timberland contain...

  17. Timber resource statistics for Washington, January 1, 1973.

    Science.gov (United States)

    Patricia M. Bassett; Grover A. Choate

    1974-01-01

    Timber resource statistics to January 1, 1973, for the State of Washington show total land area, commercial timberland area, and growing stock and sawtimber inventory volumes by county and owner group. Growth and removals are shown by Forest Survey inventory unit for 1972. Each National Forest is updated to January 1, 1973.

  18. Large-scale silviculture experiments of western Oregon and Washington.

    Science.gov (United States)

    Nathan J. Poage; Paul D. Anderson

    2007-01-01

    We review 12 large-scale silviculture experiments (LSSEs) in western Washington and Oregon with which the Pacific Northwest Research Station of the USDA Forest Service is substantially involved. We compiled and arrayed information about the LSSEs as a series of matrices in a relational database, which is included on the compact disc published with this report and...

  19. Alternative Fuels Data Center: Washington Transportation Data for

    Science.gov (United States)

    stations in Washington with alternative fuels Fuel Public Private Biodiesel (B20 and above) 8 33 Compressed Partnerships Spark Biodiesel Success for Essential Baking Company Partnerships Spark Biodiesel Success for Videos on YouTube Video thumbnail for Seattle Bakery Delivers With Biodiesel Trucks Seattle Bakery

  20. A 2015 comparison of operational performance : Washington state ferries to ferry operators worldwide.

    Science.gov (United States)

    2015-03-01

    This report provides an update to the 2010 report A Comparison of Operational Performance: : Washington State Ferries to Ferry Operators Worldwide, observing changes in Washington State : Ferries, 23 other ferry systems, and the ferry industry ...

  1. Marijuana, other drugs, and alcohol use by drivers in Washington State.

    Science.gov (United States)

    2016-07-01

    In Washington State legal sales of marijuana began July 8, 2014. A voluntary, anonymous roadside study was conducted to assess the prevalence of drivers testing positive for alcohol and other drugs, including marijuana, on Washingtons roads. Data ...

  2. Marijuana, other drugs, and alcohol use by drivers in Washington state : appendices.

    Science.gov (United States)

    2016-07-01

    In Washington State legal sales of marijuana began July 8, 2014. A voluntary, anonymous roadside study was conducted to assess the prevalence of drivers testing positive for alcohol and other drugs, including marijuana, on Washingtons roads. Data ...

  3. 78 FR 13887 - Notice of Inventory Completion: Washington State Parks and Recreation Commission, Olympia, WA

    Science.gov (United States)

    2013-03-01

    ... Washington State Parks and Recreation Commission at the address below by April 1, 2013. ADDRESSES: Alicia... contact Alicia Woods, Washington State Parks and Recreation Commission, PO Box 42650, Olympia, WA 98504...

  4. 77 FR 48535 - Notice of Inventory Completion: Washington State Parks and Recreation Commission, Olympia, WA

    Science.gov (United States)

    2012-08-14

    ...: Alicia Woods, Washington State Parks and Recreation Commission, P.O. Box 42650, Olympia, WA 98504-2650... it satisfies the criteria in 43 CFR 10.11(c)(1) should contact Alicia Woods, Washington State Parks...

  5. 77 FR 61782 - Notice of Inventory Completion: Washington State Parks and Recreation Commission, Olympia, WA

    Science.gov (United States)

    2012-10-11

    ... Washington State Parks and Recreation Commission at the address below by November 13, 2012. ADDRESSES: Alicia... affiliated with the human remains should contact Alicia Woods, Washington State Parks and Recreation...

  6. Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes.

    Science.gov (United States)

    Hirsch, Cory D; Evans, Joseph; Buell, C Robin; Hirsch, Candice N

    2014-07-01

    Technology and software improvements in the last decade now provide methodologies to access the genome sequence of not only a single accession, but also multiple accessions of plant species. This provides a means to interrogate species diversity at the genome level. Ample diversity among accessions in a collection of species can be found, including single-nucleotide polymorphisms, insertions and deletions, copy number variation and presence/absence variation. For species with small, non-repetitive rich genomes, re-sequencing of query accessions is robust, highly informative, and economically feasible. However, for species with moderate to large sized repetitive-rich genomes, technical and economic barriers prevent en masse genome re-sequencing of accessions. Multiple approaches to access a focused subset of loci in species with larger genomes have been developed, including reduced representation sequencing, exome capture and transcriptome sequencing. Collectively, these approaches have enabled interrogation of diversity on a genome scale for large plant genomes, including crop species important to worldwide food security. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  7. EUPAN enables pan-genome studies of a large number of eukaryotic genomes.

    Science.gov (United States)

    Hu, Zhiqiang; Sun, Chen; Lu, Kuang-Chen; Chu, Xixia; Zhao, Yue; Lu, Jinyuan; Shi, Jianxin; Wei, Chaochun

    2017-08-01

    Pan-genome analyses are routinely carried out for bacteria to interpret the within-species gene presence/absence variations (PAVs). However, pan-genome analyses are rare for eukaryotes due to the large sizes and higher complexities of their genomes. Here we proposed EUPAN, a eukaryotic pan-genome analysis toolkit, enabling automatic large-scale eukaryotic pan-genome analyses and detection of gene PAVs at a relatively low sequencing depth. In the previous studies, we demonstrated the effectiveness and high accuracy of EUPAN in the pan-genome analysis of 453 rice genomes, in which we also revealed widespread gene PAVs among individual rice genomes. Moreover, EUPAN can be directly applied to the current re-sequencing projects primarily focusing on single nucleotide polymorphisms. EUPAN is implemented in Perl, R and C ++. It is supported under Linux and preferred for a computer cluster with LSF and SLURM job scheduling system. EUPAN together with its standard operating procedure (SOP) is freely available for non-commercial use (CC BY-NC 4.0) at http://cgm.sjtu.edu.cn/eupan/index.html . ccwei@sjtu.edu.cn or jianxin.shi@sjtu.edu.cn. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  8. Researcher Mobility at a US Research-Intensive University: Implications for Research and Internationalization Strategies

    Science.gov (United States)

    Payumo, Jane G.; Lan, George; Arasu, Prema

    2018-01-01

    This study offers a unique lens on the patterns, productivity, and impact of researcher mobility at a US research-intensive university. Bibliometric data for Washington State University (WSU) was extracted from Elsevier's Scopus database and analyzed for the 10-year period from 2002 to 2012. We grouped researchers into four categories based on…

  9. SNUGB: a versatile genome browser supporting comparative and functional fungal genomics

    Directory of Open Access Journals (Sweden)

    Kim Seungill

    2008-12-01

    Full Text Available Abstract Background Since the full genome sequences of Saccharomyces cerevisiae were released in 1996, genome sequences of over 90 fungal species have become publicly available. The heterogeneous formats of genome sequences archived in different sequencing centers hampered the integration of the data for efficient and comprehensive comparative analyses. The Comparative Fungal Genomics Platform (CFGP was developed to archive these data via a single standardized format that can support multifaceted and integrated analyses of the data. To facilitate efficient data visualization and utilization within and across species based on the architecture of CFGP and associated databases, a new genome browser was needed. Results The Seoul National University Genome Browser (SNUGB integrates various types of genomic information derived from 98 fungal/oomycete (137 datasets and 34 plant and animal (38 datasets species, graphically presents germane features and properties of each genome, and supports comparison between genomes. The SNUGB provides three different forms of the data presentation interface, including diagram, table, and text, and six different display options to support visualization and utilization of the stored information. Information for individual species can be quickly accessed via a new tool named the taxonomy browser. In addition, SNUGB offers four useful data annotation/analysis functions, including 'BLAST annotation.' The modular design of SNUGB makes its adoption to support other comparative genomic platforms easy and facilitates continuous expansion. Conclusion The SNUGB serves as a powerful platform supporting comparative and functional genomics within the fungal kingdom and also across other kingdoms. All data and functions are available at the web site http://genomebrowser.snu.ac.kr/.

  10. The Sequenced Angiosperm Genomes and Genome Databases.

    Science.gov (United States)

    Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

    2018-01-01

    Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

  11. Genome-wide study of correlations between genomic features and their relationship with the regulation of gene expression.

    Science.gov (United States)

    Kravatsky, Yuri V; Chechetkin, Vladimir R; Tchurikov, Nikolai A; Kravatskaya, Galina I

    2015-02-01

    The broad class of tasks in genetics and epigenetics can be reduced to the study of various features that are distributed over the genome (genome tracks). The rapid and efficient processing of the huge amount of data stored in the genome-scale databases cannot be achieved without the software packages based on the analytical criteria. However, strong inhomogeneity of genome tracks hampers the development of relevant statistics. We developed the criteria for the assessment of genome track inhomogeneity and correlations between two genome tracks. We also developed a software package, Genome Track Analyzer, based on this theory. The theory and software were tested on simulated data and were applied to the study of correlations between CpG islands and transcription start sites in the Homo sapiens genome, between profiles of protein-binding sites in chromosomes of Drosophila melanogaster, and between DNA double-strand breaks and histone marks in the H. sapiens genome. Significant correlations between transcription start sites on the forward and the reverse strands were observed in genomes of D. melanogaster, Caenorhabditis elegans, Mus musculus, H. sapiens, and Danio rerio. The observed correlations may be related to the regulation of gene expression in eukaryotes. Genome Track Analyzer is freely available at http://ancorr.eimb.ru/. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  12. Basic Education for Adults: Pathways to College and Careers for Washington's Emerging Workforce. Washington's Community and Technical Colleges

    Science.gov (United States)

    Washington State Board for Community and Technical Colleges, 2015

    2015-01-01

    This brief describes the Basic Education for Adults (BEdA) programs that bridge the gap between school and work, thereby creating pathways to college and careers for Washington's emerging workforce. BEdA programs teach foundational skills--reading, writing, math, technology and English language--so adults can move through college and into…

  13. 78 FR 53235 - 50th Anniversary of the March on Washington for Jobs and Freedom

    Science.gov (United States)

    2013-08-28

    ... Anniversary of the March on Washington for Jobs and Freedom By the President of the United States of America A... waters of the reflecting pool, to the proud base of the Washington Monument. They were men and women..., and justice for all. The March on Washington capped off a summer of discontent, a time when the...

