Sample records for radiation-induced genomic instability

  1. Radiation-induced Genomic Instability and Radiation Sensitivity

    SciTech Connect (OSTI)

    Varnum, Susan M.; Sowa, Marianne B.; Kim, Grace J.; Morgan, William F.

    2013-01-19T23:59:59.000Z

    The obvious relationships between reactive oxygen and nitrogen species, mitochondrial dysfunction, inflammatory type responses and reactive chemokines and cytokines suggests a general stress response induced by ionizing radiation most likely leads to the non-targeted effects described after radiation exposure. We argue that true bystander effects do not occur in the radiation therapy clinic. But there is no question that effects outside the target volume do occur. These “out of field effects” are considered very low dose effects in the context of therapy. So what are the implications of non-targeted effects on radiation sensitivity? The primary goal of therapy is to eradicate the tumor. Given the genetic diversity of the human population, lifestyle and environment factors it is likely some combination of these will influence patient outcome. Non-targeted effects may contribute to a greater or lesser extent. But consider the potential situation involving a partial body exposure due to a radiation accident or radiological terrorism. Non-targeted effects suggest that the tissue at risk for demonstrating possible detrimental effects of radiation exposure might be greater than the volume actually irradiated.

  2. Saturation of radiation-induced parametric instabilities by excitation of Langmuir turbulence

    SciTech Connect (OSTI)

    Dubois, D.F.; Rose, H.A. [Los Alamos National Lab., NM (United States); Russell, D. [Lodestar Research Inc., Boulder, CO (United States)

    1995-12-01T23:59:59.000Z

    Progress made in the last few years in the calculation of the saturation spectra of parametric instabilities which involve Langmuir daughter waves will be reviewed. These instabilities include the ion acoustic decay instability, the two plasmon decay instability (TPDI), and stimulated Raman scattering (SRS). In particular I will emphasize spectral signatures which can be directly compared with experiment. The calculations are based on reduced models of driven Laugmuir turbulence. Thomson scattering from hf-induced Langmuir turbulence in the unpreconditioned ionosphere has resulted in detailed agreement between theory and experiment at early times. Strong turbulence signatures dominate in this regime where the weak turbulence approximation fails completely. Recent experimental studies of the TPDI have measured the Fourier spectra of Langmuir waves as well as the angular and frequency, spectra of light emitted near 3/2 of the pump frequency again permitting some detailed comparisons with theory. The experiments on SRS are less detailed but by Thomson scattering the secondary decay of the daughter Langmuir wave has been observed. Scaling laws derived from a local model of SRS saturation are compared with full simulations and recent Nova experiments.

  3. Radiation-induced instability of MnS precipitates and its possible consequences on irradiation-induced stress corrosion cracking of austenitic stainless steels

    SciTech Connect (OSTI)

    Chung, H.M.; Sanecki, J.E. [Argonne National Lab., IL (United States); Garner, F.A. [Pacific Northwest National Lab., Richland, WA (United States)

    1996-12-01T23:59:59.000Z

    Irradiation-assisted stress corrosion cracking (IASCC) is a significant materials issue for the light water reactor (LWR) industry and may also pose a problem for fusion power reactors that will use water as coolant. A new metallurgical process is proposed that involves the radiation-induced release into solution of minor impurity elements not usually thought to participate in IASCC. MnS-type precipitates, which contain most of the sulfur in stainless steels, are thought to be unstable under irradiation. First, Mn transmutes strongly to Fe in thermalized neutron spectra. Second, cascade-induced disordering and the inverse Kirkendall effect operating at the incoherent interfaces of MnS precipitates are thought to act as a pump to export Mn from the precipitate into the alloy matrix. Both of these processes will most likely allow sulfur, which is known to exert a deleterious influence on intergranular cracking, to re-enter the matrix. To test this hypothesis, compositions of MnS-type precipitates contained in several unirradiated and irradiated heats of Type 304, 316, and 348 stainless steels (SSs) were analyzed by Auger electron spectroscopy. Evidence is presented that shows a progressive compositional modification of MnS precipitates as exposure to neutrons increases in boiling water reactors. As the fluence increases, the Mn level in MnS decreases, whereas the Fe level increases. The S level also decreases relative to the combined level of Mn and Fe. MnS precipitates were also found to be a reservoir of other deleterious impurities such as F and O which could be also released due to radiation-induced instability of the precipitates.

  4. Mechanisms of Low Dose Radio-Suppression of Genomic Instability

    SciTech Connect (OSTI)

    Engelward, Bevin P

    2009-09-16T23:59:59.000Z

    The major goal of this project is to contribute toward the elucidation of the impact of long term low dose radiation on genomic stability. We have created and characterized novel technologies for delivering long term low dose radiation to animals, and we have studied genomic stability by applying cutting edge molecular analysis technologies. Remarkably, we have found that a dose rate that is 300X higher than background radiation does not lead to any detectable genomic damage, nor is there any significant change in gene expression for genes pertinent to the DNA damage response. These results point to the critical importance of dose rate, rather than just total dose, when evaluating public health risks and when creating regulatory guidelines. In addition to these studies, we have also further developed a mouse model for quantifying cells that have undergone a large scale DNA sequence rearrangement via homologous recombination, and we have applied these mice in studies of both low dose radiation and space radiation. In addition to more traditional approaches for assessing genomic stability, we have also explored radiation and possible beneficial effects (adaptive response), long term effects (persistent effects) and effects on communication among cells (bystander effects), both in vitro and in vivo. In terms of the adaptive response, we have not observed any significant induction of an adaptive response following long term low dose radiation in vivo, delivered at 300X background. In terms of persistent and bystander effects, we have revealed evidence of a bystander effect in vivo and with researchers at and demonstrated for the first time the molecular mechanism by which cells “remember” radiation exposure. Understanding the underlying molecular mechanisms by which radiation can induce genomic instability is fundamental to our ability to assess the biological impact of low dose radiation. Finally, in a parallel set of studies we have explored the effects of heavy iron particle radiation on large scale sequence rearrangements and we have discovered tissue specific differences in sensitivity to homologous recombination. DOE support has given rise to critical new knowledge about the biological impact of low dose rate radiation and about the underlying mechanisms that govern genomic stability in response to radiation exposure. This work has spurred interest in radiation among MIT scientists, and has fostered ongoing research projects that will continue to contribute toward our understanding of the biological effects of low dose radiation exposure.

  5. Breast tumor copy number aberration phenotypes and genomic instability

    E-Print Network [OSTI]

    2006-01-01T23:59:59.000Z

    the hypothesis that deregulation of the Rb pathway is a3]. Nevertheless, deregulation of functions that maintainto instability include deregulation of CCNE1 and AURKA

  6. Genomic instability and bystander effects induced by high-LET radiation Eric J Hall*,1

    E-Print Network [OSTI]

    of the radiobiological effects of high- linear energy transfer (LET) radiation is essential for radiation protectionGenomic instability and bystander effects induced by high-LET radiation Eric J Hall*,1 and Tom K, it has always been accepted that the deleterious effects of ionizing radiation, such as mutation

  7. Overexpressed of RAD51 suppresses recombination defects: a possible mechanism to reverse genomic instability

    SciTech Connect (OSTI)

    Schild, David; Wiese, Claudia

    2009-10-15T23:59:59.000Z

    RAD51, a key protein in the homologous recombinational DNA repair (HRR) pathway, is the major strand-transferase required for mitotic recombination. An important early step in HRR is the formation of single-stranded DNA (ss-DNA) coated by RPA (a ss-DNA binding protein). Displacement of RPA by RAD51 is highly regulated and facilitated by a number of different proteins known as the 'recombination mediators'. To assist these recombination mediators, a second group of proteins also is required and we are defining these proteins here as 'recombination co-mediators'. Defects in either recombination mediators or comediators, including BRCA1 and BRCA2, lead to impaired HRR that can genetically be complemented for (i.e. suppressed) by overexpression of RAD51. Defects in HRR have long been known to contribute to genomic instability leading to tumor development. Since genomic instability also slows cell growth, precancerous cells presumably require genomic restabilization to gain a growth advantage. RAD51 is overexpressed in many tumors, and therefore, we hypothesize that the complementing ability of elevated levels of RAD51 in tumors with initial HRR defects limits genomic instability during carcinogenic progression. Of particular interest, this model may also help explain the high frequency of TP53 mutations in human cancers, since wild-type p53 represses RAD51.

  8. Radiation-Induced Reduction of Ceria in Single and Polycrystalline...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Radiation-Induced Reduction of Ceria in Single and Polycrystalline Thin Films. Radiation-Induced Reduction of Ceria in Single and Polycrystalline Thin Films. Abstract: Ceria (CeO2)...

  9. Progressive Genomic Instability in the FVB/Kras[superscript LA2] Mouse Model of Lung Cancer

    E-Print Network [OSTI]

    Jacks, Tyler E.

    Alterations in DNA copy number contribute to the development and progression of cancers and are common in epithelial tumors. We have used array Comparative Genomic Hybridization (aCGH) to visualize DNA copy number alterations ...

  10. Living with genome instability: the adaptation of phytoplasmas todiverse environments of their insect and plant hosts

    SciTech Connect (OSTI)

    Bai, Xiaodong; Zhang, Jianhua; Ewing, Adam; Miller, Sally A.; Radek, Agnes; Shevchenko, Dimitriy; Tsukerman, Kiryl; Walunas, Theresa; Lapidus, Alla; Campbell, John W.; Hogenhout Saskia A.

    2006-02-17T23:59:59.000Z

    Phytoplasmas (Candidatus Phytoplasma, Class Mollicutes) cause disease in hundreds of economically important plants, and are obligately transmitted by sap-feeding insects of the order Hemiptera, mainly leafhoppers and psyllids. The 706,569-bp chromosome and four plasmids of aster yellows phytoplasma strain witches broom (AY-WB) were sequenced and compared to the onion yellows phytoplasma strain M (OY-M) genome. The phytoplasmas have small repeat-rich genomes. The repeated DNAs are organized into large clusters, potential mobile units (PMUs), which contain tra5 insertion sequences (ISs), and specialized sigma factors and membrane proteins. So far, PMUs are unique to phytoplasmas. Compared to mycoplasmas, phytoplasmas lack several recombination and DNA modification functions, and therefore phytoplasmas probably use different mechanisms of recombination, likely involving PMUs, for the creation of variability, allowing phytoplasmas to adjust to the diverse environments of plants and insects. The irregular GC skews and presence of ISs and large repeated sequences in the AY-WB and OY-M genomes are indicative of high genomic plasticity. Nevertheless, segments of {approx}250 kb, located between genes lplA and glnQ are syntenic between the two phytoplasmas, contain the majority of the metabolic genes and no ISs. AY-WB is further along in the reductive evolution process than OY-M. The AY-WB genome is {approx}154 kb smaller than the OY-M genome, primarily as a result of fewer multicopy sequences, including PMUs. Further, AY-WB lacks genes that are truncated and are part of incomplete pathways in OY-M. This is the first comparative phytoplasma genome analysis and report of the existence of PMUs in phytoplasma genomes.

  11. aminoguanidine alleviates radiation-induced: Topics by E-print...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sputtering. In this paper we study several aspects of debris and radiation-induced damage to candidate EUVL source collector optics materials. The first study concerns the use...

  12. Radiation induced strand breakage analyzed by tunel technique 

    E-Print Network [OSTI]

    Reynolds, Marissa Dawn

    2003-01-01T23:59:59.000Z

    The objective of this research is to fully characterize the effectiveness and limits of using the terminal deoxynucleotidyl transferase mediated biotin-dUTP nick end labeling (TUNEL) technique for analysis of radiation induced strand breakage...

  13. Radiation induced by relativistic beams passing over a diffraction...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    August 2000 FEL 2000 1 Radiation Induced by Relativistic Beams Passing Over a Diffraction Grating J.H. Brownell, J. Walsh, J. Swartz, S. Trotz Dept. of Physics and Astronomy,...

  14. Radiation induced strand breakage analyzed by tunel technique

    E-Print Network [OSTI]

    Reynolds, Marissa Dawn

    2003-01-01T23:59:59.000Z

    The objective of this research is to fully characterize the effectiveness and limits of using the terminal deoxynucleotidyl transferase mediated biotin-dUTP nick end labeling (TUNEL) technique for analysis of radiation induced strand breakage...

  15. Differences in synchrotron radiation induced gas desorption from stainless steel and aluminium alloy

    E-Print Network [OSTI]

    Andritschky, M; Mathewson, A G; Souchet, R; Strubin, Pierre M; Trickett, B A

    1990-01-01T23:59:59.000Z

    Differences in synchrotron radiation induced gas desorption from stainless steel and aluminium alloy

  16. Modeling radiation-induced mixing at interfaces between low solubility metals

    E-Print Network [OSTI]

    Zhang, Liang, Ph. D. Massachusetts Institute of Technology

    2014-01-01T23:59:59.000Z

    This thesis studies radiation-induced mixing at interfaces between low solubility metals using molecular dynamics (MD) computer simulations. It provides original contributions on the fundamental mechanisms of radiation-induced ...

  17. Transient radiation-induced absorption in laser materials

    SciTech Connect (OSTI)

    Brannon, P.J.

    1994-12-31T23:59:59.000Z

    Transient radiation-induced absorption losses in laser materials have been measured using a pulsed nuclear reactor. Reactor pulse widths of 70 to 90 {mu}s and absorbed doses of 1 to 7.5 krad have been used. Transmission recovery times and peak absorption coefficients are given. Materials tested include LiNbO{sub 3}, GSGG, silica substrates, and filter glasses used in the laser cavity. The filter glasses are tested at discrete wavelengths in the range 440--750 nm. Lithium niobate , MgO doped LiNbO{sub 3}, GSGG, and the silica substrates are tested at 1061 nm.

  18. Measurements of prompt radiation induced conductivity in Teflon (PTFE).

    SciTech Connect (OSTI)

    Hartman, E. Frederick; Zarick, Thomas Andrew; Sheridan, Timothy J.; Preston, E. [ITT Exelis Mission Systems, Colorado Springs, CO

    2013-05-01T23:59:59.000Z

    We performed measurements of the prompt radiation induced conductivity (RIC) in thin samples of Teflon (PTFE) at the Little Mountain Medusa LINAC facility in Ogden, UT. Three mil (76.2 microns) samples were irradiated with a 0.5 %CE%BCs pulse of 20 MeV electrons, yielding dose rates of 1E9 to 1E11 rad/s. We applied variable potentials up to 2 kV across the samples and measured the prompt conduction current. Details of the experimental apparatus and analysis are reported in this report on prompt RIC in Teflon.