  14. 77 FR 50157 - Notice of Public Meeting, Eastern Washington Resource Advisory Council Meeting

    Science.gov (United States)

    2012-08-20

    ...; HAG 12-0260] Notice of Public Meeting, Eastern Washington Resource Advisory Council Meeting AGENCY.... Department of the Interior, Bureau of Land Management (BLM) Eastern Washington Resource Advisory Council... Bureau of Land Management's Eastern Washington and San Juan Resource Management Plan and the U.S. Forest...

  15. 77 FR 23495 - Notice of Public Meeting, Eastern Washington Resource Advisory Council Meeting

    Science.gov (United States)

    2012-04-19

    ...; HAG 12-0164] Notice of Public Meeting, Eastern Washington Resource Advisory Council Meeting AGENCY... 1972, the U.S. Department of the Interior, Bureau of Land Management (BLM) Eastern Washington Resource... of Land Management's Eastern Washington and San Juan Resource Management Plan, and the U.S. Forest...

  16. Anticipation of Personal Genomics Data Enhances Interest and Learning Environment in Genomics and Molecular Biology Undergraduate Courses.

    Science.gov (United States)

    Weber, K Scott; Jensen, Jamie L; Johnson, Steven M

    2015-01-01

    An important discussion at colleges is centered on determining more effective models for teaching undergraduates. As personalized genomics has become more common, we hypothesized it could be a valuable tool to make science education more hands on, personal, and engaging for college undergraduates. We hypothesized that providing students with personal genome testing kits would enhance the learning experience of students in two undergraduate courses at Brigham Young University: Advanced Molecular Biology and Genomics. These courses have an emphasis on personal genomics the last two weeks of the semester. Students taking these courses were given the option to receive personal genomics kits in 2014, whereas in 2015 they were not. Students sent their personal genomics samples in on their own and received the data after the course ended. We surveyed students in these courses before and after the two-week emphasis on personal genomics to collect data on whether anticipation of obtaining their own personal genomic data impacted undergraduate student learning. We also tested to see if specific personal genomic assignments improved the learning experience by analyzing the data from the undergraduate students who completed both the pre- and post-course surveys. Anticipation of personal genomic data significantly enhanced student interest and the learning environment based on the time students spent researching personal genomic material and their self-reported attitudes compared to those who did not anticipate getting their own data. Personal genomics homework assignments significantly enhanced the undergraduate student interest and learning based on the same criteria and a personal genomics quiz. We found that for the undergraduate students in both molecular biology and genomics courses, incorporation of personal genomic testing can be an effective educational tool in undergraduate science education.

  17. THE APPLE JUICE CONCENTRATE ANTI-DUMPING CASE AGAINST CHINA: AN ESTIMATE OF CHANGE IN WASHINGTON'S REVENUES

    OpenAIRE

    van Voorthuizen, Hilde; Cho, Sung-Yeol; Schotzko, R. Thomas; Mittelhammer, Ronald C.

    2001-01-01

    Increasing volumes of apple juice concentrate imports from China into the U.S. began in the mid 90s as a result of low Chinese prices. In 1999, the U.S. Apple Association launched a complaint with the US International Trade Commission (USITC) regarding the Chinese price strategy. During the course of investigation, the U.S. Apple Association requested that the Department of Agricultural Economics at Washington State University analyze the impact on the total value of juice apples utilized in ...

  18. Our Universe

    Science.gov (United States)

    Stern, Alan

    2001-03-01

    The Universe in which we live is unimaginably vast and ancient, with countless star systems, galaxies, and extraordinary phenomena such as black holes, dark matter, and gamma ray bursts. What phenomena remain mysteries, even to seasoned scientists? Our Universe is a fascinating collection of essays by some of the world's foremost astrophysicists. Some are theorists, some computational modelers, some observers, but all offer their insights into the most cutting-edge, difficult, and curious aspects of astrophysics. Compiled, the essays describe more than the latest techniques and findings. Each of the ten contributors offers a more personal perspective on their work, revealing what motivates them and how their careers and lives have been shaped by their desire to understand our universe. S. Alan Stern is Director of the Department of Space Studies at Southwest Research Institute in Boulder, Colorado. He is a planetary scientist and astrophysicist with both observational and theoretical interests. Stern is an avid pilot and a principal investigator in NASA's planetary research program, and he was selected to be a NASA space shuttle mission specialist finalist. He is the author of more than 100 papers and popular articles. His most recent book is Pluto & Charon (Wiley, 1997). Contributors: Dr. John Huchra, Harvard University Dr. Esther Hu, University of Hawaii, Honolulu Dr. John Mather, NASA Goddard Space Flight Center Dr. Nick Gnedin, University of Colorado, Boulder Dr. Doug Richstone, University of Michigan, Ann Arbor Dr. Bohdan Paczynski, Princeton University, NJ Dr. Megan Donahue, Space Telescope Science Institute, Baltimore, MD Dr. Jerry Ostriker, Princeton University, New Jersey G. Bothun, University of Oregon, Eugene

  19. Modeling hazardous mass flows Geoflows09: Mathematical and computational aspects of modeling hazardous geophysical mass flows; Seattle, Washington, 9–11 March 2009

    Science.gov (United States)

    Iverson, Richard M.; LeVeque, Randall J.

    2009-01-01

    A recent workshop at the University of Washington focused on mathematical and computational aspects of modeling the dynamics of dense, gravity-driven mass movements such as rock avalanches and debris flows. About 30 participants came from seven countries and brought diverse backgrounds in geophysics; geology; physics; applied and computational mathematics; and civil, mechanical, and geotechnical engineering. The workshop was cosponsored by the U.S. Geological Survey Volcano Hazards Program, by the U.S. National Science Foundation through a Vertical Integration of Research and Education (VIGRE) in the Mathematical Sciences grant to the University of Washington, and by the Pacific Institute for the Mathematical Sciences. It began with a day of lectures open to the academic community at large and concluded with 2 days of focused discussions and collaborative work among the participants.

  20. Basic Research at the University of Washington to Counter Improvised Explosive Devices

    Science.gov (United States)

    2011-01-31

    frequency equal to ωS = ω1 + ω2. As a concrete example of this process, when photons having wavelengths of 1064 nm and 532 nm illuminate the surface of...Second, common obscuring materials (e.g., cellulose, plastic) are translucent to THz radiation, so detection and imaging of spectral signatures inside

  1. 75 FR 5105 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2010-02-01

    ... majority of dates for the site fall in the range of 1250 to 1650 years ago. Burial context in a shell... projectile point. Historical documentation indicates that the southern Lopez Island area is part of the...

  2. Final Report for the ADMX Phase 2a Project at the University of Washington

    International Nuclear Information System (INIS)

    Rosenberg, Leslie J.

    2015-01-01

    This is a final report of the ADMX (Axion Dark Matter eXperiment) Phase 2a program. This program is a project allowing for a sensitive axion dark-matter search at higher axion masses. The Phase 2a program also prepares the project for lower temperature anticipated in later operations. The Phase 2a program includes sensitive data-taking operations at two cavity modes, TM010 and TM020, allowing for faster data-taking operations and extending the search to higher and plausible dark-matter axion masses.

  3. 76 FR 28806 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2011-05-18

    ... remains of a female. In 1922, a Tlingit individual identified her as a shaman or Indian doctor known to... Tlingit included placing the human remains of shamans in a little house or cave (DeLaguna 1990) with some...

  4. Documentation for University of Washington Seaglider records archived at NODC (NODC Accession 0092291)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Seagliders are small (1.8m hull), reusable, long-range, and buoyancy-driven autonomous underwater vehicles (AUVs) designed to glide from the ocean surface to as deep...

  5. 78 FR 59956 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2013-09-30

    .... Material culture observed at the site include projectile points, mauls, adze blades, red ochre, bone bipoints and faunal material is consistent with Native American Coast Salish material culture. Based on...

  6. 77 FR 59649 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2012-09-28

    ... sites and are considered part of the Gulf of Georgia Culture Area. Material culture observed at the... with Native American Coast Salish material culture. Oral history indicates that Orcas Island was... part of the Gulf of Georgia Culture Area. The human remains from these three sites are consistent with...

  7. 78 FR 50443 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2013-08-19

    ... midden component and dates to approximately 670 radiocarbon years ago. Material culture observed at the sites, projectile points, carved antler fragments, ochre, toggling harpoons, faunal material and basketry, is consistent with Native American Coast Salish material culture. Linguistically, Native American...

  8. 75 FR 436 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

    Science.gov (United States)

    2010-01-05

    ... steam shovel crew. The human remains were transferred to the King County Coroner's Office and..., bossing of the cranium, presence of wormian bones, or shovel shaped incisors. Information available in the... bones, or shovel shaped incisors. Information available in the original accession files helped affirm...

  9. Ego Development and Conformity: A Construct Validity Study of the Washington University Sentence Completion Test

    Science.gov (United States)

    Hoppe, Carl F.; Loevinger, Jane

    1977-01-01

    Self and peer evaluations and experimental measures of conformity were given to 107 adolescent private school boys. Student discipline records also indicated the number of demerits. The self-report measures and the demerits showed maximum conformity between the self-protective and conscientious ego stages as measured by the Sentence Completion…

  10. 78 FR 21401 - Notice of Inventory Completion: Central Washington University, Ellensburg, WA

    Science.gov (United States)

    2013-04-10

    ... Graves Protection and Repatriation Act (NAGPRA), 25 U.S.C. 3003, of the completion of an inventory of... administrative responsibilities under NAGPRA, 25 U.S.C. 3003(d)(3) and 43 CFR 10.11(d). The determinations in...-pams or Sokulks were Shahap-tam Indians and occupied both banks of the Columbia from a short distance...

  11. 75 FR 36717 - Washington State University; Notice of Acceptance for Docketing and Opportunity for Hearing on...

    Science.gov (United States)

    2010-06-28

    ... to SGI if the request is granted, including the identity of any expert, consultant, or assistant who... party or its counsel may be shown by reliance on a qualified expert, consultant, or assistant who... access to SUNSI or SGI, and motions for protective orders, in a timely fashion in order to minimize any...

  12. A Brief History of the Resting State: the Washington University Perspective

    Science.gov (United States)

    Snyder, Abraham Z.; Raichle, Marcus E.

    2012-01-01

    We present a history of the concepts and developments that have led us to focus on the resting state as an object of study. We then discuss resting state research performed in our laboratory since 2005 with an emphasis on papers of particular interest. PMID:22266172

  13. Clinical experience of therapy with cyclotron neutrons at the University of Washington

    International Nuclear Information System (INIS)

    Parker, R.G.; Gerdes, A.J.; Berry, H.C.; Soronen, M.D.

    1975-01-01

    Proper clinical evaluation of fast neutron teletherapy of human cancers will be difficult and time-consuming and will require extension over many years. Fast neutron teletherapy may not have significant advantage over modern conventional supervoltage/megavoltage radiation therapy. A negative answer will be acceptable only if based on sound evidence. If fast neutron teletherapy has an advantage over modern conventional radiation therapy, the advantage may be small and tumor- and site-specific. Detection of a small advantage will require study of a large number of patients and this will be possible only in carefully planned cooperative clinical trials. The study of a large number of patients over a long period will require installation of dedicated neutron generators in research-oriented medical centers. Cooperative clinical trials must be preceded by careful definition of target tumors, normal tissue tolerances, reasonable doses and advantageous patterns of application. Any improvement in local tumor control attributed to fast neutron teletherapy might be dissipated by a concurrent increase in treatment-related sequelae. Much related physics and radiobiology remains to be done and must be supported concurrent with the clinical programs

  14. Incorporating inquiry and the process of science into introductory astronomy labs at the George Washington University

    Science.gov (United States)

    Cobb, Bethany E.

    2018-01-01

    Since 2013, the Physics Department at GWU has used student-centered active learning in the introductory astronomy course “Introduction to the Cosmos.” Class time is spent in groups on questions, math problems, and hands-on activities, with multiple instructors circulating to answer questions and engage with the students. The students have responded positively to this active-learning. Unfortunately, in transitioning to active-learning there was no time to rewrite the labs. Very quickly, the contrast between the dynamic classroom and the traditional labs became apparent. The labs were almost uniformly “cookie-cutter” in that the procedure and analysis were specified step-by-step and there was just one right answer. Students rightly criticized the labs for lacking a clear purpose and including busy-work. Furthermore, this class fulfills the GWU scientific reasoning general education requirement and thus includes learning objectives related to understanding the scientific method, testing hypotheses with data, and considering uncertainty – but the traditional labs did not require these skills. I set out to rejuvenate the lab sequence by writing new inquiry labs based on both topic-specific and scientific reasoning learning objectives. While inquiry labs can be challenging for the students, as they require active thinking and creativity, these labs engage the students more thoroughly in the scientific process. In these new labs, whenever possible, I include real astronomical data and ask the students to use digital tools (SDSS SkyServer, SOHO archive) as if they are real astronomers. To allow students to easily plot, manipulate and analyze data, I built “smart” Excel files using formulas, dropdown menus and macros. The labs are now much more authentic and thought-provoking. Whenever possible, students independently develop questions, hypotheses, and procedures and the scientific method is “scaffolded” over the semester by providing more guidance in the early labs and more independence later on. Finally, in every lab, students must identify and reflect on sources of error. These labs are more challenging for the instructors to run and to grade, but they are much more satisfying when it comes to student learning.

  15. Genomic analyses of the CAM plant pineapple.

    Science.gov (United States)

    Zhang, Jisen; Liu, Juan; Ming, Ray

    2014-07-01

    The innovation of crassulacean acid metabolism (CAM) photosynthesis in arid and/or low CO2 conditions is a remarkable case of adaptation in flowering plants. As the most important crop that utilizes CAM photosynthesis, the genetic and genomic resources of pineapple have been developed over many years. Genetic diversity studies using various types of DNA markers led to the reclassification of the two genera Ananas and Pseudananas and nine species into one genus Ananas and two species, A. comosus and A. macrodontes with five botanical varieties in A. comosus. Five genetic maps have been constructed using F1 or F2 populations, and high-density genetic maps generated by genotype sequencing are essential resources for sequencing and assembling the pineapple genome and for marker-assisted selection. There are abundant expression sequence tag resources but limited genomic sequences in pineapple. Genes involved in the CAM pathway has been analysed in several CAM plants but only a few of them are from pineapple. A reference genome of pineapple is being generated and will accelerate genetic and genomic research in this major CAM crop. This reference genome of pineapple provides the foundation for studying the origin and regulatory mechanism of CAM photosynthesis, and the opportunity to evaluate the classification of Ananas species and botanical cultivars. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  16. Intelligent Universe

    Energy Technology Data Exchange (ETDEWEB)

    Hoyle, F

    1983-01-01

    The subject is covered in chapters, entitled: chance and the universe (synthesis of proteins; the primordial soup); the gospel according to Darwin (discussion of Darwin theory of evolution); life did not originate on earth (fossils from space; life in space); the interstellar connection (living dust between the stars; bacteria in space falling to the earth; interplanetary dust); evolution by cosmic control (microorganisms; genetics); why aren't the others here (a cosmic origin of life); after the big bang (big bang and steady state); the information rich universe; what is intelligence up to; the intelligent universe.

  17. The genome draft of coconut (Cocos nucifera).

    Science.gov (United States)

    Xiao, Yong; Xu, Pengwei; Fan, Haikuo; Baudouin, Luc; Xia, Wei; Bocs, Stéphanie; Xu, Junyang; Li, Qiong; Guo, Anping; Zhou, Lixia; Li, Jing; Wu, Yi; Ma, Zilong; Armero, Alix; Issali, Auguste Emmanuel; Liu, Na; Peng, Ming; Yang, Yaodong

    2017-11-01

    antiporter gene family and ion channel gene families between C. nucifera and Arabidopsis thaliana indicated that significant gene expansion may have occurred in the coconut involving Na+/H+ antiporter, carnitine/acylcarnitine translocase, potassium-dependent sodium-calcium exchanger, and potassium channel genes. Despite its agronomic importance, C. nucifera is still under-studied. In this report, we present a draft genome of C. nucifera and provide genomic information that will facilitate future functional genomics and molecular-assisted breeding in this crop species. © The Author 2017. Published by Oxford University Press.

  18. ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.

    Science.gov (United States)

    Sablok, Gaurav; Chen, Ting-Wen; Lee, Chi-Ching; Yang, Chi; Gan, Ruei-Chi; Wegrzyn, Jill L; Porta, Nicola L; Nayak, Kinshuk C; Huang, Po-Jung; Varotto, Claudio; Tang, Petrus

    2017-06-01

    Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  19. Opportunities for addressing laminated root rot caused by Phellinus sulphuracens in Washington's forests: A Report from the Washington State Academy of Sciences in cooperation with the Washington State Department of Natural Resources

    Science.gov (United States)

    R. James Cook; Robert L. Edmonds; Ned B. Klopfenstein; Willis Littke; Geral McDonald; Daniel Omdahl; Karen Ripley; Charles G. Shaw; Rona Sturrock; Paul Zambino

    2013-01-01

    This report from the Washington State Academy of Sciences (WSAS) is in response to a request from the Washington State Department of Natural Resources (DNR) to "identify approaches and opportunities ripe for research on understanding and managing root diseases of Douglas-fir." Similar to the process used by the National Research Council, the WSAS upon...

  20. Reaching Higher. A Parent's Guide to the Washington Assessment of Learning. Revised = Para llegar mas arriba. Una guia para padres sobre la evaluacion del aprendizaje de los estudiantes del estado de Washington (Washington Assessment of Student Learning). Revisado.

    Science.gov (United States)

    Washington Office of the State Superintendent of Public Instruction, Olympia.

    This guide in English and Spanish is designed to answer questions parents may have about the Washington Assessment of Student Learning (WASL), including how it will help improve their children's education, how it is scored, and how to use the information it provides. In Washington, clear educational goals for subject content, thinking skills, and…

  1. USAID University

    Data.gov (United States)

    US Agency for International Development — USAID University is USAID's learning management system. Features include 1) Access online courses 2) Register for instructor-led courses 3)Access your student...

  2. Runaway universe

    Energy Technology Data Exchange (ETDEWEB)

    Davies, P

    1978-01-01

    The subject is covered in chapters entitled: the emerging universe (general introduction, history of astronomical and cosmological research, origins, the expanding universe, stars, galaxies, electromagnetic radiation); primeval fire (the big bang model, origin of the elements, properties of the elements and of sub-atomic particles); order out of chaos (galactic evolution, star formation, nuclear fusion, the solar system, origin of life on Earth); a star called Sol (properties of the sun and of other stars); life in the universe; the catastrophe principle (the rise and fall of cosmic order); stardoom (star evolution, neutron stars); black holes and superholes (gravitational collapse); technology and survival; the dying universe (second law of thermodynamics); worlds without end (cosmological models).

  3. Rhodes University

    African Journals Online (AJOL)

    Samridhi Sharma

    2013-10-29

    Oct 29, 2013 ... been taken may improve the reception, by the target audience, of the intended communication. This may ... alcohol marketing. Similarly .... of the intended users (Rhodes University support staff ..... Digital Human Modeling and.

  4. Undulant Universe

    Energy Technology Data Exchange (ETDEWEB)

    Barenboim, Gabriela; /Valencia U.; Mena, Olga; Quigg, Chris; /Fermilab

    2004-12-01

    If the equation of state for ''dark energy'' varies periodically, the expansion of the Universe may have undergone alternating eras of acceleration and deceleration. We examine a specific form that survives existing observational tests, does not single out the present state of the Universe as exceptional, and suggests a future much like the matter-dominated past: a smooth expansion without a final inflationary epoch.

  5. Routine environmental audit of the Hanford Site, Richland, Washington

    Energy Technology Data Exchange (ETDEWEB)

    1994-05-01

    This report documents the results of the routine environmental audit of the Hanford Site (Hanford), Richland, Washington. During this audit, the activities conducted by the audit team included reviews of internal documents an reports from previous audits and assessments; interviews with US Department of Energy (DOE), State of Washington regulatory, and contractor personnel; and inspections and observations of selected facilities and operations. The onsite portion of the audit was conducted May 2--13, 1994, by the DOE Office of Environmental Audit (EH-24), located within the Office of Environment, Safety and Health (EH). The audit evaluated the status of programs to ensure compliance with Federal, State, and local environmental laws and regulations; compliance with DOE orders, guidance, and directives; and conformance with accepted industry practices and standards of performance. The audit also evaluated the status and adequacy of the management systems developed to address environmental requirements.