  19. Nature of Radiation-Induced Defects in Quartz

    E-Print Network [OSTI]

    Bu Wang; Yingtian Yu; Isabella Pignatelli; Gaurav N. Sant; Mathieu Bauchy

    2015-04-10T23:59:59.000Z

    Although quartz ($\\rm \\alpha$-form) is a mineral used in numerous applications wherein radiation exposure is an issue, the nature of the atomistic defects formed during radiation-induced damage have not been fully clarified. Especially, the extent of oxygen vacancy formation is still debated, which is an issue of primary importance as optical techniques based on charged oxygen vacancies have been utilized to assess the level of radiation damage in quartz. In this paper, molecular dynamics (MD) simulations are applied to study the effects of ballistic impacts on the atomic network of quartz. We show that the defects that are formed mainly consist of over-coordinated Si and O, as well as Si--O connectivity defects, e.g., small Si--O rings and edge-sharing Si tetrahedra. Oxygen vacancies, on the contrary, are found in relatively low abundance, suggesting that characterizations based on $E^{\\prime}$ centers do not adequately capture radiation-induced structural damage in quartz. Finally, we evaluate the dependence on the incident energy, of the amount of each type of the point defects formed, and quantify unambiguously the threshold displacement energies for both O and Si atoms. These results provide a comprehensive basis to assess the nature and extent of radiation damage in quartz.

  20. Radiative acceleration and transient, radiation-induced electric fields

    E-Print Network [OSTI]

    L. Zampieri; R. Turolla; L. Foschini; A. Treves

    2003-04-14T23:59:59.000Z

    The radiative acceleration of particles and the electrostatic potential fields that arise in low density plasmas hit by radiation produced by a transient, compact source are investigated. We calculate the dynamical evolution and asymptotic energy of the charged particles accelerated by the photons and the radiation-induced electric double layer in the full relativistic, Klein-Nishina regime. For fluxes in excess of $10^{27}$ ${\\rm erg} {\\rm cm}^{-2} {\\rm s}^{-1}$, the radiative force on a diluted plasma ($n\\la 10^{11}$ cm$^{-3}$) is so strong that electrons are accelerated rapidly to relativistic speeds while ions lag behind owing to their larger inertia. The ions are later effectively accelerated by the strong radiation-induced double layer electric field up to Lorentz factors $\\approx 100$, attainable in the case of negligible Compton drag. The asymptotic energies achieved by both ions and electrons are larger by a factor 2--4 with respect to what one could naively expect assuming that the electron-ion assembly is a rigidly coupled system. The regime we investigate may be relevant within the framework of giant flares from soft gamma-repeaters.

  1. Nature of Radiation-Induced Defects in Quartz

    E-Print Network [OSTI]

    Wang, Bu; Pignatelli, Isabella; Sant, Gaurav N; Bauchy, Mathieu

    2015-01-01T23:59:59.000Z

    Although quartz ($\\rm \\alpha$-form) is a mineral used in numerous applications wherein radiation exposure is an issue, the nature of the atomistic defects formed during radiation-induced damage have not been fully clarified. Especially, the extent of oxygen vacancy formation is still debated, which is an issue of primary importance as optical techniques based on charged oxygen vacancies have been utilized to assess the level of radiation damage in quartz. In this paper, molecular dynamics (MD) simulations are applied to study the effects of ballistic impacts on the atomic network of quartz. We show that the defects that are formed mainly consist of over-coordinated Si and O, as well as Si--O connectivity defects, e.g., small Si--O rings and edge-sharing Si tetrahedra. Oxygen vacancies, on the contrary, are found in relatively low abundance, suggesting that characterizations based on $E^{\\prime}$ centers do not adequately capture radiation-induced structural damage in quartz. Finally, we evaluate the dependenc...

  2. Spatiotemporal characterization of ionizing radiation induced DNA damage foci and their relation to chromatin organization

    E-Print Network [OSTI]

    Costes, Sylvain V

    2010-01-01T23:59:59.000Z

    to ionizing radiation are nuclear marks of permanentto ionizing radiation are nuclear marks of permanentvisible nuclear domains referred to as radiation-induced

  3. Radiation-induced solitary waves in hot plasmas of accretion disks

    E-Print Network [OSTI]

    Fedor V. Prigara

    2005-07-08T23:59:59.000Z

    It is shown that the existence of radiation-induced solitary waves in hot plasmas of accretion disks depends on the radial temperature profile.

  4. attenuates ionizing radiation-induced: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Article Influence of XRCC1 Genetic Polymorphisms on Ionizing Radiation-Induced DNA Damage and Repair CiteSeer Summary: License, which permits unrestricted use, distribution,...

  5. ameliorates radiation-induced lung: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sputtering. In this paper we study several aspects of debris and radiation-induced damage to candidate EUVL source collector optics materials. The first study concerns the use...

  6. alleviates radiation-induced small-bowel: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sputtering. In this paper we study several aspects of debris and radiation-induced damage to candidate EUVL source collector optics materials. The first study concerns the use...

  7. Irradiated Esophageal Cells are Protected from Radiation-Induced Recombination by MnSOD Gene Therapy

    E-Print Network [OSTI]

    Engelward, Bevin

    Irradiated Esophageal Cells are Protected from Radiation-Induced Recombination by MnSOD Gene. Irradiated Esophageal Cells are Protected from Radiation- Induced Recombination by MnSOD Gene Therapy. Radiat,a Bevin Engelward,b Michael Epperlya and Joel S. Greenbergera,1 a Departments of Radiation Oncology

  8. Mechanism of radiation-induced bystander effect: Role of the cyclooxygenase-2 signaling pathway

    E-Print Network [OSTI]

    Brenner, David Jonathan

    impact on our thinking as well as immediate application in radiation protection. RadiationMechanism of radiation-induced bystander effect: Role of the cyclooxygenase-2 signaling pathway 25, 2005 (received for review June 30, 2005) The radiation-induced bystander effect is defined

  9. Effects of exogenous carbon monoxide on radiation-induced bystander effect in zebrafish embryos in vivo

    E-Print Network [OSTI]

    Yu, K.N.

    -no-threshed (LNT) model widely accepted for radiation protection saying that biological effects caused by ionizingEffects of exogenous carbon monoxide on radiation-induced bystander effect in zebrafish embryos) on the radiation induced bystander effect (RIBE) in vivo between embryos of the zebrafish was studied. RIBE

  10. Mini-review Radiation-induced bystander effect: Early process and rapid assessment

    E-Print Network [OSTI]

    Yu, K.N.

    by the radiation protection agencies. How- ever, this dogma has been challenged by scientific findings since 1990sMini-review Radiation-induced bystander effect: Early process and rapid assessment Hongzhi Wang September 2013 Accepted 26 September 2013 Keywords: Radiation-induced bystander effect Rapid assessment

  11. Dosimetric Analysis of Radiation-induced Gastric Bleeding

    SciTech Connect (OSTI)

    Feng, Mary, E-mail: maryfeng@umich.edu [Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan (United States)] [Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan (United States); Normolle, Daniel [Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania (United States)] [Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania (United States); Pan, Charlie C. [Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan (United States)] [Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan (United States); Dawson, Laura A. [Department of Radiation Oncology, Princess Margaret Hospital, University of Toronto, Toronto, Ontario (Canada)] [Department of Radiation Oncology, Princess Margaret Hospital, University of Toronto, Toronto, Ontario (Canada); Amarnath, Sudha [Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan (United States)] [Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan (United States); Ensminger, William D. [Department of Internal Medicine, Division of Hematology Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan (United States)] [Department of Internal Medicine, Division of Hematology Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan (United States); Lawrence, Theodore S.; Ten Haken, Randall K. [Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan (United States)] [Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan (United States)

    2012-09-01T23:59:59.000Z

    Purpose: Radiation-induced gastric bleeding has been poorly understood. In this study, we described dosimetric predictors for gastric bleeding after fractionated radiation therapy. Methods and Materials: The records of 139 sequential patients treated with 3-dimensional conformal radiation therapy (3D-CRT) for intrahepatic malignancies were reviewed. Median follow-up was 7.4 months. The parameters of a Lyman normal tissue complication probability (NTCP) model for the occurrence of {>=}grade 3 gastric bleed, adjusted for cirrhosis, were fitted to the data. The principle of maximum likelihood was used to estimate parameters for NTCP models. Results: Sixteen of 116 evaluable patients (14%) developed gastric bleeds at a median time of 4.0 months (mean, 6.5 months; range, 2.1-28.3 months) following completion of RT. The median and mean maximum doses to the stomach were 61 and 63 Gy (range, 46-86 Gy), respectively, after biocorrection of each part of the 3D dose distributions to equivalent 2-Gy daily fractions. The Lyman NTCP model with parameters adjusted for cirrhosis predicted gastric bleed. Best-fit Lyman NTCP model parameters were n=0.10 and m=0.21 and with TD{sub 50} (normal) = 56 Gy and TD{sub 50} (cirrhosis) = 22 Gy. The low n value is consistent with the importance of maximum dose; a lower TD{sub 50} value for the cirrhosis patients points out their greater sensitivity. Conclusions: This study demonstrates that the Lyman NTCP model has utility for predicting gastric bleeding and that the presence of cirrhosis greatly increases this risk. These findings should facilitate the design of future clinical trials involving high-dose upper abdominal radiation.

  12. affecting radiation-induced neurological: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    therapeutic effects of IR. Alternate p53 Su, Tin Tin 40 Debris and Radiation-Induced Damage Effects on EUV Nanolithography Source Collector Mirror Optics Performance CiteSeer...

  13. attenuates murine radiation-induced: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2-3. Rupert A. C. Croft; Gabriel Altay 2007-09-14 52 Debris and Radiation-Induced Damage Effects on EUV Nanolithography Source Collector Mirror Optics Performance CiteSeer...

  14. Radiation-induced esophageal injury: A spectrum from esophagitis to cancer

    SciTech Connect (OSTI)

    Vanagunas, A.; Jacob, P.; Olinger, E. (Northwestern Univ. Medical School, Chicago, IL (USA))

    1990-07-01T23:59:59.000Z

    Radiation esophagitis is a common but frequently unrecognized complication of therapeutic radiation to the neck, chest, or mediastinum. The spectrum of injury ranges from acute self-limited esophagitis to life-threatening esophageal perforation. Complications such as stricture or primary esophageal cancer may occur many years after irradiation, and their linkage to radiation may not be considered. Five cases of radiation-induced injury are described, and the spectrum of radiation-induced esophageal injury is reviewed.

  15. Time dependent annealing of radiation - induced leakage currents in MOS devices

    SciTech Connect (OSTI)

    Terrell, J.M. (Booz Allen and Hamilton, Inc. Bethesda, MD (US)); Olkham, T.R.; Lelis, A.J.; Benedetto, J.M. (Harry Diamond Labs., Adelphi, MD (US))

    1989-12-01T23:59:59.000Z

    Results are presented showing the radiation response of several unhardened commercial 1.25-{mu}m bulk CMOS processes using LOCOS isolation technology. In all cases studied radiation-induced failure is caused by effects in the field oxide, and the radiation-induced {delta}V{sub T} in the channel region is usually small at the failure dose. Time dependent leakage current data for the field oxides are presented and discussed.

  16. Abstract Due to reduction in device feature size and supply voltage, the sensitivity to radiation induced transient faults of

    E-Print Network [OSTI]

    Marculescu, Diana

    , the protection from radiation induced transient faults has become as important as other product characteristics to radiation induced transient faults of digital systems increases dramatically. In this paper, we present two targeting radiation hardening leading up to 80% SER reduction when applied to a subset of ISCAS'89

  17. Debris and Radiation-Induced Damage Effects on EUV Nanolithography Source Collector Mirror Optics Performance

    E-Print Network [OSTI]

    Harilal, S. S.

    Debris and Radiation-Induced Damage Effects on EUV Nanolithography Source Collector Mirror Optics, Argonne, Illinois ABSTRACT Exposure of collector mirrors facing the hot, dense pinch plasma in plasma region of the lamp are known to induce serious damage to nearby collector mirrors. Candidate collector

  18. EXTRAPOLATING RADIATION-INDUCED CANCER RISKS FROM LOW DOSES TO VERY LOW DOSES

    E-Print Network [OSTI]

    Brenner, David Jonathan

    risk; National Council on Radiation Protection and Measurements INTRODUCTION THERE IS considerablePaper EXTRAPOLATING RADIATION-INDUCED CANCER RISKS FROM LOW DOSES TO VERY LOW DOSES David J. Brenner* Abstract--There is strong evidence that ionizing radiation increases cancer risks at high doses

  19. Repression of ATR pathway by miR-185 enhances radiation-induced apoptosis and proliferation

    E-Print Network [OSTI]

    Cai, Long

    of miR-34a expression may be responsible for important protective mechanisms counteracting radiationOPEN Repression of ATR pathway by miR-185 enhances radiation-induced apoptosis and proliferation of a human microRNA (miRNA), hsa-miR-185, is downregulated in response to ionizing radiation. Elevation of mi

  20. A Prospective Cohort Study on Radiation-induced Hypothyroidism: Development of an NTCP Model

    SciTech Connect (OSTI)

    Boomsma, Marjolein J.; Bijl, Hendrik P.; Christianen, Miranda E.M.C.; Beetz, Ivo; Chouvalova, Olga; Steenbakkers, Roel J.H.M. [Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen (Netherlands); Laan, Bernard F.A.M. van der [Department of Otorhinolaryngology/Head and Neck Surgery, University Medical Center Groningen, University of Groningen, Groningen (Netherlands); Wolffenbuttel, Bruce H.R. [Department of Endocrinology, University Medical Center Groningen, University of Groningen, Groningen (Netherlands)] [Department of Endocrinology, University Medical Center Groningen, University of Groningen, Groningen (Netherlands); Oosting, Sjoukje F. [Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen (Netherlands)] [Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen (Netherlands); Schilstra, Cornelis [Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen (Netherlands)] [Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen (Netherlands); Langendijk, Johannes A., E-mail: j.a.langendijk@umcg.nl [Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen (Netherlands)

    2012-11-01T23:59:59.000Z

    Purpose: To establish a multivariate normal tissue complication probability (NTCP) model for radiation-induced hypothyroidism. Methods and Materials: The thyroid-stimulating hormone (TSH) level of 105 patients treated with (chemo-) radiation therapy for head-and-neck cancer was prospectively measured during a median follow-up of 2.5 years. Hypothyroidism was defined as elevated serum TSH with decreased or normal free thyroxin (T4). A multivariate logistic regression model with bootstrapping was used to determine the most important prognostic variables for radiation-induced hypothyroidism. Results: Thirty-five patients (33%) developed primary hypothyroidism within 2 years after radiation therapy. An NTCP model based on 2 variables, including the mean thyroid gland dose and the thyroid gland volume, was most predictive for radiation-induced hypothyroidism. NTCP values increased with higher mean thyroid gland dose (odds ratio [OR]: 1.064/Gy) and decreased with higher thyroid gland volume (OR: 0.826/cm{sup 3}). Model performance was good with an area under the curve (AUC) of 0.85. Conclusions: This is the first prospective study resulting in an NTCP model for radiation-induced hypothyroidism. The probability of hypothyroidism rises with increasing dose to the thyroid gland, whereas it reduces with increasing thyroid gland volume.

  1. Torus instability

    E-Print Network [OSTI]

    B. Kliem; T. Toeroek

    2006-08-04T23:59:59.000Z

    The expansion instability of a toroidal current ring in low-beta magnetized plasma is investigated. Qualitative agreement is obtained with experiments on spheromak expansion and with essential properties of solar coronal mass ejections, unifying the two apparently disparate classes of fast and slow coronal mass ejections.

  2. Radiation-induced complications in prostate cancer patients treated with radiotherapy

    SciTech Connect (OSTI)

    Azuddin, A. Yusof [School of Applied Physics, Faculty of Sciences and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia and Faculty of Health Sciences, Universiti Kebangsaan Malaysia, 53000 Kuala Lumpur (Malaysia); Rahman, I. Abdul; Mohamed, F. [School of Applied Physics, Faculty of Sciences and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor (Malaysia); Siah, N. J. [Faculty of Health Sciences, Universiti Kebangsaan Malaysia, 53000 Kuala Lumpur (Malaysia); Saadc, M. [Department of Oncology, University Malaya Medical Center, 50603 Kuala Lumpur (Malaysia); Ismail, F. [Department of Oncology and Radiotherapy, Universiti Kebangsaan Malaysia Medical Centre, 56000 Cheras, Kuala Lumpur (Malaysia)

    2014-09-03T23:59:59.000Z

    The purpose of the study is to determine the relationship between radiation-induced complications with dosimetric and radiobiological parameters for prostate cancer patients that underwent the conformal radiotherapy treatment. 17 prostate cancer patients that have been treated with conformal radiotherapy were retrospectively analysed. The dosimetric data was retrieved in the form of dose-volume histogram (DVH) from Radiotherapy Treatment Planning System. The DVH was utilised to derived Normal Tissue Complication Probability (NTCP) in radiobiological data. Follow-up data from medical records were used to grade the occurrence of acute gastrointestinal (GI) and genitourinary (GU) complications using Radiation Therapy Oncology Group (RTOG) scoring system. The chi-square test was used to determine the relationship between radiation-induced complication with dosimetric and radiobiological parameters. 8 (47%) and 7 (41%) patients were having acute GI and GU complications respectively. The acute GI complication can be associated with V60{sub rectum}, rectal mean dose and NTCP{sub rectum} with p-value of 0.016, 0.038 and 0.049 respectively. There are no significant relationships of acute GU complication with dosimetric and radiobiological variables. Further study can be done by increase the sample size and follow up duration for deeper understanding of the factors that effecting the GU and GI complication in prostate cancer radiotherapy.

  3. Cancer Vulnerabilities Unveiled by Genomic Loss

    E-Print Network [OSTI]

    Nijhawan, Deepak

    Due to genome instability, most cancers exhibit loss of regions containing tumor suppressor genes and collateral loss of other genes. To identify cancer-specific vulnerabilities that are the result of copy number losses, ...

  4. Radiation-Induced Segregation and Phase Stability in Candidate Alloys for the Advanced Burner Reactor

    SciTech Connect (OSTI)

    Gary S. Was; Brian D. Wirth

    2011-05-29T23:59:59.000Z

    Major accomplishments of this project were the following: 1) Radiation induced depletion of Cr occurs in alloy D9, in agreement with that observed in austenitic alloys. 2) In F-M alloys, Cr enriches at PAG grain boundaries at low dose (<7 dpa) and at intermediate temperature (400°C) and the magnitude of the enrichment decreases with temperature. 3) Cr enrichment decreases with dose, remaining enriched in alloy T91 up to 10 dpa, but changing to depletion above 3 dpa in HT9 and HCM12A. 4) Cr has a higher diffusivity than Fe by a vacancy mechanism and the corresponding atomic flux of Cr is larger than Fe in the opposite direction to the vacancy flux. 5) Cr concentration at grain boundaries decreases as a result of vacancy transport during electron or proton irradiation, consistent with Inverse Kirkendall models. 6) Inclusion of other point defect sinks into the KLMC simulation of vacancy-mediated diffusion only influences the results in the low temperature, recombination dominated regime, but does not change the conclusion that Cr depletes as a result of vacancy transport to the sink. 7) Cr segregation behavior is independent of Frenkel pair versus cascade production, as simulated for electron versus proton irradiation conditions, for the temperatures investigated. 8) The amount of Cr depletion at a simulated planar boundary with vacancy-mediated diffusion reaches an apparent saturation value by about 1 dpa, with the precise saturation concentration dependent on the ratio of Cr to Fe diffusivity. 9) Cr diffuses faster than Fe by an interstitial transport mechanism, and the corresponding atomic flux of Cr is much larger than Fe in the same direction as the interstitial flux. 10) Observed experimental and computational results show that the radiation induced segregation behavior of Cr is consistent with an Inverse Kirkendall mechanism.

  5. The Role of Platelet Factor 4 in Radiation-Induced Thrombocytopenia

    SciTech Connect (OSTI)

    Lambert, Michele P., E-mail: lambertm@email.chop.edu [Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA (United States); Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA (United States); Xiao Liqing; Nguyen, Yvonne [Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA (United States); Kowalska, M. Anna [Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA (United States); Center for Medical Biology, Polish Academy of Science, Lodz (Poland); Poncz, Mortimer [Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA (United States); Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA (United States)

    2011-08-01T23:59:59.000Z

    Purpose: Factors affecting the severity of radiation-induced thrombocytopenia (RIT) are not well described. We address whether platelet factor 4 (PF4; a negative paracrine for megakaryopoiesis) affects platelet recovery postradiation. Methods and Materials: Using conditioned media from irradiated bone marrow (BM) cells from transgenic mice overexpressing human (h) PF4 (hPF4+), megakaryocyte colony formation was assessed in the presence of this conditioned media and PF4 blocking agents. In a model of radiation-induced thrombocytopenia, irradiated mice with varying PF4 expression levels were treated with anti-hPF4 and/or thrombopoietin (TPO), and platelet count recovery and survival were examined. Results: Conditioned media from irradiated BM from hPF4+ mice inhibited megakaryocyte colony formation, suggesting that PF4 is a negative paracrine released in RIT. Blocking with an anti-hPF4 antibody restored colony formation of BM grown in the presence of hPF4+ irradiated media, as did antibodies that block the megakaryocyte receptor for PF4, low-density lipoprotein receptor-related protein 1 (LRP1). Irradiated PF4 knockout mice had higher nadir platelet counts than irradiated hPF4+/knockout litter mates (651 vs. 328 x 106/mcL, p = 0.02) and recovered earlier (15 days vs. 22 days, respectively, p <0.02). When irradiated hPF4+ mice were treated with anti-hPF4 antibody and/or TPO, they showed less severe thrombocytopenia than untreated mice, with improved survival and time to platelet recovery, but no additive effect was seen. Conclusions: Our studies show that in RIT, damaged megakaryocytes release PF4 locally, inhibiting platelet recovery. Blocking PF4 enhances recovery while released PF4 from megakaryocytes limits TPO efficacy, potentially because of increased release of PF4 stimulated by TPO. The clinical value of blocking this negative paracrine pathway post-RIT remains to be determined.

  6. DNA repair efficiency in germ cells and early mouse embryos and consequences for radiation-induced transgenerational genomic damage

    E-Print Network [OSTI]

    Marchetti, Francesco

    2009-01-01T23:59:59.000Z

    Kastan, M. B. (1997). DNA damage induces phosphorylation ofby ATM in response to DNA damage. Science 281, Barber, R. ,Nussenzweig, A. (2002). DNA damage-induced G2-M checkpoint

  7. DNA repair efficiency in germ cells and early mouse embryos and consequences for radiation-induced transgenerational genomic damage

    E-Print Network [OSTI]

    Marchetti, Francesco

    2009-01-01T23:59:59.000Z

    mutation rate in the post-chernobyl families from ukraine.mutation rate after the Chernobyl accident. Nature 380, 683-fallout following the Chernobyl accident (Dubrova et al. ,

  8. Radiation-Induced Decomposition of U(VI) Phase to Nanocrystals of UO2

    SciTech Connect (OSTI)

    S. Utsunomiya; R.C. Ewing; L. Wang

    2005-06-13T23:59:59.000Z

    U{sup 6+}-phases are common alteration products, under oxidizing conditions, of uraninite and the UO{sub 2} in spent nuclear fuel. These U{sup 6+}-phases are subjected to a radiation field caused by the {alpha}-decay of U, or in the case of spent nuclear fuel, incorporated actinides, such as {sup 239}Pu and {sup 237}Np. In order to evaluate the effects of {alpha}-decay events on the stability of the U{sup 6+}-phases, we report, for the first time, the results of ion beam irradiations (1.0 MeV Kr{sup 2+}) of U{sup 6+}-phases. The heavy-particle irradiations are used to simulate the ballistic interactions of the recoil-nucleus of an {alpha}-decay event with the surrounding structure. The Kr{sup 2+}-irradiation decomposed the U{sup 6+}-phases to UO{sub 2} nanocrystals at doses as low as 0.006 displacements per atom (dpa). U{sup 6+}-phases accumulate substantial radiation doses ({approx}1.0 displacement per atom) within 100,000 years if the concentration of incorporated {sup 239}Pu is as high as 1 wt%. Similar nanocrystals of UO{sub 2} were observed in samples from the natural fission reactors at Oklo, Gabon. Multiple cycles of radiation-induced decomposition to UO{sub 2} followed by alteration to U{sup 6+}-phases provide a mechanism for the remobilization of incorporated radionuclides.

  9. Roles of Sensory Nerves in the Regulation of Radiation-Induced Structural and Functional Changes in the Heart

    SciTech Connect (OSTI)

    Sridharan, Vijayalakshmi; Tripathi, Preeti [Department of Pharmaceutical Sciences, Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas (United States); Sharma, Sunil [Department of Radiation Oncology, Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas (United States); Moros, Eduardo G. [Department of Radiation Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida (United States); Zheng, Junying [Department of Pharmaceutical Sciences, Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas (United States); Hauer-Jensen, Martin [Department of Pharmaceutical Sciences, Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas (United States); Surgical Service, Central Arkansas Veterans Healthcare System, Little Rock, Arkansas (United States); Boerma, Marjan, E-mail: mboerma@uams.edu [Department of Pharmaceutical Sciences, Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas (United States)

    2014-01-01T23:59:59.000Z

    Purpose: Radiation-induced heart disease (RIHD) is a chronic severe side effect of radiation therapy of intrathoracic and chest wall tumors. The heart contains a dense network of sensory neurons that not only are involved in monitoring of cardiac events such as ischemia and reperfusion but also play a role in cardiac tissue homeostasis, preconditioning, and repair. The purpose of this study was to examine the role of sensory nerves in RIHD. Methods and Materials: Male Sprague-Dawley rats were administered capsaicin to permanently ablate sensory nerves, 2 weeks before local image-guided heart x-ray irradiation with a single dose of 21 Gy. During the 6 months of follow-up, heart function was assessed with high-resolution echocardiography. At 6 months after irradiation, cardiac structural and molecular changes were examined with histology, immunohistochemistry, and Western blot analysis. Results: Capsaicin pretreatment blunted the effects of radiation on myocardial fibrosis and mast cell infiltration and activity. By contrast, capsaicin pretreatment caused a small but significant reduction in cardiac output 6 months after irradiation. Capsaicin did not alter the effects of radiation on cardiac macrophage number or indicators of autophagy and apoptosis. Conclusions: These results suggest that sensory nerves, although they play a predominantly protective role in radiation-induced cardiac function changes, may eventually enhance radiation-induced myocardial fibrosis and mast cell activity.

  10. Long-term Evaluation of Radiation-Induced Optic Neuropathy After Single-Fraction Stereotactic Radiosurgery

    SciTech Connect (OSTI)

    Leavitt, Jacqueline A., E-mail: leavitt.jacqueline@mayo.edu [Department of Ophthalmology, Mayo Clinic and Foundation, Rochester, Minnesota (United States); Stafford, Scott L. [Department of Radiation Oncology, Mayo Clinic and Foundation, Rochester, Minnesota (United States); Link, Michael J. [Department of Neurosurgery, Mayo Clinic and Foundation, Rochester, Minnesota (United States); Pollock, Bruce E. [Department of Radiation Oncology, Mayo Clinic and Foundation, Rochester, Minnesota (United States); Department of Neurosurgery, Mayo Clinic and Foundation, Rochester, Minnesota (United States)

    2013-11-01T23:59:59.000Z

    Purpose: To determine the long-term risk of radiation-induced optic neuropathy (RION) in patients having single-fraction stereotactic radiosurgery (SRS) for benign skull base tumors. Methods and Materials: Retrospective review of 222 patients having Gamma Knife radiosurgery for benign tumors adjacent to the anterior visual pathway (AVP) between 1991 and 1999. Excluded were patients with prior or concurrent external beam radiation therapy or SRS. One hundred twenty-nine patients (58%) had undergone previous surgery. Tumor types included confirmed World Health Organization grade 1 or presumed cavernous sinus meningioma (n=143), pituitary adenoma (n=72), and craniopharyngioma (n=7). The maximum dose to the AVP was ?8.0 Gy (n=126), 8.1-10.0 Gy (n=39), 10.1-12.0 Gy (n=47), and >12 Gy (n=10). Results: The mean clinical and imaging follow-up periods were 83 and 123 months, respectively. One patient (0.5%) who received a maximum radiation dose of 12.8 Gy to the AVP developed unilateral blindness 18 months after SRS. The chance of RION according to the maximum radiation dose received by the AVP was 0 (95% confidence interval [CI] 0-3.6%), 0 (95% CI 0-10.7%), 0 (95% CI 0-9.0%), and 10% (95% CI 0-43.0%) for patients receiving ?8 Gy, 8.1-10.0 Gy, 10.1-12.0 Gy, and >12 Gy, respectively. The overall risk of RION in patients receiving >8 Gy to the AVP was 1.0% (95% CI 0-6.2%). Conclusions: The risk of RION after single-fraction SRS in patients with benign skull base tumors who have no prior radiation exposure is very low if the maximum dose to the AVP is ?12 Gy. Physicians performing single-fraction SRS should remain cautious when treating lesions adjacent to the AVP, especially when the maximum dose exceeds 10 Gy.