  6. El Consenso de Washington: aciertos, yerros y omisiones

    Directory of Open Access Journals (Sweden)

    Juan Carlos Moreno-Brid

    2004-12-01

    Full Text Available This paper analyses the economic and social development of Latin America after nearly two decades of macroeconomic policies and reforms in line with the “Washington Consensus”. It shows that these policies did lower inflation and induced an export boom, but failed to boost domestic investment and to remove the balance of payments binding constraint on the region’s long–term path of economic expansion. Four alternative explanations of such poor performance of the Washington Consensus are compared. It is argued, in particular, that, contrary to mainstream opinion, in Latin America there is no clear association between the depth of macroeconomic reforms and economic growth performance.

  7. Routine environmental audit of the Hanford Site, Richland, Washington

    International Nuclear Information System (INIS)

    1994-05-01

    This report documents the results of the routine environmental audit of the Hanford Site (Hanford), Richland, Washington. During this audit, the activities conducted by the audit team included reviews of internal documents an reports from previous audits and assessments; interviews with US Department of Energy (DOE), State of Washington regulatory, and contractor personnel; and inspections and observations of selected facilities and operations. The onsite portion of the audit was conducted May 2--13, 1994, by the DOE Office of Environmental Audit (EH-24), located within the Office of Environment, Safety and Health (EH). The audit evaluated the status of programs to ensure compliance with Federal, State, and local environmental laws and regulations; compliance with DOE orders, guidance, and directives; and conformance with accepted industry practices and standards of performance. The audit also evaluated the status and adequacy of the management systems developed to address environmental requirements

  8. Status of birds at the Hanford Site in southeastern Washington

    International Nuclear Information System (INIS)

    Landeen, D.S.; Johnson, A.R.; Mitchell, R.M.

    1992-06-01

    The US Department of Energy has entered into agreements with the Washington State Department of Ecology, the US Environmental Protection Agency, and Hanford Site contractors to focus work activities on cleanup and stabilization of radioactive and hazardous waste sites located at the Hanford Site in southeastern Washington. Ecological characterization is an essential part of the remediation process, and the identification of biotic components such as bird species that could be impacted by cleanup activities is an important part of the initial environmental characterizations. Site characterization work has resulted in this list of 238 birds that have been observed at the Hanford Site. This list is presented with a status rating for abundance and seasonal occurrence

  9. Draft genome of the gayal, Bos frontalis

    Science.gov (United States)

    Wang, Ming-Shan; Zeng, Yan; Wang, Xiao; Nie, Wen-Hui; Wang, Jin-Huan; Su, Wei-Ting; Xiong, Zi-Jun; Wang, Sheng; Qu, Kai-Xing; Yan, Shou-Qing; Yang, Min-Min; Wang, Wen; Dong, Yang; Zhang, Ya-Ping

    2017-01-01

    Abstract Gayal (Bos frontalis), also known as mithan or mithun, is a large endangered semi-domesticated bovine that has a limited geographical distribution in the hill-forests of China, Northeast India, Bangladesh, Myanmar, and Bhutan. Many questions about the gayal such as its origin, population history, and genetic basis of local adaptation remain largely unresolved. De novo sequencing and assembly of the whole gayal genome provides an opportunity to address these issues. We report a high-depth sequencing, de novo assembly, and annotation of a female Chinese gayal genome. Based on the Illumina genomic sequencing platform, we have generated 350.38 Gb of raw data from 16 different insert-size libraries. A total of 276.86 Gb of clean data is retained after quality control. The assembled genome is about 2.85 Gb with scaffold and contig N50 sizes of 2.74 Mb and 14.41 kb, respectively. Repetitive elements account for 48.13% of the genome. Gene annotation has yielded 26 667 protein-coding genes, of which 97.18% have been functionally annotated. BUSCO assessment shows that our assembly captures 93% (3183 of 4104) of the core eukaryotic genes and 83.1% of vertebrate universal single-copy orthologs. We provide the first comprehensive de novo genome of the gayal. This genetic resource is integral for investigating the origin of the gayal and performing comparative genomic studies to improve understanding of the speciation and divergence of bovine species. The assembled genome could be used as reference in future population genetic studies of gayal. PMID:29048483

  10. GFVO: the Genomic Feature and Variation Ontology

    KAUST Repository

    Baran, Joachim

    2015-05-05

    Falling costs in genomic laboratory experiments have led to a steady increase of genomic feature and variation data. Multiple genomic data formats exist for sharing these data, and whilst they are similar, they are addressing slightly different data viewpoints and are consequently not fully compatible with each other. The fragmentation of data format specifications makes it hard to integrate and interpret data for further analysis with information from multiple data providers. As a solution, a new ontology is presented here for annotating and representing genomic feature and variation dataset contents. The Genomic Feature and Variation Ontology (GFVO) specifically addresses genomic data as it is regularly shared using the GFF3 (incl. FASTA), GTF, GVF and VCF file formats. GFVO simplifies data integration and enables linking of genomic annotations across datasets through common semantics of genomic types and relations. Availability and implementation. The latest stable release of the ontology is available via its base URI; previous and development versions are available at the ontology’s GitHub repository: https://github.com/BioInterchange/Ontologies; versions of the ontology are indexed through BioPortal (without external class-/property-equivalences due to BioPortal release 4.10 limitations); examples and reference documentation is provided on a separate web-page: http://www.biointerchange.org/ontologies.html. GFVO version 1.0.2 is licensed under the CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0) and therefore de facto within the public domain; the ontology can be appropriated without attribution for commercial and non-commercial use.

  11. Groundwater levels for selected wells in Upper Kittitas County, Washington

    Science.gov (United States)

    Fasser, E.T.; Julich, R.J.

    2011-01-01

    Groundwater levels for selected wells in Upper Kittitas County, Washington, are presented on an interactive, web-based map to document the spatial distribution of groundwater levels in the study area measured during spring 2011. Groundwater-level data and well information were collected by the U.S. Geological Survey using standard techniques and are stored in the U.S. Geological Survey National Water Information System, Groundwater Site-Inventory database.

  12. Memorial—John A. Washington II, M.D.▿

    OpenAIRE

    2010-01-01

    John A. Washington II, M.D., former Head of Clinical Microbiology at the Mayo Clinic from 1972 to 1986 and Chairman of the Department of Microbiology at the Cleveland Clinic from 1986 to 1992, died on 5 September 2010 at the age of 74. John was an internationally recognized, widely respected leader in the disciplines of clinical microbiology and infectious diseases, authoring more than 450 scientific articles, books, and book chapters and training scores of pathology residents and clinical mi...

  13. Bioinformatics decoding the genome

    CERN Multimedia

    CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

    2006-01-01

    Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

  14. Genomic research in Eucalyptus.

    Science.gov (United States)

    Poke, Fiona S; Vaillancourt, René E; Potts, Brad M; Reid, James B

    2005-09-01

    Eucalyptus L'Hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to Australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. With the sequencing of the genomes of Arabidopsis thaliana and Oryza sativa and the recent completion of the first tree genome sequence, Populus trichocarpa, attention has turned to the current status of genomic research in Eucalyptus. For several eucalypt species, large segregating families have been established, high-resolution genetic maps constructed and large EST databases generated. Collaborative efforts have been initiated for the integration of diverse genomic projects and will provide the framework for future research including exploiting the sequence of the entire eucalypt genome which is currently being sequenced. This review summarises the current position of genomic research in Eucalyptus and discusses the direction of future research.

  15. Genome Variation Map: a data repository of genome variations in BIG Data Center.

    Science.gov (United States)

    Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

    2018-01-04

    The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Volatile substance misuse deaths in Washington State, 2003-2012.

    Science.gov (United States)

    Ossiander, Eric M

    2015-01-01

    Volatile substance misuse (VSM - also known as huffing or sniffing) causes some deaths, but because there are no specific cause-of-death codes for VSM, these deaths are rarely tabulated. Count and describe VSM deaths occurring in Washington State during 2003-2012. We used the textual cause-of-death information on death certificates to count VSM-associated deaths that occurred in Washington State during 2003-2012. We extracted records that contained words suggesting either a method of inhalation or a substance commonly used for VSM, and reviewed those records to identify deaths on which the inhalation of a volatile substance was mentioned. We conducted a descriptive analysis of those deaths. Fifty-six deaths involving VSM occurred in Washington State during 2003-2012. VSM deaths occurred primarily among adults age 20 and over (91%), males (88%), and whites (93%). Twelve different chemicals were associated with deaths, but 1 of them, difluoroethane, was named on 30 death certificates (54%), and its involvement increased during the study period. Gas duster products were named as the source of difluoroethane for 12 deaths; no source was named for the other 18 difluoroethane deaths. Most VSM deaths occurred among white male adults, and gas duster products containing difluoroethane were the primary source of inhalants. Approaches to deter VSM, such as the addition of bitterants to gas dusters, should be explored.

  17. GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface.

    Science.gov (United States)

    Lajugie, Julien; Fourel, Nicolas; Bouhassira, Eric E

    2015-01-01

    Parallel visualization of multiple individual human genomes is a complex endeavor that is rapidly gaining importance with the increasing number of personal, phased and cancer genomes that are being generated. It requires the display of variants such as SNPs, indels and structural variants that are unique to specific genomes and the introduction of multiple overlapping gaps in the reference sequence. Here, we describe GenPlay Multi-Genome, an application specifically written to visualize and analyze multiple human genomes in parallel. GenPlay Multi-Genome is ideally suited for the comparison of allele-specific expression and functional genomic data obtained from multiple phased genomes in a graphical interface with access to multiple-track operation. It also allows the analysis of data that have been aligned to custom genomes rather than to a standard reference and can be used as a variant calling format file browser and as a tool to compare different genome assembly, such as hg19 and hg38. GenPlay is available under the GNU public license (GPL-3) from http://genplay.einstein.yu.edu. The source code is available at https://github.com/JulienLajugie/GenPlay. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  18. Genome packaging in viruses

    OpenAIRE

    Sun, Siyang; Rao, Venigalla B.; Rossmann, Michael G.