  11. Poor Baseline Pulmonary Function May Not Increase the Risk of Radiation-Induced Lung Toxicity

    SciTech Connect (OSTI)

    Wang, Jingbo [Department of Radiation Oncology, University of Michigan/Ann Arbor Veterans Health System, Ann Arbor, Michigan (United States) [Department of Radiation Oncology, University of Michigan/Ann Arbor Veterans Health System, Ann Arbor, Michigan (United States); Department of Radiation Oncology, Cancer Hospital, Chinese Academic Medical Sciences and Peking Union Medical College, Beijing (China); Cao, Jianzhong [Department of Radiation Oncology, Cancer Hospital, Chinese Academic Medical Sciences and Peking Union Medical College, Beijing (China)] [Department of Radiation Oncology, Cancer Hospital, Chinese Academic Medical Sciences and Peking Union Medical College, Beijing (China); Yuan, Shuanghu [Department of Radiation Oncology, University of Michigan/Ann Arbor Veterans Health System, Ann Arbor, Michigan (United States)] [Department of Radiation Oncology, University of Michigan/Ann Arbor Veterans Health System, Ann Arbor, Michigan (United States); Ji, Wei [Department of Radiation Oncology, Cancer Hospital, Chinese Academic Medical Sciences and Peking Union Medical College, Beijing (China)] [Department of Radiation Oncology, Cancer Hospital, Chinese Academic Medical Sciences and Peking Union Medical College, Beijing (China); Arenberg, Douglas [Department of Internal Medicine, University of Michigan/Ann Arbor Veterans Health System, Ann Arbor, Michigan (United States)] [Department of Internal Medicine, University of Michigan/Ann Arbor Veterans Health System, Ann Arbor, Michigan (United States); Dai, Jianrong [Department of Radiation Oncology, Cancer Hospital, Chinese Academic Medical Sciences and Peking Union Medical College, Beijing (China)] [Department of Radiation Oncology, Cancer Hospital, Chinese Academic Medical Sciences and Peking Union Medical College, Beijing (China); Stanton, Paul; Tatro, Daniel; Ten Haken, Randall K. [Department of Radiation Oncology, University of Michigan/Ann Arbor Veterans Health System, Ann Arbor, Michigan (United States)] [Department of Radiation Oncology, University of Michigan/Ann Arbor Veterans Health System, Ann Arbor, Michigan (United States); Wang, Luhua, E-mail: wlhwq@yahoo.com [Department of Radiation Oncology, Cancer Hospital, Chinese Academic Medical Sciences and Peking Union Medical College, Beijing (China)] [Department of Radiation Oncology, Cancer Hospital, Chinese Academic Medical Sciences and Peking Union Medical College, Beijing (China); Kong, Feng-Ming, E-mail: fengkong@med.umich.edu [Department of Radiation Oncology, University of Michigan/Ann Arbor Veterans Health System, Ann Arbor, Michigan (United States)] [Department of Radiation Oncology, University of Michigan/Ann Arbor Veterans Health System, Ann Arbor, Michigan (United States)

    2013-03-01T23:59:59.000Z

    Purpose: Poor pulmonary function (PF) is often considered a contraindication to definitive radiation therapy for lung cancer. This study investigated whether baseline PF was associated with radiation-induced lung toxicity (RILT) in patients with non-small cell lung cancer (NSCLC) receiving conformal radiation therapy (CRT). Methods and Materials: NSCLC patients treated with CRT and tested for PF at baseline were eligible. Baseline predicted values of forced expiratory volume in 1 sec (FEV1), forced vital capacity (FVC), and diffusion capacity of lung for carbon monoxide (DLCO) were analyzed. Additional factors included age, gender, smoking status, Karnofsky performance status, coexisting chronic obstructive pulmonary disease (COPD), tumor location, histology, concurrent chemotherapy, radiation dose, and mean lung dose (MLD) were evaluated for RILT. The primary endpoint was symptomatic RILT (SRILT), including grade ?2 radiation pneumonitis and fibrosis. Results: There was a total of 260 patients, and SRILT occurred in 58 (22.3%) of them. Mean FEV1 values for SRILT and non-SRILT patients were 71.7% and 65.9% (P=.077). Under univariate analysis, risk of SRILT increased with MLD (P=.008), the absence of COPD (P=.047), and FEV1 (P=.077). Age (65 split) and MLD were significantly associated with SRILT in multivariate analysis. The addition of FEV1 and age with the MLD-based model slightly improved the predictability of SRILT (area under curve from 0.63-0.70, P=.088). Conclusions: Poor baseline PF does not increase the risk of SRILT, and combining FEV1, age, and MLD may improve the predictive ability.

  12. RADIATION-INDUCED DECOMPOSITION OF U(VI) ALTERATION PHASES OF UO2

    SciTech Connect (OSTI)

    S. Utsunomiya; R.C. Ewing

    2005-09-08T23:59:59.000Z

    U{sup 6+}-phases are common alteration products of spent nuclear fuel under oxidizing conditions, and they may potentially incorporate actinides, such as long-lived {sup 239}Pu and {sup 237}Np, delaying their transport to the biosphere. In order to evaluate the ballistic effects of {alpha}-decay events on the stability of the U{sup 6+}-phases, we report, for the first time, the results of ion beam irradiations (1.0 MeV Kr{sup 2+}) for six different structures of U{sup 6+}-phases: uranophane, kasolite, boltwoodite, saleeite, carnotite, and liebigite. The target uranyl-minerals were characterized by powder X-ray diffraction and identification confirmed by SAED (selected area electron diffraction) in TEM (transmission electron microscopy). The TEM observation revealed no initial contamination of uraninite in these U{sup 6+} phases. All of the samples were irradiated with in situ TEM observation using 1.0 MeV Kr{sup 2+} in the IVEM (intermediate-voltage electron microscope) at the IVEM-Tandem Facility of Argonne National Laboratory. The ion flux was 6.3 x 10{sup 11} ions/cm{sup 2}/sec. The specimen temperatures during irradiation were 298 and 673 K, respectively. The Kr{sup 2+}-irradiation decomposed the U{sup 6+}-phases to nanocrystals of UO{sub 2} at doses as low as 0.006 dpa. The cumulative doses for the pure U{sup 6+}-phases, e.g., uranophane, at 0.1 and 1 million years (m.y.) are calculated to be 0.009 and 0.09 dpa using SRIM2003. However, with the incorporation of 1 wt.% {sup 239}Pu, the calculated doses reach 0.27 and {approx}1.00 dpa in ten thousand and one hundred thousand years, respectively. Under oxidizing conditions, multiple cycles of radiation-induced decomposition to UO{sub 2} followed by alteration to U{sup 6+}-phases should be further investigated to determine the fate of trace elements that may have been incorporated in the U{sup 6+}-phases.

  13. Clinical Outcomes of 174 Nasopharyngeal Carcinoma Patients With Radiation-Induced Temporal Lobe Necrosis

    SciTech Connect (OSTI)

    Lam, Tai-Chung, E-mail: lamtaichung@gmail.com [Department of Clinical Oncology, Tuen Mun Hospital (Hong Kong); Wong, Frank C.S. [Department of Clinical Oncology, Tuen Mun Hospital (Hong Kong); Leung, To-Wai [Department of Clinical Oncology, Queen Mary Hospital (Hong Kong); Ng, S.H. [Department of Medicine and Geriatrics, Tuen Mun Hospital (Hong Kong); Tung, Stewart Y. [Department of Clinical Oncology, Tuen Mun Hospital (Hong Kong)

    2012-01-01T23:59:59.000Z

    Purpose: To retrospectively study the clinical outcomes of nasopharyngeal carcinoma patients with radiation-induced temporal lobe necrosis (TLN) treated with steroids, surgery, or observation only. Methods and Patients: We performed a retrospective analysis of 174 consecutive patients diagnosed with TLN between 1990 and 2008. Before 1998, symptomatic patients were treated with oral steroids, while asymptomatic patients were treated conservatively. After 1998, most symptomatic and asymptomatic patients with a large volume of necrosis were treated by intravenously pulsed-steroid therapy with a standardized protocol. We examined factors affecting grade 4 complication-free survival and overall survival. Outcomes of the three treatment groups, those receiving conservative treatment, those receiving oral steroid, and those receiving intravenous pulse steroid, were compared. Results: The mean follow-up time was 115 months. Rates of grade 4 complication-free survival at 2 years and at 5 years after diagnosis of TLN were 72.2% and 54.1%, respectively. The 2-year and 5-year overall survival rates were 57.5% and 35.4%, respectively. Multivariate analysis revealed that being symptomatic at diagnosis (relative risk [RR], 4.5; p = 0.0001), re-irradiation of the nasopharynx (NP) (RR, 1.56; p = 0.008), salvage brachytherapy to the NP (RR, 1.75; p = 0.012), and a short latency period before the diagnosis of TLN (RR, 0.96, p < 0.0001) were independent prognosticators of poor grade 4 complication-free survival. Patients with all four factors had a 100% risk of developing grade 4 complications within 5 years; whereas if no factor was present, the risk was 12.5%. Intravenous pulse steroid therapy was associated with a higher clinical response rate compared with conventional steroid therapy (p < 0.0001); however, it did not affect complication-free survival in multivariate analysis. Conclusions: TLN patients with good prognosticators could be observed without active treatment. Although treatment with intravenously pulsed steroid was associated with better clinical response than conventional steroid delivery, it did not affect the complication-free survival rate of TLN patients.

  14. Amifostine, a radioprotectant agent, protects rat brain tissue lipids against ionizing radiation induced damage: An FTIR microspectroscopic imaging study

    SciTech Connect (OSTI)

    Cakmak G.; Miller L.; Zorlu, F.; Severcan, F.

    2012-03-03T23:59:59.000Z

    Amifostine is the only approved radioprotective agent by FDA for reducing the damaging effects of radiation on healthy tissues. In this study, the protective effect of amifostine against the damaging effects of ionizing radiation on the white matter (WM) and grey matter (GM) regions of the rat brain were investigated at molecular level. Sprague-Dawley rats, which were administered amifostine or not, were whole-body irradiated at a single dose of 800 cGy, decapitated after 24 h and the brain tissues of these rats were analyzed using Fourier transform infrared microspectroscopy (FTIRM). The results revealed that the total lipid content and CH{sub 2} groups of lipids decreased significantly and the carbonyl esters, olefinic=CH and CH{sub 3} groups of lipids increased significantly in the WM and GM after exposure to ionizing radiation, which could be interpreted as a result of lipid peroxidation. These changes were more prominent in the WM of the brain. The administration of amifostine before ionizing radiation inhibited the radiation-induced lipid peroxidation in the brain. In addition, this study indicated that FTIRM provides a novel approach for monitoring ionizing radiation induced-lipid peroxidation and obtaining different molecular ratio images can be used as biomarkers to detect lipid peroxidation in biological systems.

  15. Radiation hardening and radiation-induced chromium depletion effects on intergranular stress corrosion cracking of austenitic stainless steels

    SciTech Connect (OSTI)

    Bruemmer, S.M.; Simonen, E.P.

    1993-03-01T23:59:59.000Z

    Available data on neutron-irradiated materials have been analyzed and correlations developed between fluence, yield strength, grain boundary chromium concentration and cracking susceptibility in high-temperature water environments. Large heat-to-heat differences in critical fluence (0.2 to 2.5 n/cm[sup 2]) for IGSCC are documented.In many cases, this variability is consistent with yield strength differences among irradiated materials. IGSCC correlated better to yield strength than to fluence for most heats suggesting a possible role of the radiation-induced hardening (and microstructure) on cracking. However, isolatedheats reveal a wide range of yield strengths from 450 to 800 MPa necessary to promote IGSCC which cannot be understood by strength effects alone. Grain boundary Cr depletion explain differences in IGSCC susceptibility for irradiated stainless steels. Cr contents versus SCC shows that all materials showing IG cracking have some grain boundary depletion ([ge]2%). Grain boundary Cr concentrations for cracking (below [approximately]16 wt %) are in good agreement with similar SCC tests on unirradiated 304 SS with controlled depletion profiles. Heats that prompt variability in the yield strength correlation, are accounted for bydifferences in their interfacial Cr contents. Certain stainless steels are more resistant to cracking even though they have significant radiation-induced Cr depletion. It is proposed that Cr depletion is required for IASCC, but observed susceptibility is modified by other microchemical and microstructural components.

  16. Radiation hardening and radiation-induced chromium depletion effects on intergranular stress corrosion cracking of austenitic stainless steels

    SciTech Connect (OSTI)

    Bruemmer, S.M.; Simonen, E.P.

    1993-03-01T23:59:59.000Z

    Available data on neutron-irradiated materials have been analyzed and correlations developed between fluence, yield strength, grain boundary chromium concentration and cracking susceptibility in high-temperature water environments. Large heat-to-heat differences in critical fluence (0.2 to 2.5 n/cm{sup 2}) for IGSCC are documented.In many cases, this variability is consistent with yield strength differences among irradiated materials. IGSCC correlated better to yield strength than to fluence for most heats suggesting a possible role of the radiation-induced hardening (and microstructure) on cracking. However, isolatedheats reveal a wide range of yield strengths from 450 to 800 MPa necessary to promote IGSCC which cannot be understood by strength effects alone. Grain boundary Cr depletion explain differences in IGSCC susceptibility for irradiated stainless steels. Cr contents versus SCC shows that all materials showing IG cracking have some grain boundary depletion ({ge}2%). Grain boundary Cr concentrations for cracking (below {approximately}16 wt %) are in good agreement with similar SCC tests on unirradiated 304 SS with controlled depletion profiles. Heats that prompt variability in the yield strength correlation, are accounted for bydifferences in their interfacial Cr contents. Certain stainless steels are more resistant to cracking even though they have significant radiation-induced Cr depletion. It is proposed that Cr depletion is required for IASCC, but observed susceptibility is modified by other microchemical and microstructural components.

  17. Quantification of radiation induced crosslinking in a commercial, toughened silicone rubber, TR-55, by 1H MQ-NMR

    SciTech Connect (OSTI)

    Maxwell, R; Chinn, S; Alviso, C; Harvey, C A; Giuliani, J; Wilson, T; Cohenour, R

    2008-11-10T23:59:59.000Z

    Radiation induced degradation in a commercial, filled silicone composite has been studied by SPME/GC-MS, DMA, DSC, swelling, and Multiple Quantum NMR. Analysis of volatile and semivolatile species indicates degradation via decomposition of the peroxide curing catalyst and radiation induced backbiting reactions. DMA, swelling, and spin-echo NMR analysis indicate a increase in crosslink density of near 100% upon exposure to a cumulative dose of 250 kGray. Analysis of the sol-fraction via Charlseby-Pinner analysis indicates a ratio of chain scission to crosslinking yields of 0.38, consistent with the dominance of the crosslinking observed by DMA, swelling and spin-echo NMR and the chain scissioning reactions observed by MS analysis. Multiple Quantum NMR has revealed a bimodal distribution of residual dipolar couplings near 1 krad/sec and 5 krad/sec in an approximately 90:10 ratio, consistent with bulk network chains and chains associated with the filler surface. Upon exposure to radiation, the mean {Omega}{sub d} for both domains and the width of both domains both increased. The MQ NMR analysis provided increase insight into the effects of ionizing radiation on the network structure of silicone polymers.

  18. Genome duplications (polyploidy) / ancientGenome duplications (polyploidy) / ancient genome duplications (genome duplications (paleopolyploidypaleopolyploidy))

    E-Print Network [OSTI]

    Utrecht, Universiteit

    Genome duplications (polyploidy) / ancientGenome duplications (polyploidy) / ancient genome duplications (genome duplications (paleopolyploidypaleopolyploidy)) Mechanism? e.g. a diploid cell undergoes;Paramecium genome duplicationsParamecium genome duplications #12;Comparison of two scaffolds originating from

  19. Genomics and Systems Biology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Genomics and Systems Biology Genomics and Systems Biology Los Alamos scientists perform research in functional genomics and structural genomics, and applications for such work...

  20. Molluscan Evolutionary Genomics

    E-Print Network [OSTI]

    Simison, W. Brian

    2010-01-01T23:59:59.000Z

    59179 Molluscan Evolutionary Genomics W. Brian Simison andBoore Molluscan Evolutionary Genomics W. Brian Simison andL. Boore Evolutionary Genomics Department, DOE Joint Genome

  1. Synchrotron radiation induced x-ray micro analysis: A realistic alternative for electron- and ion beam microscopy?

    SciTech Connect (OSTI)

    Janssens, K.; Adams, F. [Universitaire Instelling Antwerpen, Antwerp (Belgium). Dept. of Chemistry; Rivers, M.L.; Jones, K.W. [Brookhaven National Lab., Upton, NY (United States)

    1992-10-01T23:59:59.000Z

    Synchrotron Radiation induced X-ray micro Fluorescence analysis ({mu}-SRXRF) is compared with more conventional microanalytical techniques such as Secondary Ion Microscopy (SIMS) and Electron Probe X-ray Microanalysis (EPXMA) for two typical microanalytical applications. SRXRF and EPXMA are employed for the analysis of individual particles, showing the complementary character of both techniques. By means of element mapping of trace constituents in a heterogeneous feldspar, the strong and weak points of SRXRF in comparison to EPXMA and SIMS are illustrated. The most striking difference between SRXRF and the other two microanalytical methods is the ability of SRXRF to probe deep into the investigated Material, whereas SIMS and EPXMA only investigate the upper surface of the material. The possibilities of SRXRF at third generation synchrotron rings is also briefly discussed.

  2. Synchrotron radiation induced x-ray micro analysis: A realistic alternative for electron- and ion beam microscopy

    SciTech Connect (OSTI)

    Janssens, K.; Adams, F. (Universitaire Instelling Antwerpen, Antwerp (Belgium). Dept. of Chemistry); Rivers, M.L.; Jones, K.W. (Brookhaven National Lab., Upton, NY (United States))

    1992-01-01T23:59:59.000Z

    Synchrotron Radiation induced X-ray micro Fluorescence analysis ([mu]-SRXRF) is compared with more conventional microanalytical techniques such as Secondary Ion Microscopy (SIMS) and Electron Probe X-ray Microanalysis (EPXMA) for two typical microanalytical applications. SRXRF and EPXMA are employed for the analysis of individual particles, showing the complementary character of both techniques. By means of element mapping of trace constituents in a heterogeneous feldspar, the strong and weak points of SRXRF in comparison to EPXMA and SIMS are illustrated. The most striking difference between SRXRF and the other two microanalytical methods is the ability of SRXRF to probe deep into the investigated Material, whereas SIMS and EPXMA only investigate the upper surface of the material. The possibilities of SRXRF at third generation synchrotron rings is also briefly discussed.

  3. A physical model of the photo- and radiation-induced degradation of ytterbium-doped silica optical fibres

    SciTech Connect (OSTI)

    Mady, Franck, E-mail: franck.mady@unice.fr; Duchez, Jean-Bernard, E-mail: franck.mady@unice.fr; Mebrouk, Yasmine, E-mail: franck.mady@unice.fr; Benabdesselam, Mourad, E-mail: franck.mady@unice.fr [University of Nice Sophia Antipolis, Laboratoire de Physique de la Matière Condensée (LPMC), CNRS UMR 7336, Parc Valrose, 06108 Nice cedex 2 (France)

    2014-10-21T23:59:59.000Z

    We propose a model to describe the photo- or/and the radiation-induced darkening of ytterbium-doped silica optical fibers. This model accounts for the well-established experimental features of photo-darkening. Degradation behaviors predicted for fibers pumped in harsh environments are also fully confirmed by experimental data reported in the work by Duchez et al. (this proceeding), which gives a detailed characterization of the interplay between the effects of the pump and those of a superimposed ionizing irradiation (actual operation conditions in space-based applications for instance). In particular, dependences of the darkening build-up on the pump power, the total ionizing dose and the dose rate are all correctly reproduced. The presented model is a ‘sufficient’ one, including the minimal physical ingredients required to reproduce experimental features. Refinements could be proposed to improve, e.g., quantitative kinetics.

  4. Evaluation of Reaction Rate Theory and Monte Carlo Methods for Application to Radiation-Induced Microstructural Characterization

    SciTech Connect (OSTI)

    Stoller, Roger E [ORNL; Golubov, Stanislav I [ORNL; Becquart, C. S. [Universite de Lille; Domain, C. [EDF R& D, Clamart, France

    2007-08-01T23:59:59.000Z

    The multiscale modeling scheme encompasses models from the atomistic to the continuum scale. Phenomena at the mesoscale are typically simulated using reaction rate theory, Monte Carlo, or phase field models. These mesoscale models are appropriate for application to problems that involve intermediate length scales, and timescales from those characteristic of diffusion to long-term microstructural evolution (~?s to years). Although the rate theory and Monte Carlo models can be used simulate the same phenomena, some of the details are handled quite differently in the two approaches. Models employing the rate theory have been extensively used to describe radiation-induced phenomena such as void swelling and irradiation creep. The primary approximations in such models are time- and spatial averaging of the radiation damage source term, and spatial averaging of the microstructure into an effective medium. Kinetic Monte Carlo models can account for these spatial and temporal correlations; their primary limitation is the computational burden which is related to the size of the simulation cell. A direct comparison of RT and object kinetic MC simulations has been made in the domain of point defect cluster dynamics modeling, which is relevant to the evolution (both nucleation and growth) of radiation-induced defect structures. The primary limitations of the OKMC model are related to computational issues. Even with modern computers, the maximum simulation cell size and the maximum dose (typically much less than 1 dpa) that can be simulated are limited. In contrast, even very detailed RT models can simulate microstructural evolution for doses up 100 dpa or greater in clock times that are relatively short. Within the context of the effective medium, essentially any defect density can be simulated. Overall, the agreement between the two methods is best for irradiation conditions which produce a high density of defects (lower temperature and higher displacement rate), and for materials that have a relatively high density of fixed sinks such as dislocations.

  5. Reproductive Status at First Diagnosis Influences Risk of Radiation-Induced Second Primary Contralateral Breast Cancer in the WECARE Study

    SciTech Connect (OSTI)

    Brooks, Jennifer D., E-mail: brooksj@mskcc.org [Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY (United States); Boice, John D. [International Epidemiology Institute, Rockville, MD and Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt School of Medicine, Nashville, TN (United States)] [International Epidemiology Institute, Rockville, MD and Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt School of Medicine, Nashville, TN (United States); Stovall, Marilyn [Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX (United States)] [Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX (United States); Reiner, Anne S. [Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY (United States)] [Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY (United States); Bernstein, Leslie [Division of Cancer Etiology, Department of Population Sciences, Beckman Research Institute and City of Hope Comprehensive Cancer Center, Duarte, CA (United States)] [Division of Cancer Etiology, Department of Population Sciences, Beckman Research Institute and City of Hope Comprehensive Cancer Center, Duarte, CA (United States); John, Esther M. [Cancer Prevention Institute of California, Fremont, CA, and Stanford University School of Medicine and Stanford Cancer Institute, Stanford, CA (United States)] [Cancer Prevention Institute of California, Fremont, CA, and Stanford University School of Medicine and Stanford Cancer Institute, Stanford, CA (United States); Lynch, Charles F. [Department of Epidemiology, University of Iowa, Iowa City, IA (United States)] [Department of Epidemiology, University of Iowa, Iowa City, IA (United States); Mellemkjaer, Lene [Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen (Denmark)] [Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen (Denmark); Knight, Julia A. [Dalla Lana School of Public Health, University of Toronto and Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario (Canada)] [Dalla Lana School of Public Health, University of Toronto and Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario (Canada); Thomas, Duncan C.; Haile, Robert W. [Department of Preventive Medicine, University of Southern California, Los Angeles, CA (United States)] [Department of Preventive Medicine, University of Southern California, Los Angeles, CA (United States); Smith, Susan A. [Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX (United States)] [Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX (United States); Capanu, Marinela; Bernstein, Jonine L. [Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY (United States)] [Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY (United States); Shore, Roy E. [Department of Environmental Medicine, New York University, New York, NY (United States) [Department of Environmental Medicine, New York University, New York, NY (United States); Radiation Effects Research Foundation, Hiroshima (Japan)

    2012-11-15T23:59:59.000Z

    Purpose: Our study examined whether reproductive and hormonal factors before, at the time of, or after radiation treatment for a first primary breast cancer modify the risk of radiation-induced second primary breast cancer. Methods and Materials: The Women's Environmental, Cancer and Radiation Epidemiology (WECARE) Study is a multicenter, population-based study of 708 women (cases) with asynchronous contralateral breast cancer (CBC) and 1399 women (controls) with unilateral breast cancer. Radiotherapy (RT) records, coupled with anthropomorphic phantom simulations, were used to estimate quadrant-specific radiation dose to the contralateral breast for each patient. Rate ratios (RR) and 95% confidence intervals (CI) were computed to assess the relationship between reproductive factors and risk of CBC. Results: Women who were nulliparous at diagnosis and exposed to {>=}1 Gy to the contralateral breast had a greater risk for CBC than did matched unexposed nulliparous women (RR = 2.2; 95% CI, 1.2-4.0). No increased risk was seen in RT-exposed parous women (RR = 1.1; 95% CI, 0.8-1.4). Women treated with RT who later became pregnant (8 cases and 9 controls) had a greater risk for CBC (RR = 6.0; 95% CI, 1.3-28.4) than unexposed women (4 cases and 7 controls) who also became pregnant. The association of radiation with risk of CBC did not vary by number of pregnancies, history of breastfeeding, or menopausal status at the time of first breast cancer diagnosis. Conclusion: Nulliparous women treated with RT were at an increased risk for CBC. Although based on small numbers, women who become pregnant after first diagnosis also seem to be at an increased risk for radiation-induced CBC.

  6. Genome Engineering

    SciTech Connect (OSTI)

    Voytas, Dan [University of Minnesota

    2014-03-20T23:59:59.000Z

    Dan Voytas, University of Minnesota, at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif

  7. Comparison of radiation exposure and associated radiation-induced cancer risks from mammography and molecular imaging of the breast

    SciTech Connect (OSTI)

    O'Connor, Michael K.; Li Hua; Rhodes, Deborah J.; Hruska, Carrie B.; Clancy, Conor B.; Vetter, Richard J. [Department of Radiology, Mayo Clinic, Rochester, Minnesota 55905 (United States); Department of Medicine, Mayo Clinic, Rochester, Minnesota 55905 (United States); Department of Radiology, Mayo Clinic, Rochester, Minnesota 55905 (United States); Department of Medical Physics, St. James's Hospital, Dublin (Ireland); Radiation Safety, Mayo Clinic, Rochester, Minnesota 55905 (United States)

    2010-12-15T23:59:59.000Z

    Purpose: Recent studies have raised concerns about exposure to low-dose ionizing radiation from medical imaging procedures. Little has been published regarding the relative exposure and risks associated with breast imaging techniques such as breast specific gamma imaging (BSGI), molecular breast imaging (MBI), or positron emission mammography (PEM). The purpose of this article was to estimate and compare the risks of radiation-induced cancer from mammography and techniques such as PEM, BSGI, and MBI in a screening environment. Methods: The authors used a common scheme for all estimates of cancer incidence and mortality based on the excess absolute risk model from the BEIR VII report. The lifetime attributable risk model was used to estimate the lifetime risk of radiation-induced breast cancer incidence and mortality. All estimates of cancer incidence and mortality were based on a population of 100 000 females followed from birth to age 80 and adjusted for the fraction that survives to various ages between 0 and 80. Assuming annual screening from ages 40 to 80 and from ages 50 to 80, the cumulative cancer incidence and mortality attributed to digital mammography, screen-film mammography, MBI, BSGI, and PEM was calculated. The corresponding cancer incidence and mortality from natural background radiation was calculated as a useful reference. Assuming a 15%-32% reduction in mortality from screening, the benefit/risk ratio for the different imaging modalities was evaluated. Results: Using conventional doses of 925 MBq Tc-99m sestamibi for MBI and BSGI and 370 MBq F-18 FDG for PEM, the cumulative cancer incidence and mortality were found to be 15-30 times higher than digital mammography. The benefit/risk ratio for annual digital mammography was >50:1 for both the 40-80 and 50-80 screening groups, but dropped to 3:1 for the 40-49 age group. If the primary use of MBI, BSGI, and PEM is in women with dense breast tissue, then the administered doses need to be in the range 75-150 MBq for Tc-99m sestamibi and 35 MBq-70 MBq for F-18 FDG in order to obtain benefit/risk ratios comparable to those of mammography in these age groups. These dose ranges should be achievable with enhancements to current technology while maintaining a reasonable examination time. Conclusions: The results of the dose estimates in this study clearly indicate that if molecular imaging techniques are to be of value in screening for breast cancer, then the administered doses need to be substantially reduced to better match the effective doses of mammography.

  8. Hydrodynamic instability in strong media

    SciTech Connect (OSTI)

    Bakhrakh, S.M.; Drennov, O.B.; Kovalev, N.P. [Russian Federal Nuclear Center (Russian Federation)] [and others

    1997-03-05T23:59:59.000Z

    This paper reviews the All Russian Scientific Research Institute of Experimental Physics open publications on hydrodynamic instability in strong media.

  9. Molecular analysis of radiation-induced albino (c)-locus mutations that cause death at preimplantation stages of development

    SciTech Connect (OSTI)

    Rinchik, E.M. (Oak Ridge National Lab., TN (United States)); Toenjes, R.R.; Paul, D. (Fraunhofer-Instituet fuer Toxikologie und Aerosolforschung, Hannover (Germany)); Potter, M.D. (Univ. of Tenn.-Oak Ridge Graduate School of Biomedical Sciences, Oak Ridge, TN (United States))

    1993-12-01T23:59:59.000Z

    Deletion mutations at the albino (c) locus have been useful for continuing the development of fine-structure physical and functional maps of the Fes-Hbb region of mouse chromosome 7. This report describes the molecular analysis of a number of radiation-induced c deletions that, when homozygous, cause death of the embryo during preimplantation stages. The distal extent of these deletions defines a locus, pid, (preimplantation development) genetically associated with this phenotype. The proximal breakpoints of eight of these deletions were mapped with respect to the Tyr (tyrosinase; albino) gene as well as to anonymous loci within the Fah-Tyr region that are defined by the Pmv-31 viral integration site and by chromosome-microdissection clones. Rearrangements corresponding to the proximal breakpoints of two of these deletions were detected by Southern blot analysis, and a size-altered restriction fragment carrying the breakpoint of one of them was cloned. A probe derived from this deletion fusion fragment defines a locus, D7Rn6, which maps within (or distal to) the pid region, and which discriminates among the distal extents of deletions eliciting the pid phenotype. Extension of physical maps from D7Rn6 should provide access both to the pid region and to loci mapping distal to pid that are defined by N-ethyl-N-nitrosourea-induced lethal mutations. 36 refs., 10 figs.

  10. The torus instability

    E-Print Network [OSTI]

    Kliem, B

    2006-01-01T23:59:59.000Z

    The expansion instability of a toroidal current ring in low-beta magnetized plasma is investigated. Qualitative agreement is obtained with experiments on spheromak expansion and with essential properties of solar coronal mass ejections (CMEs), unifying the two apparently disparate classes of fast and slow CMEs.