    2010-01-01

    Genome packaging is a fundamental process in a viral life cycle. Many viruses assemble preformed capsids into which the genomic material is subsequently packaged. These viruses use a packaging motor protein that is driven by the hydrolysis of ATP to condense the nucleic acids into a confined space. How these motor proteins package viral genomes had been poorly understood until recently, when a few X-ray crystal structures and cryo-electron microscopy structures became available. Here we discu...

  19. Ichthyophonus in Puget Sound rockfish from the San Juan Islands archipelago and Puget Sound, Washington, USA

    Science.gov (United States)

    Halos, D.; Hart, S.A.; Hershberger, P.; Kocan, R.

    2005-01-01

    In vitro explant cultures identified Ichthyophonus in 10.9% of 302 Puget Sound rockfish Sebastes emphaeus sampled from five sites in the San Juan Islands archipelago and Puget Sound, Washington, in 2003. None of the infected fish exhibited visible lesions and only a single fish was histologically positive. Significantly more females were infected (12.4%) than males (6.8%), and while infected males were only detected at two of the five sites, infected females were identified at all sites, with no significant differences in infection prevalence. Genomic sequences of Ichthyophonus isolates obtained from Puget Sound rockfish, Pacific herring Clupea pallasii, and Yukon River Chinook salmon Oncorhynchus tshawytscha were identical in both the A and B regions of the small subunit 18S ribosomal DNA but were different from Ichthyophonus sequences previously isolated from four different species of rockfish from the northeastern Pacific Ocean. Ichthyophonus in Puget Sound rockfish may not have been previously detected because the infection is subclinical in this species and earlier investigators did not utilize in vitro techniques for diagnosis of ichthyophoniasis. However, since clinical ichthyophoniasis has recently been identified in several other species of northeast Pacific rockfishes, it is hypothesized that this either is an emerging disease resulting from changing marine conditions or the result of introduction by infected southern species that appear during periodic El Nin??o events. ?? Copyright by the American Fisheries Society 2005.

  20. Between Two Fern Genomes

    Science.gov (United States)

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

  1. Causes of genome instability

    DEFF Research Database (Denmark)

    Langie, Sabine A S; Koppen, Gudrun; Desaulniers, Daniel

    2015-01-01

    function, chromosome segregation, telomere length). The purpose of this review is to describe the crucial aspects of genome instability, to outline the ways in which environmental chemicals can affect this cancer hallmark and to identify candidate chemicals for further study. The overall aim is to make......Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus...

  2. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  3. MIPS plant genome information resources.

    Science.gov (United States)

    Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

    2007-01-01

    The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

  4. Plasma universe

    International Nuclear Information System (INIS)

    Alfven, H.

    1986-04-01

    Traditionally the views in our cosmic environment have been based on observations in the visual octave of the electromagnetic spectrum, during the last half-century supplemented by infrared and radio observations. Space research has opened the full spectrum. Of special importance are the X-ray-gamma-ray regions, in which a number of unexpected phenomena have been discovered. Radiations in these regions are likely to originate mainly from magnetised cosmic plasma. Such a medium may also emit synchrotron radiation which is observable in the radio region. If we try to base a model of the universe on the plasma phenomena mentioned we find that the plasma universe is drastically different from the traditional visual universe. Information about the plasma universe can also be obtained by extrapolation of laboratory experiments and magnetospheric in situ measurements of plasma. This approach is possible because it is likely that the basic properties of plasma are the same everywhere. In order to test the usefulness of the plasma universe model we apply it to cosmogony. Such an approach seems to be rather successful. For example, the complicated structure of the Saturnian C ring can be accounted for. It is possible to reconstruct certain phenomena 4-5 bilions years ago with an accuracy of better than 1 percent

  5. Baby universes

    International Nuclear Information System (INIS)

    Strominger, A.

    1988-01-01

    This paper discusses how the subject of baby universes and their effects on spacetime coupling constants is in its infancy and rapidly developing. The subject is based on the non-existent (even by physicists' standards) Euclidean formulation of quantum gravity, and it is therefore necessary to make a number of assumptions in order to proceed. Nevertheless, the picture which has emerged is quite appealing: all spacetime coupling constants become dynamical variables when the effects of baby universes are taken into account. This fact might even solve the puzzle of the cosmological constant. The subject therefore seems worth further investigation

  6. The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data.

    Science.gov (United States)

    Clarke, Laura; Fairley, Susan; Zheng-Bradley, Xiangqun; Streeter, Ian; Perry, Emily; Lowy, Ernesto; Tassé, Anne-Marie; Flicek, Paul

    2017-01-04

    The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups. Here, we present the new data and analysis that IGSR has made available. We have also introduced a new data portal that increases discoverability of our data-previously only browseable through our FTP site-by focusing on particular samples, populations or data sets of interest. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Computational genomics of hyperthermophiles

    NARCIS (Netherlands)

    Werken, van de H.J.G.

    2008-01-01

    With the ever increasing number of completely sequenced prokaryotic genomes and the subsequent use of functional genomics tools, e.g. DNA microarray and proteomics, computational data analysis and the integration of microbial and molecular data is inevitable. This thesis describes the computational

  8. Safeguarding genome integrity

    DEFF Research Database (Denmark)

    Sørensen, Claus Storgaard; Syljuåsen, Randi G

    2012-01-01

    Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with D...

  9. Human genome I

    International Nuclear Information System (INIS)

    Anon.

    1989-01-01

    An international conference, Human Genome I, was held Oct. 2-4, 1989 in San Diego, Calif. Selected speakers discussed: Current Status of the Genome Project; Technique Innovations; Interesting regions; Applications; and Organization - Different Views of Current and Future Science and Procedures. Posters, consisting of 119 presentations, were displayed during the sessions. 119 were indexed for inclusion to the Energy Data Base

  10. Stiegler's University

    Science.gov (United States)

    Featherstone, Mark

    2017-01-01

    In this article, Mark Featherstone proposes to explore Bernard Stiegler's work through the lens of the politics of education and in particular the idea of the university, which becomes a pharmacological space of, on the one hand, utopian possibility, and, on the other hand, dystopian limitation, destruction, and death in his recent "States of…

  11. Rumen microbial genomics

    International Nuclear Information System (INIS)

    Morrison, M.; Nelson, K.E.

    2005-01-01

    Improving microbial degradation of plant cell wall polysaccharides remains one of the highest priority goals for all livestock enterprises, including the cattle herds and draught animals of developing countries. The North American Consortium for Genomics of Fibrolytic Ruminal Bacteria was created to promote the sequencing and comparative analysis of rumen microbial genomes, offering the potential to fully assess the genetic potential in a functional and comparative fashion. It has been found that the Fibrobacter succinogenes genome encodes many more endoglucanases and cellodextrinases than previously isolated, and several new processive endoglucanases have been identified by genome and proteomic analysis of Ruminococcus albus, in addition to a variety of strategies for its adhesion to fibre. The ramifications of acquiring genome sequence data for rumen microorganisms are profound, including the potential to elucidate and overcome the biochemical, ecological or physiological processes that are rate limiting for ruminal fibre degradation. (author)

  12. Microbial Genomes Multiply

    Science.gov (United States)

    Doolittle, Russell F.

    2002-01-01

    The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

  13. Musa sebagai Model Genom

    Directory of Open Access Journals (Sweden)

    RITA MEGIA

    2005-12-01

    Full Text Available During the meeting in Arlington, USA in 2001, the scientists grouped in PROMUSA agreed with the launching of the Global Musa Genomics Consortium. The Consortium aims to apply genomics technologies to the improvement of this important crop. These genome projects put banana as the third model species after Arabidopsis and rice that will be analyzed and sequenced. Comparing to Arabidopsis and rice, banana genome provides a unique and powerful insight into structural and in functional genomics that could not be found in those two species. This paper discussed these subjects-including the importance of banana as the fourth main food in the world, the evolution and biodiversity of this genetic resource and its parasite.

  14. The genome editing revolution

    DEFF Research Database (Denmark)

    Stella, Stefano; Montoya, Guillermo

    2016-01-01

    -Cas system has become the main tool for genome editing in many laboratories. Currently the targeted genome editing technology has been used in many fields and may be a possible approach for human gene therapy. Furthermore, it can also be used to modifying the genomes of model organisms for studying human......In the last 10 years, we have witnessed a blooming of targeted genome editing systems and applications. The area was revolutionized by the discovery and characterization of the transcription activator-like effector proteins, which are easier to engineer to target new DNA sequences than...... sequence). This ribonucleoprotein complex protects bacteria from invading DNAs, and it was adapted to be used in genome editing. The CRISPR ribonucleic acid (RNA) molecule guides to the specific DNA site the Cas9 nuclease to cleave the DNA target. Two years and more than 1000 publications later, the CRISPR...

  15. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  16. 76 FR 56157 - Brandeis University, et al.; Notice of Consolidated Decision on Applications for Duty-Free Entry...

    Science.gov (United States)

    2011-09-12

    ... DEPARTMENT OF COMMERCE International Trade Administration Brandeis University, et al.; Notice of Consolidated Decision on Applications for Duty-Free Entry of Electron Microscope This is a decision... Constitution Avenue, NW., Washington, DC. Docket Number: 11-042. Applicant: Brandeis University, Waltham, MA...