  11. JGI Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2012-01-01T23:59:59.000Z

    JGI Fungal Genomics Program Igor V. Grigoriev 1 Lawrenceof California. JGI Fungal Genomics Program Contact: IgorJGI). Its key project, the Genomics Encyclopedia of Fungi,

  12. JGI Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2011-01-01T23:59:59.000Z

    View Supports functional genomics, user data deposition andJGI Fungal Genomics Program Igor V. Grigoriev 1 DOE Jointof California. JGI Fungal Genomics Program Contact: Igor

  13. Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor

    2012-01-01T23:59:59.000Z

    strains Comparative genomics and transcriptomics of xyloseFungal Genomics Program Igor Grigoriev 1 * (complex communities Fungal Genomics Program Igor Grigoriev

  14. Traffic Dynamic Instability

    E-Print Network [OSTI]

    Louis Reese; Anna Melbinger; Erwin Frey

    2015-05-05T23:59:59.000Z

    Here we study a driven lattice gas model for microtubule depolymerizing molecular motors, where traffic jams of motors induce stochastic switching between microtubule growth and shrinkage. We term this phenomenon \\enquote{traffic dynamic instability} because it is reminiscent of microtubule dynamic instability [T. Mitchison and M. Kirschner, Nature 312, 237 (1984)]. The intermittent dynamics of growth and shrinking emerges from the interplay between the arrival of motors at the microtubule tip, motor induced depolymerization, and motor detachment from the tip. The switching dynamics correlates with low and high motor density on the lattice. This leads to an effectively bistable particle density in the system. A refined domain wall theory predicts this transient appearance of different phases in the system. The theoretical results are supported by stochastic simulations.

  15. Traffic Dynamic Instability

    E-Print Network [OSTI]

    Reese, Louis; Frey, Erwin

    2015-01-01T23:59:59.000Z

    Here we study a driven lattice gas model for microtubule depolymerizing molecular motors, where traffic jams of motors induce stochastic switching between microtubule growth and shrinkage. We term this phenomenon \\enquote{traffic dynamic instability} because it is reminiscent of microtubule dynamic instability [T. Mitchison and M. Kirschner, Nature 312, 237 (1984)]. The intermittent dynamics of growth and shrinking emerges from the interplay between the arrival of motors at the microtubule tip, motor induced depolymerization, and motor detachment from the tip. The switching dynamics correlates with low and high motor density on the lattice. This leads to an effectively bistable particle density in the system. A refined domain wall theory predicts this transient appearance of different phases in the system. The theoretical results are supported by stochastic simulations.

  16. The prediction of radiation-induced liver dysfunction using a local dose and regional venous perfusion model

    SciTech Connect (OSTI)

    Cao Yue; Platt, Joel F.; Francis, Isaac R; Balter, James M.; Pan, Charlie; Normolle, Daniel; Ben-Josef, Edgar; Haken, Randall K. ten; Lawrence, Theodore S. [Departments of Radiation Oncology and Radiology, University of Michigan, Ann Arbor, Michigan 48109-0010 (United States); Department of Radiology, University of Michigan, Ann Arbor, Michigan 48109-0010 (United States); Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48109-0010 (United States)

    2007-02-15T23:59:59.000Z

    We have shown that high dose conformal radiation combined with chemotherapy appears to prolong the survival of patients with unresectable intrahepatic cancers. The ability to safely deliver higher doses is primarily limited by the development of radiation-induced liver disease, characterized by venous occlusion. In this study, we investigated whether portal venous perfusion measured prior to the end of radiation therapy (RT) together with dose could predict liver venous perfusion dysfunction after treatment. Ten patients with unresectable intrahepatic cancer participated in an IRB-approved computer tomography (CT) perfusion study. Hepatic arterial and portal vein perfusion distributions were estimated by using dynamic contrast enhanced CT and the single compartmental model. Scans were obtained at four time points: prior to treatment, after 15 and 30 fractions of 1.5 Gy treatments, and one month following the completion of RT. Multivariant linear regression was used to determine covariances among the first three time point measurements plus dose for prediction of the post RT measurement. The reduction in the regional venous perfusion one month following RT was predicted by the local accumulated dose and the change in the regional venous perfusion after {approx}30 fractions (F=90.6,p<0.000 01). Each Gy produced an approximately 1.2% of reduction in the venous perfusion. This local dose and venous perfusion model has the potential to predict individual sensitivity to radiation. This is the first step toward developing a method to deliver higher and potentially more curative radiation doses to the patients who can safely receive these higher doses.

  17. A Systems Genetic Approach to Identify Low Dose Radiation-Induced Lymphoma Susceptibility/DOE2013FinalReport

    SciTech Connect (OSTI)

    Balmain, Allan [University of California, San Francisco; Song, Ihn Young [University of California, San Francisco

    2013-05-15T23:59:59.000Z

    The ultimate goal of this project is to identify the combinations of genetic variants that confer an individual's susceptibility to the effects of low dose (0.1 Gy) gamma-radiation, in particular with regard to tumor development. In contrast to the known effects of high dose radiation in cancer induction, the responses to low dose radiation (defined as 0.1 Gy or less) are much less well understood, and have been proposed to involve a protective anti-tumor effect in some in vivo scientific models. These conflicting results confound attempts to develop predictive models of the risk of exposure to low dose radiation, particularly when combined with the strong effects of inherited genetic variants on both radiation effects and cancer susceptibility. We have used a Â?Â?Systems Genetics approach in mice that combines genetic background analysis with responses to low and high dose radiation, in order to develop insights that will allow us to reconcile these disparate observations. Using this comprehensive approach we have analyzed normal tissue gene expression (in this case the skin and thymus), together with the changes that take place in this gene expression architecture a) in response to low or high- dose radiation and b) during tumor development. Additionally, we have demonstrated that using our expression analysis approach in our genetically heterogeneous/defined radiation-induced tumor mouse models can uniquely identify genes and pathways relevant to human T-ALL, and uncover interactions between common genetic variants of genes which may lead to tumor susceptibility.

  18. Weibel instability with nonextensive distribution

    SciTech Connect (OSTI)

    Qiu, Hui-Bin; Liu, Shi-Bing [Strong-field and Ultrafast Photonics Lab, Institute of Laser Engineering, Beijing University of Technology, Beijing 100124 (China)] [Strong-field and Ultrafast Photonics Lab, Institute of Laser Engineering, Beijing University of Technology, Beijing 100124 (China)

    2013-10-15T23:59:59.000Z

    Weibel instability in plasma, where the ion distribution is isotropic and the electron component of the plasma possesses the anisotropic temperature distribution, is investigated based on the kinetic theory in context of nonextensive statistics mechanics. The instability growth rate is shown to be dependent on the nonextensive parameters of both electron and ion, and in the extensive limit, the result in Maxwellian distribution plasma is recovered. The instability growth rate is found to be enhanced as the nonextensive parameter of electron increases.

  19. Radiation-Induced Rib Fractures After Hypofractionated Stereotactic Body Radiation Therapy: Risk Factors and Dose-Volume Relationship

    SciTech Connect (OSTI)

    Asai, Kaori [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan)] [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan); Shioyama, Yoshiyuki, E-mail: shioyama@radiol.med.kyushu-u.ac.jp [Department of Heavy Particle Therapy and Radiation Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan)] [Department of Heavy Particle Therapy and Radiation Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan); Nakamura, Katsumasa; Sasaki, Tomonari; Ohga, Saiji; Nonoshita, Takeshi [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan)] [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan); Yoshitake, Tadamasa [Department of Heavy Particle Therapy and Radiation Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan)] [Department of Heavy Particle Therapy and Radiation Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan); Ohnishi, Kayoko [Department of Radiology, National Center for Global Health and Medicine, Tokyo (Japan)] [Department of Radiology, National Center for Global Health and Medicine, Tokyo (Japan); Terashima, Kotaro; Matsumoto, Keiji [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan)] [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan); Hirata, Hideki [Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan)] [Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan); Honda, Hiroshi [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan)] [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan)

    2012-11-01T23:59:59.000Z

    Purpose: The purpose of this study was to clarify the incidence, the clinical risk factors, and the dose-volume relationship of radiation-induced rib fracture (RIRF) after hypofractionated stereotactic body radiation therapy (SBRT). Methods and Materials: One hundred sixteen patients treated with SBRT for primary or metastatic lung cancer at our institution, with at least 6 months of follow-up and no previous overlapping radiation exposure, were included in this study. To determine the clinical risk factors associated with RIRF, correlations between the incidence of RIRF and the variables, including age, sex, diagnosis, gross tumor volume diameter, rib-tumor distance, and use of steroid administration, were analyzed. Dose-volume histogram analysis was also conducted. Regarding the maximum dose, V10, V20, V30, and V40 of the rib, and the incidences of RIRF were compared between the two groups divided by the cutoff value determined by the receiver operating characteristic curves. Results: One hundred sixteen patients and 374 ribs met the inclusion criteria. Among the 116 patients, 28 patients (46 ribs) experienced RIRF. The estimated incidence of rib fracture was 37.7% at 3 years. Limited distance from the rib to the tumor (<2.0 cm) was the only significant risk factor for RIRF (p = 0.0001). Among the dosimetric parameters used for receiver operating characteristic analysis, the maximum dose showed the highest area under the curve. The 3-year estimated risk of RIRF and the determined cutoff value were 45.8% vs. 1.4% (maximum dose, {>=}42.4 Gy or less), 51.6% vs. 2.0% (V40, {>=}0.29 cm{sup 3} or less), 45.8% vs. 2.2% (V30, {>=}1.35 cm{sup 3} or less), 42.0% vs. 8.5% (V20, {>=}3.62 cm{sup 3} or less), or 25.9% vs. 10.5% (V10, {>=}5.03 cm{sup 3} or less). Conclusions: The incidence of RIRF after hypofractionated SBRT is relatively high. The maximum dose and high-dose volume are strongly correlated with RIRF.

  20. Normal Tissue Complication Probability Modeling of Radiation-Induced Hypothyroidism After Head-and-Neck Radiation Therapy

    SciTech Connect (OSTI)

    Bakhshandeh, Mohsen [Department of Medical Physics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran (Iran, Islamic Republic of)] [Department of Medical Physics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran (Iran, Islamic Republic of); Hashemi, Bijan, E-mail: bhashemi@modares.ac.ir [Department of Medical Physics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran (Iran, Islamic Republic of)] [Department of Medical Physics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran (Iran, Islamic Republic of); Mahdavi, Seied Rabi Mehdi [Department of Medical Physics, Faculty of Medical Sciences, Tehran University of Medical Sciences, Tehran (Iran, Islamic Republic of)] [Department of Medical Physics, Faculty of Medical Sciences, Tehran University of Medical Sciences, Tehran (Iran, Islamic Republic of); Nikoofar, Alireza; Vasheghani, Maryam [Department of Radiation Oncology, Hafte-Tir Hospital, Tehran University of Medical Sciences, Tehran (Iran, Islamic Republic of)] [Department of Radiation Oncology, Hafte-Tir Hospital, Tehran University of Medical Sciences, Tehran (Iran, Islamic Republic of); Kazemnejad, Anoshirvan [Department of Biostatistics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran (Iran, Islamic Republic of)] [Department of Biostatistics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran (Iran, Islamic Republic of)

    2013-02-01T23:59:59.000Z

    Purpose: To determine the dose-response relationship of the thyroid for radiation-induced hypothyroidism in head-and-neck radiation therapy, according to 6 normal tissue complication probability models, and to find the best-fit parameters of the models. Methods and Materials: Sixty-five patients treated with primary or postoperative radiation therapy for various cancers in the head-and-neck region were prospectively evaluated. Patient serum samples (tri-iodothyronine, thyroxine, thyroid-stimulating hormone [TSH], free tri-iodothyronine, and free thyroxine) were measured before and at regular time intervals until 1 year after the completion of radiation therapy. Dose-volume histograms (DVHs) of the patients' thyroid gland were derived from their computed tomography (CT)-based treatment planning data. Hypothyroidism was defined as increased TSH (subclinical hypothyroidism) or increased TSH in combination with decreased free thyroxine and thyroxine (clinical hypothyroidism). Thyroid DVHs were converted to 2 Gy/fraction equivalent doses using the linear-quadratic formula with {alpha}/{beta} = 3 Gy. The evaluated models included the following: Lyman with the DVH reduced to the equivalent uniform dose (EUD), known as LEUD; Logit-EUD; mean dose; relative seriality; individual critical volume; and population critical volume models. The parameters of the models were obtained by fitting the patients' data using a maximum likelihood analysis method. The goodness of fit of the models was determined by the 2-sample Kolmogorov-Smirnov test. Ranking of the models was made according to Akaike's information criterion. Results: Twenty-nine patients (44.6%) experienced hypothyroidism. None of the models was rejected according to the evaluation of the goodness of fit. The mean dose model was ranked as the best model on the basis of its Akaike's information criterion value. The D{sub 50} estimated from the models was approximately 44 Gy. Conclusions: The implemented normal tissue complication probability models showed a parallel architecture for the thyroid. The mean dose model can be used as the best model to describe the dose-response relationship for hypothyroidism complication.

  1. 6. Instabilities 6.1 Surface tension driven instabilities

    E-Print Network [OSTI]

    Bico,José

    6. Instabilities Apple® #12;6.1 Surface tension driven instabilities ? ? Es min, but slow Es · · #P1 a b Pb Pa #P2 - + viscous stress $ unstable surface tension $ stable (at the onset ! non linear;dynamics: viscous forces or inertia? viscous flow: Ohnesorge number inertia: ! inertia! viscous 6.1 Surface

  2. Final Technical Report - Mechanisms and pathways controlling genomic instability

    SciTech Connect (OSTI)

    Dynan, William S. [Georgia Regents University] [Georgia Regents University

    2013-05-31T23:59:59.000Z

    This project used model organisms, the zebrafish and the Japanese medaka fish to investigate the effects of low-dose radiation exposure on the vertebrate embryo. Endpoints measured included apoptotic cell death, aging, and oxidative stress.

  3. the Adaptive Response, Genetic Haplo-Insufficiency and Genomic Instability

    SciTech Connect (OSTI)

    Geard, Charles R.

    2014-12-12T23:59:59.000Z

    The linear no-threshold (LNT) hypothesis is the driving force in the establishment of radiation protection standards. However, the scientific basis for linearity has been brought into question, particularly due to the concerns about induced radiation resistance as it pertains to oxidative stress. Specifically, we investigated the observation that tumor hypoxia is associated with malignant progression, increased metastases, chemo- and radioresistance and poor prognosis. Experiments were conducted with non-malignant 3T3/NIH cells and normal human lung fibroblasts (NHLF) that were subjected to ?-irradiation under the levels of oxygen resembling those in growing tumors, and related our data to the concentrations of dissolved oxygen (DO), which is a better indicator of the amounts of residual oxygen inside the cells cultured in the hypoxic or anoxic atmosphere. We found that at DO levels about 0.5 mg/L cells subjected to both short-term (17 hours) and prolonged (48-72 hours) hypoxia continued to proliferate, and that apoptotic events were decreased at the early hours of hypoxic treatment. We showed that the short-term hypoxia up-regulated p53-binding protein 1 (53BP1) and resulted in facilitated 53BP1 nuclear foci formation and disappearance, thus indicating the higher efficiency of DNA double strand breaks repair processes. The latter was confirmed by the lower micronuclei incidence in irradiated hypoxic cells.

  4. Instabilities of Advection-Dominated Accretion Flows

    E-Print Network [OSTI]

    Xingming Chen

    1996-01-22T23:59:59.000Z

    Accretion disk instabilities are briefly reviewed. Some details are given to the short-wavelength thermal instabilities and the convective instabilities. Time-dependent calculations of two-dimensional advection-dominated accretion flows are presented.

  5. The bar instability revisited

    E-Print Network [OSTI]

    Chiodi, Filippo; Claudin, Philippe

    2012-01-01T23:59:59.000Z

    The river bar instability is revisited, using a hydrodynamical model based on Reynolds averaged Navier-Stokes equations. The results are contrasted with the standard analysis based on shallow water Saint-Venant equations. We first show that the stability of both transverse modes (ripples) and of small wavelength inclined modes (bars) predicted by the Saint-Venant approach are artefacts of this hydrodynamical approximation. When using a more reliable hydrodynamical model, the dispersion relation does not present any maximum of the growth rate when the sediment transport is assumed to be locally saturated. The analysis therefore reveals the fundamental importance of the relaxation of sediment transport towards equilibrium as it it is responsible for the stabilisation of small wavelength modes. This dynamical mechanism is characterised by the saturation number, defined as the ratio of the saturation length to the water depth Lsat/H. This dimensionless number controls the transition from ripples (transverse patte...

  6. The bar instability revisited

    E-Print Network [OSTI]

    Filippo Chiodi; Bruno Andreotti; Philippe Claudin

    2012-10-11T23:59:59.000Z

    The river bar instability is revisited, using a hydrodynamical model based on Reynolds averaged Navier-Stokes equations. The results are contrasted with the standard analysis based on shallow water Saint-Venant equations. We first show that the stability of both transverse modes (ripples) and of small wavelength inclined modes (bars) predicted by the Saint-Venant approach are artefacts of this hydrodynamical approximation. When using a more reliable hydrodynamical model, the dispersion relation does not present any maximum of the growth rate when the sediment transport is assumed to be locally saturated. The analysis therefore reveals the fundamental importance of the relaxation of sediment transport towards equilibrium as it it is responsible for the stabilisation of small wavelength modes. This dynamical mechanism is characterised by the saturation number, defined as the ratio of the saturation length to the water depth Lsat/H. This dimensionless number controls the transition from ripples (transverse patterns) at small Lsat/H to bars (inclined patterns) at large Lsat/H. At a given value of the saturation number, the instability presents a threshold and a convective-absolute transition, both controlled by the channel aspect ratio {\\beta}. We have investigated the characteristics of the most unstable mode as a function of the main parameters, Lsat/H, {\\beta} and of a subdominant parameter controlling the relative influence of drag and gravity on sediment transport. As previously found, the transition from alternate bars to multiple bars is mostly controlled by the river aspect ratio {\\beta}. By contrast, in the alternate bar regime (large Lsat/H), the selected wavelength does not depend much on {\\beta} and approximately scales as H^(2/3)L^(1/3)/C, where C is the Ch\\'ezy number.

  7. Genomics and Systems Biology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Genomics and Systems Biology LANL leads the world in computational finishing of microbial genomes Read caption + In 2013, Los Alamos scientist Richard Sayre and his team...

  8. Genomics and Bioinformatics Doug Brutlag

    E-Print Network [OSTI]

    IX #12;Genomics, Bioinformatics & Computational Biology Computational Biology Computational Molecular Biology BioinformaticsGenomics ProteomicsStructural Genomics #12;Genomics, Bioinformatics & Computational Biology Computational Biology Computational Molecular Biology BioinformaticsGenomics Proteomics

  9. Convective Instability of Thickening Mantle Lithosphere

    E-Print Network [OSTI]

    Conrad, Clint

    , 1997; Platt and England, 1994; Platt et al., 1998]. The gravitational instability of mantle lithosphere

  10. Environmental Influences on Crossflow Instability 

    E-Print Network [OSTI]

    Downs, Robert 1982-

    2012-08-28T23:59:59.000Z

    The laminar-to-turbulent transition process in swept-wing boundary layers is often dominated by an inflectional instability arising from crossflow. It is now known that freestream turbulence and surface roughness are two of the key disturbance...

  11. Preliminary Observations on Program Instability

    E-Print Network [OSTI]

    Rebentisch, Eric

    1996-10-10T23:59:59.000Z

    This white paper reports emerging findings at the end of Phase I of the Lean Aircraft Initiative in the Policy focus group area. Specifically, it provides details about research on program instability. Its objective is to ...

  12. INTRODUCTION TO GENOMIC MEDICINE

    E-Print Network [OSTI]

    INTRODUCTION TO GENOMIC MEDICINE Genomics play a role in 21st century research and clinical related to genomic medicine. Tentative Schedule: WHEN: WHERE: WHO CAN ATTEND? INTRODUCTION January 31 Implications of Genomics in Clinical Medicine February 7 Molecular Biology/Genetics Refresher - 1 February 14

  13. Personal Genomics, Personalized Medicine,

    E-Print Network [OSTI]

    Napp, Nils

    Personal Genomics, Personalized Medicine, & YOU Carrie Iwema, PhD, MLS 21st May 2012 AAAS/Science Translational Medicine panel discussion; MLA 2012 #12;Timeline: Human Genome Sequence HSLS, U.Pitt 1995 2014 2000 2003 2007 2007 2010 Human Genome Draft Sequence Complete Human Reference Genome Individual Human

  14. Nonlinear ideal magnetohydrodynamics instabilities

    SciTech Connect (OSTI)

    Pfirsch, D. (Max-Planck-Institut fuer Plasmaphysik, EURATOM Association, D-8046 Garching (Germany)); Sudan, R.N. (Laboratory of Plasma Studies, Cornell University, Ithaca, New York 14853 (United States))

    1993-07-01T23:59:59.000Z

    Explosive phenomena such as internal disruptions in toroidal discharges and solar flares are difficult to explain in terms of linear instabilities. A plasma approaching a linear stability limit can, however, become nonlinearly and explosively unstable, with noninfinitesimal perturbations even before the marginal state is reached. For such investigations, a nonlinear extension of the usual MHD (magnetohydrodynamic) energy principle is helpful. (This was obtained by Merkel and Schlueter, Sitzungsberichted. Bayer. Akad. Wiss., Munich, 1976, No. 7, for Cartesian coordinate systems.) A coordinate system independent Eulerian formulation for the Lagrangian allowing for equilibria with flow and with built-in conservation laws for mass, magnetic flux, and entropy is developed in this paper which is similar to Newcomb's Lagrangian method of 1962 [Nucl. Fusion, Suppl., Pt. II, 452 (1962)]. For static equilibria nonlinear stability is completely determined by the potential energy. For a potential energy which contains second- and [ital n]th order or some more general contributions only, it is shown in full generality that linearly unstable and marginally stable systems are explosively unstable even for infinitesimal perturbations; linearly absolutely stable systems require finite initial perturbations. For equilibria with Abelian symmetries symmetry breaking initial perturbations are needed, which should be observed in numerical simulations. Nonlinear stability is proved for two simple examples, [ital m]=0 perturbations of a Bennet Z-pinch and [ital z]-independent perturbations of a [theta] pinch. The algebra for treating these cases reduces considerably if symmetries are taken into account from the outset, as suggested by M. N. Rosenbluth (private communication, 1992).

  15. Combining Physical and Biologic Parameters to Predict Radiation-Induced Lung Toxicity in Patients With Non-Small-Cell Lung Cancer Treated With Definitive Radiation Therapy

    SciTech Connect (OSTI)

    Stenmark, Matthew H. [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States)] [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Cai Xuwei [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States) [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Radiation Oncology, Shanghai Cancer Hospital, Fudan University, Shanghai (China); Shedden, Kerby [Department of Biostatistics, University of Michigan Medical Center, Ann Arbor, Michigan (United States)] [Department of Biostatistics, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Hayman, James A. [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States)] [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Yuan Shuanghu [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States) [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Radiation Oncology, Shangdong Cancer Hospital, Jinan (China); Ritter, Timothy [Veterans Affairs Medical Center, Ann Arbor, Michigan (United States)] [Veterans Affairs Medical Center, Ann Arbor, Michigan (United States); Ten Haken, Randall K.; Lawrence, Theodore S. [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States)] [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Kong Fengming, E-mail: fengkong@med.umich.edu [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Veterans Affairs Medical Center, Ann Arbor, Michigan (United States)

    2012-10-01T23:59:59.000Z

    Purpose: To investigate the plasma dynamics of 5 proinflammatory/fibrogenic cytokines, including interleukin-1beta (IL-1{beta}), IL-6, IL-8, tumor necrosis factor alpha (TNF-{alpha}), and transforming growth factor beta1 (TGF-{beta}1) to ascertain their value in predicting radiation-induced lung toxicity (RILT), both individually and in combination with physical dosimetric parameters. Methods and Materials: Treatments of patients receiving definitive conventionally fractionated radiation therapy (RT) on clinical trial for inoperable stages I-III lung cancer were prospectively evaluated. Circulating cytokine levels were measured prior to and at weeks 2 and 4 during RT. The primary endpoint was symptomatic RILT, defined as grade 2 and higher radiation pneumonitis or symptomatic pulmonary fibrosis. Minimum follow-up was 18 months. Results: Of 58 eligible patients, 10 (17.2%) patients developed RILT. Lower pretreatment IL-8 levels were significantly correlated with development of RILT, while radiation-induced elevations of TGF-ss1 were weakly correlated with RILT. Significant correlations were not found for any of the remaining 3 cytokines or for any clinical or dosimetric parameters. Using receiver operator characteristic curves for predictive risk assessment modeling, we found both individual cytokines and dosimetric parameters were poor independent predictors of RILT. However, combining IL-8, TGF-ss1, and mean lung dose into a single model yielded an improved predictive ability (P<.001) compared to either variable alone. Conclusions: Combining inflammatory cytokines with physical dosimetric factors may provide a more accurate model for RILT prediction. Future study with a larger number of cases and events is needed to validate such findings.

  16. JGI Fungal Genomics Program

    SciTech Connect (OSTI)

    Grigoriev, Igor V.

    2011-03-14T23:59:59.000Z

    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

  17. Genomic Encyclopedia of Fungi

    SciTech Connect (OSTI)

    Grigoriev, Igor

    2012-08-10T23:59:59.000Z

    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.

  18. Genomics and the human genome project: implications for psychiatry

    E-Print Network [OSTI]

    Kelsoe, J R

    2004-01-01T23:59:59.000Z

    and psychosis: a convergent functional genomics approach.Physiology & Genomics, 4, 83–91. O LIPHANT , A. , B ARKER ,2004), 16(4), 294–300 Genomics and the Human Genome Project:

  19. Vortex driven flame dynamics and combustion instability

    E-Print Network [OSTI]

    Altay, Hurrem Murat

    2005-01-01T23:59:59.000Z

    Combustion instability in premixed combustors mostly arises due to the coupling between heat release rate dynamics and system acoustics. It is crucial to understand the instability mechanisms to design reliable, high ...

  20. Magnetic dipole discharges. III. Instabilities

    SciTech Connect (OSTI)

    Stenzel, R. L.; Urrutia, J. M. [Department of Physics and Astronomy, University of California Los Angeles, California 90095-1547 (United States)] [Department of Physics and Astronomy, University of California Los Angeles, California 90095-1547 (United States); Ionita, C.; Schrittwieser, R. [Institute for Ion Physics and Applied Physics, University of Innsbruck A-6020 Innsbruck (Austria)] [Institute for Ion Physics and Applied Physics, University of Innsbruck A-6020 Innsbruck (Austria)

    2013-08-15T23:59:59.000Z

    Instabilities in a cross-field discharge around a permanent magnet have been investigated. The permanent magnet serves as a cold cathode and the chamber wall as an anode. The magnet is biased strongly negative and emits secondary electrons due to impact of energetic ions. The electrons outside the sheath are confined by the strong dipolar magnetic field and by the ion-rich sheath surrounding the magnet. The electron energy peaks in the equatorial plane where most ionization occurs and the ions are trapped in a negative potential well. The discharge mechanism is the same as that of cylindrical and planar magnetrons, but here extended to a 3-D cathode geometry using a single dipole magnet. While the basic properties of the discharge are presented in a companion paper, the present focus is on various observed instabilities. The first is an ion sheath instability which oscillates the plasma potential outside the sheath below the ion plasma frequency. It arises in ion-rich sheaths with low electron supply, which is the case for low secondary emission yields. Sheath oscillations modulate the discharge current creating oscillating magnetic fields. The second instability is current-driven ion sound turbulence due to counter-streaming electrons and ions. The fluctuations have a broad spectrum and short correlation lengths in all directions. The third type of fluctuations is spiky potential and current oscillations in high density discharges. These appear to be due to unstable emission properties of the magnetron cathode.

  1. Control of Motorcycle Steering Instabilities

    E-Print Network [OSTI]

    Cambridge, University of

    Control of Motorcycle Steering Instabilities SIMOS EVANGELOU, DAVID J.N. LIMEBEER, ROBIN S. SHARP, and MALCOLM C. SMITH dvances in modeling bicycle and motor- cycle dynamics are providing improved of these modes are wobble and weave. Wobble is a steering oscillation that is reminis- cent of the caster shimmy

  2. Control of laser plasma instabilities in hohlraums

    SciTech Connect (OSTI)

    Kruer, W.L.

    1996-12-01T23:59:59.000Z

    Laser plasma instabilities are an important constraint on the operating regime for inertial fusion. Many techniques have been developed to control the various laser-driven instabilities. Experiments with long scale length plasmas are testing these instability levels, the nonlinear regimes, and the control mechanisms.

  3. Dynamical instability of collapsing radiating fluid

    SciTech Connect (OSTI)

    Sharif, M., E-mail: msharif.math@pu.edu.pk; Azam, M., E-mail: azammath@gmail.com [University of the Punjab, Department of Mathematics (Pakistan)

    2013-06-15T23:59:59.000Z

    We take the collapsing radiative fluid to investigate the dynamical instability with cylindrical symmetry. We match the interior and exterior cylindrical geometries. Dynamical instability is explored at radiative and non-radiative perturbations. We conclude that the dynamical instability of the collapsing cylinder depends on the critical value {gamma} < 1 for both radiative and nonradiative perturbations.

  4. Transverse instability at the recycler ring

    SciTech Connect (OSTI)

    Ng, K.Y.; /Fermilab

    2004-10-01T23:59:59.000Z

    Sporadic transverse instabilities have been observed at the Fermilab Recycler Ring leading to increase in transverse emittances and beam loss. The driving source of these instabilities has been attributed to the resistive-wall impedance with space-charge playing an important role in suppressing Landau damping. Growth rates of the instabilities are computed. Remaining problems are discussed.