  17. The language of the protein universe.

    Science.gov (United States)

    Scaiewicz, Andrea; Levitt, Michael

    2015-12-01

    Proteins, the main cell machinery which play a major role in nearly every cellular process, have always been a central focus in biology. We live in the post-genomic era, and inferring information from massive data sets is a steadily growing universal challenge. The increasing availability of fully sequenced genomes can be regarded as the 'Rosetta Stone' of the protein universe, allowing the understanding of genomes and their evolution, just as the original Rosetta Stone allowed Champollion to decipher the ancient Egyptian hieroglyphics. In this review, we consider aspects of the protein domain architectures repertoire that are closely related to those of human languages and aim to provide some insights about the language of proteins. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Genome Annotation and Transcriptomics of Oil-Producing Algae

    Science.gov (United States)

    2015-03-16

    AFRL-OSR-VA-TR-2015-0103 GENOME ANNOTATION AND TRANSCRIPTOMICS OF OIL-PRODUCING ALGAE Sabeeha Merchant UNIVERSITY OF CALIFORNIA LOS ANGELES Final...2010 To 12-31-2014 4. TITLE AND SUBTITLE GENOME ANNOTATION AND TRANSCRIPTOMICS OF OIL-PRODUCING ALGAE 5a. CONTRACT NUMBER FA9550-10-1-0095 5b...NOTES 14. ABSTRACT Most algae accumulate triacylglycerols (TAGs) when they are starved for essential nutrients like N, S, P (or Si in the case of some

  19. GENOMICS, BIOTECHNOLOGY AND GLOBALHEALTH: THE WORK OF THE UNIVERSITY OF TORONTO JOINT CENTRE FOR BIOETHICS GENÓMICA, BIOTECNOLOGÍA Y SALUD MUNDIAL: EL TRABAJO DEL CENTRO ASOCIADO DE BIOÉTICA DE LA UNIVERSIDAD DE TORONTO GENÓMICA, BIOTECNOLOGIA E SAÚDE MUNDIAL: O TRABALHO DO CENTRO ASSOCIADO DE BIOÉTICA DA UNIVERSIDADE DE TORONTO

    Directory of Open Access Journals (Sweden)

    Abdallah S Daar

    2004-01-01

    Full Text Available The new and rapidly advancing field of genomics and related biotechnologies has the ability to either improve or worsen global health inequities. In general, developing countries are left behind in the development of new technologies and advances in genomic medicine. In this view, the University of Toronto Joint Centre for Bioethics (JCB through the Canadian Program on Genomics and Global Health has developed 25 research projects on capacity enhancement for developing countries for improving global health equity, including public health via genomics and related biotechnologies. One project with a great impact was the “Top Ten Biotechnologies for Improving Health in Developing Countries” for its influence in the “Grand Challenges in Global Health Initiative” foster by the Melinda Gates Foundation. Additionally, the UN Millennium Development Project has asked JCB to become the genomics working group for improving global health through genomics biotechnology and JCB has started by studying applications of genomics/biotechnologies in seven developing countries: Brazil, China, Cuba, Egypt, India, South Africa and South Korea, which may set examples for other developing nationsEl nuevo campo de la genómica y sus biotecnologías relacionadas, de rápido desarrollo, tiene la habilidad tanto de mejorar como de empeorar las desigualdades globales en salud. En general, los países en desarrollo quedan atrás en el desarrollo de nuevas tecnologías y avances en la medicina genómica. En vista de esta situación, el Centro Asociado de Bioética de la Universidad de Toronto (JCB a través del Programa Canadiense sobre Genómica y Salud Global ha desarrollado 25 proyectos de investigación sobre desarrollo de capacidades en países en desarrollo para mejorar la equidad en salud global, incluyendo la salud pública a través de la genómica y sus biotecnologías relacionadas. Entre estos, un proyecto de gran impacto fue “Diez Biotecnologías de Mayor

  20. Organics Verification Study for Sinclair and Dyes Inlets, Washington

    Energy Technology Data Exchange (ETDEWEB)

    Kohn, Nancy P.; Brandenberger, Jill M.; Niewolny, Laurie A.; Johnston, Robert K.

    2006-09-28

    Sinclair and Dyes Inlets near Bremerton, Washington, are on the State of Washington 1998 303(d) list of impaired waters because of fecal coliform contamination in marine water, metals in sediment and fish tissue, and organics in sediment and fish tissue. Because significant cleanup and source control activities have been conducted in the inlets since the data supporting the 1998 303(d) listings were collected, two verification studies were performed to address the 303(d) segments that were listed for metal and organic contaminants in marine sediment. The Metals Verification Study (MVS) was conducted in 2003; the final report, Metals Verification Study for Sinclair and Dyes Inlets, Washington, was published in March 2004 (Kohn et al. 2004). This report describes the Organics Verification Study that was conducted in 2005. The study approach was similar to the MVS in that many surface sediment samples were screened for the major classes of organic contaminants, and then the screening results and other available data were used to select a subset of samples for quantitative chemical analysis. Because the MVS was designed to obtain representative data on concentrations of contaminants in surface sediment throughout Sinclair Inlet, Dyes Inlet, Port Orchard Passage, and Rich Passage, aliquots of the 160 MVS sediment samples were used in the analysis for the Organics Verification Study. However, unlike metals screening methods, organics screening methods are not specific to individual organic compounds, and are not available for some target organics. Therefore, only the quantitative analytical results were used in the organics verification evaluation. The results of the Organics Verification Study showed that sediment quality outside of Sinclair Inlet is unlikely to be impaired because of organic contaminants. Similar to the results for metals, in Sinclair Inlet, the distribution of residual organic contaminants is generally limited to nearshore areas already within the

  1. Prevalence of corporal punishment among students in Washington State schools.

    Science.gov (United States)

    Grossman, D C; Rauh, M J; Rivara, F P

    1995-05-01

    To determine the prevalence of corporal punishment in Washington State and the factors associated with its use in Washington elementary and secondary schools. Cross-sectional mail survey performed during the summer of 1992. All elementary and secondary schools in the state of Washington. One thousand eighteen schools (47%) responded to the survey, of which 80% were publicly funded and 63% were located in urban areas. The study sample closely resembled the profile of all schools in the state. Almost 11% of participating schools permitted corporal punishment at the time of the survey and 3.2% reported its actual use during the 1991-1992 school year, resulting in an estimated prevalence of 7.2 incidents per 1000 students per year. Sixteen percent of corporal punishment actions occurred in schools not permitting its use. Ninety percent of public schools relied on district policy regarding corporal punishment. School characteristics associated with the use of corporal punishment included rural location (crude odds ratio, 2.2; 95% confidence interval, 1.5 to 3.4), enrollment of less than 500 students (crude odds ratio, 1.7; 95% confidence interval, 1.1 to 2.7), and kindergarten to eighth-grade or kindergarten to 12th-grade enrollment (crude odds ratio, 2.5; 95% confidence interval, 1.6 to 3.9). The lack of a statewide ban on school corporal punishment at the time of this survey was associated with the continued use of corporal punishment against children in districts that continued to permit it. School policies against corporal punishment were associated with much lower prevalence. Continued efforts are needed to enact and enforce laws in the remaining states that have not yet banned corporal punishment.

  2. The founding charter of the Genomic Observatories Network.

    Science.gov (United States)

    Davies, Neil; Field, Dawn; Amaral-Zettler, Linda; Clark, Melody S; Deck, John; Drummond, Alexei; Faith, Daniel P; Geller, Jonathan; Gilbert, Jack; Glöckner, Frank Oliver; Hirsch, Penny R; Leong, Jo-Ann; Meyer, Chris; Obst, Matthias; Planes, Serge; Scholin, Chris; Vogler, Alfried P; Gates, Ruth D; Toonen, Rob; Berteaux-Lecellier, Véronique; Barbier, Michèle; Barker, Katherine; Bertilsson, Stefan; Bicak, Mesude; Bietz, Matthew J; Bobe, Jason; Bodrossy, Levente; Borja, Angel; Coddington, Jonathan; Fuhrman, Jed; Gerdts, Gunnar; Gillespie, Rosemary; Goodwin, Kelly; Hanson, Paul C; Hero, Jean-Marc; Hoekman, David; Jansson, Janet; Jeanthon, Christian; Kao, Rebecca; Klindworth, Anna; Knight, Rob; Kottmann, Renzo; Koo, Michelle S; Kotoulas, Georgios; Lowe, Andrew J; Marteinsson, Viggó Thór; Meyer, Folker; Morrison, Norman; Myrold, David D; Pafilis, Evangelos; Parker, Stephanie; Parnell, John Jacob; Polymenakou, Paraskevi N; Ratnasingham, Sujeevan; Roderick, George K; Rodriguez-Ezpeleta, Naiara; Schonrogge, Karsten; Simon, Nathalie; Valette-Silver, Nathalie J; Springer, Yuri P; Stone, Graham N; Stones-Havas, Steve; Sansone, Susanna-Assunta; Thibault, Kate M; Wecker, Patricia; Wichels, Antje; Wooley, John C; Yahara, Tetsukazu; Zingone, Adriana

    2014-03-07

    The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated.

  3. Landslides and engineering geology of the Seattle, Washington, area

    Science.gov (United States)

    Baum, Rex L.; Godt, Jonathan W.; Highland, Lynn M.

    2008-01-01

    This volume brings together case studies and summary papers describing the application of state-of-the-art engineering geologic methods to landslide hazard analysis for the Seattle, Washington, area. An introductory chapter provides a thorough description of the Quaternary and bedrock geology of Seattle. Nine additional chapters review the history of landslide mapping in Seattle, present case studies of individual landslides, describe the results of spatial assessments of landslide hazard, discuss hydrologic controls on landsliding, and outline an early warning system for rainfall-induced landslides.

  4. Details of microearthquake swarms in the Columbia basin, Washington

    International Nuclear Information System (INIS)

    Malone, S.D.; Rothe, G.H.; Smith, S.W.

    1975-01-01

    Three microearthquake swarms in the Columbia River basin of eastern Washington were studied by means of a small portable seismic network. Earthquakes in this area typically occur in swarms, concentrated both temporally and spatially. One unusual characteristic of the three swarms studied was the shallow focal depths of all events. Most events located had depths less than 1 km; none were deeper than 2 km. Composite focal mechanism solutions indicate that more than one fault surface is active in any one swarm. All events had some thrust component with the axis of maximum compression oriented roughly in a north-south direction. (auth)

  5. Surficial geology map of the Great Heath, Washington County, Maine

    Science.gov (United States)

    Cameron, Cornelia Clermont; Mullen, Michael K.

    1983-01-01

    The major portion of the Great Heath, comprising 2,645 acres in the Cherryfield quadrangle, Washington County, Maine, generally averaging 13 feet in thickness, but with as great an average as 15 feet, contain an estimated 6,953 ,000 short tons air-dried peat. The peat #s chiefly sphagnum moss with some reed-sedge of high quality according to ASTM standards for agricultural and horticultural use. This same volume of peat may be considered for use as fuel because BTO per pound ranges from 8,600 to 10,500 with low sulfur and high hydrogen contents.

  6. Mixed waste management in Washington and the Northwest Compact Region

    International Nuclear Information System (INIS)

    Carlin, E.M.

    1988-01-01

    The state of Washington's concerns about the management of mixed waste have evolved over the past year. One concern that receives increasing attention is the Northwest Compact Region's need to plan for disposal of its own mixed waste. An informal survey of the region's potential mixed waste generators has indicated that mixed waste volumes are low. However, the opening of a disposal facility may result in increased waste volumes. A preliminary proposal for such a facility has been reviewed by the federal and state agencies that dually regulate mixed waste. Initial conclusions reached by the regulators are presented

  7. Seismic reflection survey conducted in Benton and Grant Counties, Washington

    International Nuclear Information System (INIS)

    Durham, T.E.; Beggs, H.G.; Heineck, R.L.

    1979-01-01

    The following report is devoted to a discussion of data acquisition procedures, data processing parameters and interpretation of results for a reflection seismic survey located on the Hanford Site in Benton and Grant Countries, Washington. The Pasco basin was the geologic setting for the survey. The main objectives of the program were to determine the subsurface structural attitudes of the numerous basalt flows known to exist within the basin. The location of areas associated with possible faulting and/or fracturing was also considered of prime concern as these conditions could significantly affect the integrity of the basalt

  8. Hydrologic bibliography of the Columbia River basalts in Washington

    International Nuclear Information System (INIS)

    Tanaka, H.H.; Wildrick, L.

    1978-07-01

    This bibliography is part of the hydrologic data compilation effort of the Columbia Plateau Hydrology Study, Rockwell Hanford Operations' Waste Isolation Program. It includes references on both surface and subsurface hydrology directly or indirectly related to the Washington State portion of the Columbia River basalts. A comprehensive, annotated bibliography of the Pasco Basin (including the Hanford site) hydrology has been prepared for Rockwell Hanford Operations under the Pasco Basin Hydrology Study. In order to avoid unnecessary duplication, no effort was made to include a complete list of bibliographic references on Hanford in this volume

  9. University writing

    Directory of Open Access Journals (Sweden)

    Miguel Zabalza Beraza

    2013-01-01

    Full Text Available Writing in the University is a basic necessity and a long-range educational purpose. One of the basic characteristics of the university context is that it requires writing both as a tool of communication and as a source of intellectual stimulation. After establishing the basic features of academic writing, this article analyzes the role of writing for students (writing to learn and for teachers (write to plan, to reflect, to document what has been done. The article also discusses the contributions of writing for both students and teachers together: writing to investigate. Finally, going beyond what writing is as academic tool, we conclude with a more playful and creative position: writing for pleasure and enjoyment.

  10. Universe unfolding

    International Nuclear Information System (INIS)

    King, I.R.

    1976-01-01

    Topics covered the setting; looking at the stars; the earth; time, place and the sky; our satellite, the moon; orbits and motion; the motions of the planets; the Copernican revolution; the planets; the other bodies of the solar system; ages, origins, and life; introducing the stars; sorting out the stars; binary stars--two are better than one; variable stars--inconstancy as a virtue; the secrets of starlight--unraveling the spectrum; the sun--our own star; the structure of a star; interstellar material; the Milky Way, our home galaxy; galaxies--the stellar continents; cosmic violence--from radio galaxies to quasars; the universe; and epilogue. The primary emphasis is on how we have come to know what we know about the universe. Star maps are included

  11. Genome-derived vaccines.

    Science.gov (United States)

    De Groot, Anne S; Rappuoli, Rino

    2004-02-01

    Vaccine research entered a new era when the complete genome of a pathogenic bacterium was published in 1995. Since then, more than 97 bacterial pathogens have been sequenced and at least 110 additional projects are now in progress. Genome sequencing has also dramatically accelerated: high-throughput facilities can draft the sequence of an entire microbe (two to four megabases) in 1 to 2 days. Vaccine developers are using microarrays, immunoinformatics, proteomics and high-throughput immunology assays to reduce the truly unmanageable volume of information available in genome databases to a manageable size. Vaccines composed by novel antigens discovered from genome mining are already in clinical trials. Within 5 years we can expect to see a novel class of vaccines composed by genome-predicted, assembled and engineered T- and Bcell epitopes. This article addresses the convergence of three forces--microbial genome sequencing, computational immunology and new vaccine technologies--that are shifting genome mining for vaccines onto the forefront of immunology research.

  12. The Banana Genome Hub

    Science.gov (United States)

    Droc, Gaëtan; Larivière, Delphine; Guignon, Valentin; Yahiaoui, Nabila; This, Dominique; Garsmeur, Olivier; Dereeper, Alexis; Hamelin, Chantal; Argout, Xavier; Dufayard, Jean-François; Lengelle, Juliette; Baurens, Franc-Christophe; Cenci, Alberto; Pitollat, Bertrand; D’Hont, Angélique; Ruiz, Manuel; Rouard, Mathieu; Bocs, Stéphanie

    2013-01-01

    Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/ PMID:23707967

  13. Genomic instability following irradiation

    International Nuclear Information System (INIS)

    Hacker-Klom, U.B.; Goehde, W.

    2001-01-01

    Ionising irradiation may induce genomic instability. The broad spectrum of stress reactions in eukaryontic cells to irradiation complicates the discovery of cellular targets and pathways inducing genomic instability. Irradiation may initiate genomic instability by deletion of genes controlling stability, by induction of genes stimulating instability and/or by activating endogeneous cellular viruses. Alternatively or additionally it is discussed that the initiation of genomic instability may be a consequence of radiation or other agents independently of DNA damage implying non nuclear targets, e.g. signal cascades. As a further mechanism possibly involved our own results may suggest radiation-induced changes in chromatin structure. Once initiated the process of genomic instability probably is perpetuated by endogeneous processes necessary for proliferation. Genomic instability may be a cause or a consequence of the neoplastic phenotype. As a conclusion from the data available up to now a new interpretation of low level radiation effects for radiation protection and in radiotherapy appears useful. The detection of the molecular mechanisms of genomic instability will be important in this context and may contribute to a better understanding of phenomenons occurring at low doses <10 cSv which are not well understood up to now. (orig.)

  14. University physics

    CERN Document Server

    Arfken, George

    1984-01-01

    University Physics provides an authoritative treatment of physics. This book discusses the linear motion with constant acceleration; addition and subtraction of vectors; uniform circular motion and simple harmonic motion; and electrostatic energy of a charged capacitor. The behavior of materials in a non-uniform magnetic field; application of Kirchhoff's junction rule; Lorentz transformations; and Bernoulli's equation are also deliberated. This text likewise covers the speed of electromagnetic waves; origins of quantum physics; neutron activation analysis; and interference of light. This publi

  15. Human universe

    CERN Document Server

    Cox, Brian

    2014-01-01

    Human life is a staggeringly strange thing. On the surface of a ball of rock falling around a nuclear fireball in the blackness of a vacuum the laws of nature conspired to create a naked ape that can look up at the stars and wonder where it came from. What is a human being? Objectively, nothing of consequence. Particles of dust in an infinite arena, present for an instant in eternity. Clumps of atoms in a universe with more galaxies than people. And yet a human being is necessary for the question itself to exist, and the presence of a question in the universe - any question - is the most wonderful thing. Questions require minds, and minds bring meaning. What is meaning? I don't know, except that the universe and every pointless speck inside it means something to me. I am astonished by the existence of a single atom, and find my civilisation to be an outrageous imprint on reality. I don't understand it. Nobody does, but it makes me smile. This book asks questions about our origins, our destiny, and our place i...

  16. Hydrographic and biological observations on the Washington continental shelf and slope during the periods: 30 March-5 April, 8-15 June, and 6-11 September 1978

    Energy Technology Data Exchange (ETDEWEB)

    Postel, J.R.; Peterson, W.K. (comps.)

    1981-01-01

    During 1978 several cruises were successfully completed along a shelf-slope section off the Washington coast. These cruises were undertaken to collect seasonal information on the processes affecting phytoplankton production and distribution and data on the settling rate of organic matter in the sea during spring, early summer, and autumn conditions. This report summarizes the data collected on three cruises aboard the R/V CAYUSE, which was operated by Oregon State University. All three cruises originated and terminated in Newport, Oregon. Sampling was conducted at established station locations along a transect off Copalis Beach, Washington. Water depth varied from about 10 m at the innermost station (approx. 3 km from the beach) to over 1500 m at the outermost station (approx. 120 km from the beach).

  17. Traditional medicine and genomics

    Directory of Open Access Journals (Sweden)

    Kalpana Joshi

    2010-01-01

    Full Text Available ′Omics′ developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics.

  18. Traditional medicine and genomics.

    Science.gov (United States)

    Joshi, Kalpana; Ghodke, Yogita; Shintre, Pooja

    2010-01-01

    'Omics' developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics.

  19. Bacillus subtilis genome diversity.

    Science.gov (United States)

    Earl, Ashlee M; Losick, Richard; Kolter, Roberto

    2007-02-01

    Microarray-based comparative genomic hybridization (M-CGH) is a powerful method for rapidly identifying regions of genome diversity among closely related organisms. We used M-CGH to examine the genome diversity of 17 strains belonging to the nonpathogenic species Bacillus subtilis. Our M-CGH results indicate that there is considerable genetic heterogeneity among members of this species; nearly one-third of Bsu168-specific genes exhibited variability, as measured by the microarray hybridization intensities. The variable loci include those encoding proteins involved in antibiotic production, cell wall synthesis, sporulation, and germination. The diversity in these genes may reflect this organism's ability to survive in diverse natural settings.

  20. Genomic taxonomy of vibrios

    Directory of Open Access Journals (Sweden)

    Iida Tetsuya

    2009-10-01

    Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

  1. Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  2. Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  3. Genomic signal processing

    CERN Document Server

    Shmulevich, Ilya

    2007-01-01

    Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathema

  4. Surface hydrologic investigations of the Columbia Plateau Region, Washington

    International Nuclear Information System (INIS)

    Leonhart, L.S.

    1979-07-01

    The Washington State portion of the Columbia Plateau is divided into six hydrologic sub-basins on the basis of the principal surface drainage systems present, structural and topographic relationships, and political and other considerations. Baseline descriptions of the surface water systems and resources are presented for the Columbia Plateau with emphasis on the Pasco Sub-basin. A preliminary evaluation of the hydrologic budget for each sub-basin is derived. For each sub-basin, recharge/discharge relationships arising from precipitation/evapotranspiration/runoff, stream losses and gains, and artificial mechanisms are determined on the basis of available data. The net exchange between surface and groundwater systems is evaluated and relative estimates of the net groundwater flow into or out of the sub-basin are obtained. An evaluation is made of hydrologic risk factors arising from: (1) tributary flooding in eastern Washington; and, (2) major flooding of the Columbia River within the Pasco Sub-basin. Scenarios are presented for credible natural and man-generated catastrophic events

  5. Deep long-period earthquakes beneath Washington and Oregon volcanoes

    Science.gov (United States)

    Nichols, M.L.; Malone, S.D.; Moran, S.C.; Thelen, W.A.; Vidale, J.E.

    2011-01-01

    Deep long-period (DLP) earthquakes are an enigmatic type of seismicity occurring near or beneath volcanoes. They are commonly associated with the presence of magma, and found in some cases to correlate with eruptive activity. To more thoroughly understand and characterize DLP occurrence near volcanoes in Washington and Oregon, we systematically searched the Pacific Northwest Seismic Network (PNSN) triggered earthquake catalog for DLPs occurring between 1980 (when PNSN began collecting digital data) and October 2009. Through our analysis we identified 60 DLPs beneath six Cascade volcanic centers. No DLPs were associated with volcanic activity, including the 1980-1986 and 2004-2008 eruptions at Mount St. Helens. More than half of the events occurred near Mount Baker, where the background flux of magmatic gases is greatest among Washington and Oregon volcanoes. The six volcanoes with DLPs (counts in parentheses) are Mount Baker (31), Glacier Peak (9), Mount Rainier (9), Mount St. Helens (9), Three Sisters (1), and Crater Lake (1). No DLPs were identified beneath Mount Adams, Mount Hood, Mount Jefferson, or Newberry Volcano, although (except at Hood) that may be due in part to poorer network coverage. In cases where the DLPs do not occur directly beneath the volcanic edifice, the locations coincide with large structural faults that extend into the deep crust. Our observations suggest the occurrence of DLPs in these areas could represent fluid and/or magma transport along pre-existing tectonic structures in the middle crust. ?? 2010 Elsevier B.V.

  6. Quantifying the Causes and Propogation of the 2015 Washington Wildfires

    Science.gov (United States)

    Engel, R.; Marlier, M. E.; Lettenmaier, D. P.

    2017-12-01

    In the summer of 2015, Washington state experienced wildfires that burned over 450,000 ha, more than five times the average and more than three times the next-most severe fire season in the 30-year record. We examine the confluence of factors that led to the extreme fire season, and evaluate whether 2015 can be used as a predictor of possible future conditions that will be affected by climate warming. In previous work, we have found that 2015 was an extremely warm summer (nearly 1 degree C warmer than the previous year in the 30-year record) but was not particularly anomalous in terms of many other climatic indicators, including reconstructed soil moisture, the Palmer Drought Severity Index (PDSI), and the Canadian Fire Weather Index. However, according to the Dead Fuel Moisture (DFM), a drying index used by the US Forest Service, 2015 was an extreme year of record. The DFM relies on temperature, precipitation, and relative humidity to establish a daily equilibrium moisture content of dead material. We examine both Washington's 2015 fire season and the 30-year fire record with respect to climatology and other potential drivers of fire (e.g. forest health, ignition). Additionally, we explore the role of land cover with respect to fire propagation through the season. While too many potential causes of extreme fires exist to establish a concrete long-term relationship at such a fine scale, we find that the 2015 fire anomaly was at least partially climatically driven.

  7. Washington's marine oil spill compensation schedule - simplified resource damage assessment

    International Nuclear Information System (INIS)

    Geselbracht, L.; Logan, R.

    1993-01-01

    The Washington State Preassessment Screening and Oil Spill Compensation Schedule Rule (Chapter 173-183 Washington Administrative Code), which simplifies natural resource damage assessment for many oil spill cases, became effective in May 1992. The approach described in the rule incorporates a number of preconstructed rankings that rate environmental sensitivity and the propensity of spilled oil to cause environmental harm. The rule also provides guidance regarding how damages calculated under the schedule should be reduced to take into account actions taken by the responsible party that reduce environmental injury. To apply the compensation schedule to marine estuarine spills, the resource trustees need only collect a limited amount of information such as type of product spilled, number of gallons spilled, compensation schedule subregions the spill entered, season of greatest spill impact, percent coverage of habitats affected by the spill, and actions taken by the responsible party. The result of adding a simplified tool to the existing assortment of damage assessment approaches is that resource trustees will now be able to assess damages for most oil spill cases and shift more effort than was possible in the past to resource restoration

  8. Surface hydrologic investigations of the Columbia Plateau region, Washington

    International Nuclear Information System (INIS)

    Leonhart, L.S.

    1979-01-01

    The Washington State portion of the Columbia Plateau is divided into six hydrologic sub-basins on the basis of the principal surface drainage systems present, structural and topographic relationships, and political and other considerations. Baseline descriptions of the surface water systems and resources are presented for the Columbia Plateau with emphasis on the Pasco Sub-basin. A preliminary evaluation of the hydrologic budget for each sub-basin is derived. For each sub-basin, recharge/discharge relationships arising from precipitation/evapotranspiration/runoff, stream losses and gains, and artificial mechanisms are determined on the basis of available data. The net exchange between surface and ground-water systems is evaluated and relative estimates of the net ground-water flow into or out of the sub-basin are obtained. An evaluation is made of hydrologic risk factors arising from: (1) tributary flooding in eastern Washington; and (2) major flooding of the Columbia River within the Pasco Sub-basin. Scenarios are presented for credible natural and man-generated catastrophic events

  9. Ergonomics and regulatory politics: the Washington State case.

    Science.gov (United States)

    Silverstein, Michael

    2007-05-01

    Every year in the State of Washington more than 50,000 workers experience a work related musculoskeletal disorder (WMSD), making up more than 30% of all worker compensation cases. In 2000, the Washington State Department of Labor and Industries (L&I) adopted a workplace ergonomics rule requiring employers to reduce worker exposure to hazards that cause or contribute to WMSDs. In 2003, the ergonomics rule was repealed by a margin of 53.5-46.5 in a statewide voter initiative. The official rulemaking record of approximately 100,000 pages, along with supplementary published and unpublished material, was reviewed. The relationship between scientific deliberation and the public policy process in adopting and repealing the ergonomics rule was assessed and described. The deliberative features of the regulatory, judicial, legislative, and ballot processes were compared. The ergonomics rule was successful in the regulatory and legal arenas where the process was most transparent and open to public involvement, differing views could be presented fully, and decision makers were expected to explain their decisions in light of the record. The rule fared most poorly in the legislature and at the ballot box when these features were lost and where considered deliberation was replaced by unconstrained political conflict. Additional checks and balances are needed.

  10. Genomics and fish adaptation

    Directory of Open Access Journals (Sweden)

    Agostinho Antunes

    2015-12-01

    Full Text Available The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied fish species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

  11. Lophotrochozoan mitochondrial genomes

    Energy Technology Data Exchange (ETDEWEB)

    Valles, Yvonne; Boore, Jeffrey L.

    2005-10-01

    Progress in both molecular techniques and phylogeneticmethods has challenged many of the interpretations of traditionaltaxonomy. One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships within thisgroup and the inclusion of some phyla remain uncertain. While much ofthis progress in phylogenetic reconstruction has been based on comparingsingle gene sequences, we are beginning to see the potential of comparinglarge-scale features of genomes, such as the relative order of genes.Even though tremendous progress is being made on the sequencedetermination of whole nuclear genomes, the dataset of choice forgenome-level characters for many animals across a broad taxonomic rangeremains mitochondrial genomes. We review here what is known aboutmitochondrial genomes of the lophotrochozoans and discuss the promisethat this dataset will enable insight into theirrelationships.

  12. Mouse Genome Informatics (MGI)

    Data.gov (United States)

    U.S. Department of Health & Human Services — MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human...

  13. Genomic definition of species

    Energy Technology Data Exchange (ETDEWEB)

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01

    The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.

  14. Structural genomics in endocrinology

    NARCIS (Netherlands)

    Smit, J. W.; Romijn, J. A.

    2001-01-01

    Traditionally, endocrine research evolved from the phenotypical characterisation of endocrine disorders to the identification of underlying molecular pathophysiology. This approach has been, and still is, extremely successful. The introduction of genomics and proteomics has resulted in a reversal of

  15. Epidemiology & Genomics Research Program

    Science.gov (United States)

    The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.

  16. Annotating individual human genomes.

    Science.gov (United States)

    Torkamani, Ali; Scott-Van Zeeland, Ashley A; Topol, Eric J; Schork, Nicholas J

    2011-10-01

    Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. Copyright © 2011 Elsevier Inc. All rights reserved.

  17. ANNOTATING INDIVIDUAL HUMAN GENOMES*

    Science.gov (United States)

    Torkamani, Ali; Scott-Van Zeeland, Ashley A.; Topol, Eric J.; Schork, Nicholas J.

    2014-01-01

    Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely to amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. PMID:21839162

  18. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  19. Genetical Genomics for Evolutionary Studies

    NARCIS (Netherlands)

    Prins, J.C.P.; Smant, G.; Jansen, R.C.

    2012-01-01

    Genetical genomics combines acquired high-throughput genomic data with genetic analysis. In this chapter, we discuss the application of genetical genomics for evolutionary studies, where new high-throughput molecular technologies are combined with mapping quantitative trait loci (QTL) on the genome

  20. The human genome project

    International Nuclear Information System (INIS)

    Worton, R.

    1996-01-01

    The Human Genome Project is a massive international research project, costing 3 to 5 billion dollars and expected to take 15 years, which will identify the all the genes in the human genome - i.e. the complete sequence of bases in human DNA. The prize will be the ability to identify genes causing or predisposing to disease, and in some cases the development of gene therapy, but this new knowledge will raise important ethical issues