  5. Observation of Parametric Instability in Advanced LIGO

    E-Print Network [OSTI]

    Evans, Matthew; Fritschel, Peter; Miller, John; Barsotti, Lisa; Martynov, Denis; Brooks, Aidan; Coyne, Dennis; Abbott, Rich; Adhikari, Rana; Arai, Koji; Bork, Rolf; Kells, Bill; Rollins, Jameson; Smith-Lefebvre, Nicolas; Vajente, Gabriele; Yamamoto, Hiroaki; Derosa, Ryan; Effler, Anamaria; Kokeyama, Keiko; Betzweiser, Joseph; Frolov, Valera; Mullavey, Adam; O`Reilly, Brian; Dwyer, Sheila; Izumi, Kiwamu; Kawabe, Keita; Landry, Michael; Sigg, Daniel; Ballmer, Stefan; Massinger, Thomas J; Staley, Alexa; Mueller, Chris; Grote, Hartmut; Ward, Robert; King, Eleanor; Blair, David; Ju, Li; Zhao, Chunnong

    2015-01-01T23:59:59.000Z

    Parametric instabilities have long been studied as a potentially limiting effect in high-power interferometric gravitational wave detectors. Until now, however, these instabilities have never been observed in a kilometer-scale interferometer. In this work we describe the first observation of parametric instability in an Advanced LIGO detector, and the means by which it has been removed as a barrier to progress.

  6. Convective and absolute instabilities in eccentric Taylor

    E-Print Network [OSTI]

    Shyamasundar, R.K.

    Convective and absolute instabilities in eccentric Taylor Laboratoire de mécanique des fluides et d and absolute instabilities in Taylor-Couette-Poiseuille flow Benoît PIER Laboratoire de mécanique des fluides flow type often disrupt oil-well drilling By implementing a detailed instability analysis, the dynamics

  7. Combustion instability modeling and analysis

    SciTech Connect (OSTI)

    Santoro, R.J.; Yang, V.; Santavicca, D.A. [Pennsylvania State Univ., University Park, PA (United States); Sheppard, E.J. [Tuskeggee Univ., Tuskegee, AL (United States). Dept. of Aerospace Engineering

    1995-12-31T23:59:59.000Z

    It is well known that the two key elements for achieving low emissions and high performance in a gas turbine combustor are to simultaneously establish (1) a lean combustion zone for maintaining low NO{sub x} emissions and (2) rapid mixing for good ignition and flame stability. However, these requirements, when coupled with the short combustor lengths used to limit the residence time for NO formation typical of advanced gas turbine combustors, can lead to problems regarding unburned hydrocarbons (UHC) and carbon monoxide (CO) emissions, as well as the occurrence of combustion instabilities. The concurrent development of suitable analytical and numerical models that are validated with experimental studies is important for achieving this objective. A major benefit of the present research will be to provide for the first time an experimentally verified model of emissions and performance of gas turbine combustors. The present study represents a coordinated effort between industry, government and academia to investigate gas turbine combustion dynamics. Specific study areas include development of advanced diagnostics, definition of controlling phenomena, advancement of analytical and numerical modeling capabilities, and assessment of the current status of our ability to apply these tools to practical gas turbine combustors. The present work involves four tasks which address, respectively, (1) the development of a fiber-optic probe for fuel-air ratio measurements, (2) the study of combustion instability using laser-based diagnostics in a high pressure, high temperature flow reactor, (3) the development of analytical and numerical modeling capabilities for describing combustion instability which will be validated against experimental data, and (4) the preparation of a literature survey and establishment of a data base on practical experience with combustion instability.

  8. Estimate of Radiation-Induced Steel Embrittlement in the BWR Core Shroud and Vessel Wall from Reactor-Grade MOX/UOX Fuel for the Nuclear Power Plant at Laguna Verde, Veracruz, Mexico

    SciTech Connect (OSTI)

    Vickers, Lisa R. [BWXT, U.S. Department of Energy, Pantex Plant, P.O. Box 30020, Hwy 60/FM 2373, Amarillo, TX 79120-0020 (United States)

    2002-07-01T23:59:59.000Z

    The government of Mexico has expressed interest to utilize the Laguna Verde boiling water reactor (BWR) nuclear power plant for the disposition of reprocessed spent uranium oxide (UOX) fuel in the form of reactor-grade mixed oxide (MOX) fuel. MOX fuel would replace spent UOX fuel as a fraction in the core from 18 - 30% depending on the fuel loading cycle. MOX fuel is expected to increase the neutron fluence, flux, fuel centerline temperature, reactor core pressure, and yield higher energy neutrons. There is concern that a core with a fraction of MOX fuel (i.e., increased {sup 239}Pu wt%) would increase the radiation-induced steel embrittlement within the core shroud and vessel wall as compared to only conventional, enriched UOX fuel in the core. The evaluation of radiation-induced steel embrittlement within the core shroud and vessel wall is a concern because of the potentially adverse affect to personnel and public safety, environment, and operating life of the reactor. The primary conclusion of this research was that the addition of the maximum fraction of 1/3 MOX fuel to the LV1 BWR core did significantly accelerate the radiation-induced steel embrittlement such that without mitigation of steel embrittlement by periodic thermal annealing or reduction in operating parameters such as, neutron fluence, core temperature and pressure, it posed a potentially adverse affect to the personnel and public safety, environment, and operating life of the reactor. (author)

  9. Phylogenetic Inference Using Whole Genomes

    E-Print Network [OSTI]

    Phylogenetic Inference Using Whole Genomes Bruce Rannala1 and Ziheng Yang2 1 Genome Center.yang@ucl.ac.uk Annu. Rev. Genomics Hum. Genet. 2008. 9:217­31 First published online as a Review in Advance on June 3, 2008 The Annual Review of Genomics and Human Genetics is online at genom.annualreviews.org This article

  10. Genome Science/Technologies

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    McDonald Bioscience Communications Email State-of-the art technology and extensive genomics expertise Protein research Read caption + Los Alamos National Laboratory graduate...

  11. Fungal Genomics Program

    SciTech Connect (OSTI)

    Grigoriev, Igor

    2012-03-12T23:59:59.000Z

    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.

  12. Webinar: Materials Genome Initative

    Broader source: Energy.gov [DOE]

    Audio recording and text version of the Fuel Cell Technologies Office webinar titled "Materials Genome Initiative," originally presented on December 2, 2014.

  13. Centrifugally driven electrostatic instability in extragalactic jets

    E-Print Network [OSTI]

    Z. Osmanov

    2008-01-29T23:59:59.000Z

    The stability problem of the rotation induced electrostatic wave in extragalactic jets is presented. Solving a set of equations describing dynamics of a relativistic plasma flow of AGN jets, an expression of the instability rate has been derived and analyzed for typical values of AGNs. The growth rate was studied versus the wave length and the inclination angle and it has been found that the instability process is much efficient with respect to the accretion disk evolution, indicating high efficiency of the instability.

  14. Hyperbaric Oxygen Treatment in Radiation-Induced Cystitis and Proctitis: A Prospective Cohort Study on Patient-Perceived Quality of Recovery

    SciTech Connect (OSTI)

    Oscarsson, Nicklas, E-mail: nicklas.oscarsson@vgregion.se [Department of Anaesthesiology and Intensive Care Medicine, Sahlgrenska Academy, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg (Sweden); Arnell, Per [Department of Anaesthesiology and Intensive Care Medicine, Sahlgrenska Academy, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg (Sweden); Lodding, Pär [Department of Urology, Sahlgrenska Academy, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg (Sweden); Ricksten, Sven-Erik; Seeman-Lodding, Heléne [Department of Anaesthesiology and Intensive Care Medicine, Sahlgrenska Academy, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg (Sweden)

    2013-11-15T23:59:59.000Z

    Purpose: In this prospective cohort study, the effects of hyperbaric oxygen treatment (HBOT) were evaluated concerning patient-perceived symptoms of late radiation-induced cystitis and proctitis secondary to radiation therapy for pelvic cancer. Methods and Materials: Thirty-nine patients, 35 men and 4 women with a mean age of 71 (range, 35-84) years were included after informed consent and institutional ethics approval. They had all been treated with radiation therapy for prostate (n=34), cervix (n=2), or rectal (n=3) cancer using external beam radiation at a dose of 25 to 75 Gy. Patients with hematuria requiring blood transfusion were excluded. The HBOT was delivered with 100% oxygen for 90 minutes at 2.0 to 2.4 atmospheres (ATA). Mean number of treatments was 36 (28-40). Symptoms were prospectively assessed using the Expanded Prostate Index Composite score before, during, and 6 to 12 months after HBOT. Results: The HBOT was successfully conducted, and symptoms were alleviated in 76% for patients with radiation cystitis, 89% for patients with radiation proctitis, and 88% of patients with combined cystitis and proctitis. Symptom reduction was demonstrated by an increased Expanded Prostate Index Composite score in the urinary domain from 50 ± 16 to 66 ± 20 after treatment (P<.001) and in the bowel domain from 48 ± 18 to 68 ± 18 after treatment (P<.001). For 31% of the patients with cystitis and 22% with proctitis, there were only trivial symptoms after HBOT. The improvement was sustained at follow-up in both domains 6 to 12 months after HBOT. No severe side effects were observed related to HBOT, and treatment compliance was high. Conclusions: HBOT can be an effective and safe treatment modality for late radiation therapy-induced soft tissue injuries in the pelvic region.

  15. Analysis of Vision Loss Caused by Radiation-Induced Optic Neuropathy After Particle Therapy for Head-and-Neck and Skull-Base Tumors Adjacent to Optic Nerves

    SciTech Connect (OSTI)

    Demizu, Yusuke, E-mail: y_demizu@nifty.co [Department of Radiology, Hyogo Ion Beam Medical Center, Tatsuno, Hyogo (Japan); Murakami, Masao; Miyawaki, Daisuke; Niwa, Yasue [Department of Radiology, Hyogo Ion Beam Medical Center, Tatsuno, Hyogo (Japan); Akagi, Takashi [Department of Accelerator Managing, Hyogo Ion Beam Medical Center, Tatsuno, Hyogo (Japan); Sasaki, Ryohei [Division of Radiology, Kobe University Graduate School of Medicine, Kobe, Hyogo (Japan); Terashima, Kazuki [Department of Radiology, Hyogo Ion Beam Medical Center, Tatsuno, Hyogo (Japan); Suga, Daisaku [Department of Radiation Technology, Hyogo Ion Beam Medical Center, Tatsuno, Hyogo (Japan); Kamae, Isao [Division of Medical Statistics, Kobe University Graduate School of Medicine, Kobe, Hyogo (Japan); Hishikawa, Yoshio [Department of Radiology, Hyogo Ion Beam Medical Center, Tatsuno, Hyogo (Japan)

    2009-12-01T23:59:59.000Z

    Purpose: To assess the incident rates of vision loss (VL; based on counting fingers or more severe) caused by radiation-induced optic neuropathy (RION) after particle therapy for tumors adjacent to optic nerves (ONs), and to evaluate factors that may contribute to VL. Methods and Materials: From August 2001 to August 2006, 104 patients with head-and-neck or skull-base tumors adjacent to ONs were treated with carbon ion or proton radiotherapy. Among them, 145 ONs of 75 patients were irradiated and followed for greater than 12 months. The incident rate of VL and the prognostic factors for occurrence of VL were evaluated. The late effects of carbon ion and proton beams were compared on the basis of a biologically effective dose at alpha/beta = 3 gray equivalent (GyE{sub 3}). Results: Eight patients (11%) experienced VL resulting from RION. The onset of VL ranged from 17 to 58 months. The median follow-up was 25 months. No significant difference was observed between the carbon ion and proton beam treatment groups. On univariate analysis, age (>60 years), diabetes mellitus, and maximum dose to the ON (>110 GyE{sub 3}) were significant, whereas on multivariate analysis only diabetes mellitus was found to be significant for VL. Conclusions: The time to the onset of VL was highly variable. There was no statistically significant difference between carbon ion and proton beam treatments over the follow-up period. Based on multivariate analysis, diabetes mellitus correlated with the occurrence of VL. A larger study with longer follow-up is warranted.

  16. Post Treatment With an FGF Chimeric Growth Factor Enhances Epithelial Cell Proliferation to Improve Recovery From Radiation-Induced Intestinal Damage

    SciTech Connect (OSTI)

    Nakayama, Fumiaki, E-mail: f_naka@nirs.go.j [Department of Radiation Emergency Medicine, National Institute of Radiological Sciences, Chiba (Japan); Hagiwara, Akiko; Umeda, Sachiko [Department of Radiation Emergency Medicine, National Institute of Radiological Sciences, Chiba (Japan); Asada, Masahiro; Goto, Megumi; Oki, Junko; Suzuki, Masashi; Imamura, Toru [Signaling Molecules Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba (Japan); Akashi, Makoto [Department of Radiation Emergency Medicine, National Institute of Radiological Sciences, Chiba (Japan)

    2010-11-01T23:59:59.000Z

    Purpose: A fibroblast growth factor (FGF) 1-FGF2 chimera (FGFC) was created previously and showed greater structural stability than FGF1. This chimera was capable of stimulating epithelial cell proliferation much more strongly than FGF1 or FGF2 even without heparin. Therefore FGFC was expected to have greater biologic activity in vivo. This study evaluated and compared the protective activity of FGFC and FGF1 against radiation-induced intestinal injuries. Methods and Materials: We administered FGFC and FGF1 intraperitoneally to BALB/c mice 24 h before or after total-body irradiation (TBI). The numbers of surviving crypts were determined 3.5 days after TBI with gamma rays at doses ranging from 8 to 12 Gy. Results: The effect of FGFC was equal to or slightly superior to FGF1 with heparin. However, FGFC was significantly more effective in promoting crypt survival than FGF1 (p < 0.01) when 10 {mu}g of each FGF was administered without heparin before irradiation. In addition, FGFC was significantly more effective at promoting crypt survival (p < 0.05) than FGF1 even when administered without heparin at 24 h after TBI at 10, 11, or 12 Gy. We found that FGFC post treatment significantly promoted 5-bromo-2'-deoxyuridine incorporation into crypts and increased crypt depth, resulting in more epithelial differentiation. However, the number of apoptotic cells in FGFC-treated mice decreased to almost the same level as that in FGF1-treated mice. Conclusions: These findings suggest that FGFC strongly enhanced radioprotection with the induction of epithelial proliferation without exogenous heparin after irradiation and is useful in clinical applications for both the prevention and post treatment of radiation injuries.

  17. SNP in TXNRD2 Associated With Radiation-Induced Fibrosis: A Study of Genetic Variation in Reactive Oxygen Species Metabolism and Signaling

    SciTech Connect (OSTI)

    Edvardsen, Hege, E-mail: hege.edvardsen@rr-research.no [Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo (Norway) [Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo (Norway); K. G. Jebsen Breast cancer centre, Institute for Clinical Medicine, University of Oslo, Oslo (Norway); Landmark-Høyvik, Hege [Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo (Norway) [Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo (Norway); K. G. Jebsen Breast cancer centre, Institute for Clinical Medicine, University of Oslo, Oslo (Norway); Reinertsen, Kristin V. [National Resource Centre for Late Effects after Cancer Treatment, OUS Radiumhospitalet, Oslo (Norway)] [National Resource Centre for Late Effects after Cancer Treatment, OUS Radiumhospitalet, Oslo (Norway); Zhao, Xi [Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo (Norway) [Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo (Norway); K. G. Jebsen Breast cancer centre, Institute for Clinical Medicine, University of Oslo, Oslo (Norway); Grenaker-Alnæs, Grethe Irene; Nebdal, Daniel [Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo (Norway)] [Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo (Norway); Syvänen, Ann-Christine [Department of Medical Sciences, Uppsala University, Uppsala (Sweden)] [Department of Medical Sciences, Uppsala University, Uppsala (Sweden); Rødningen, Olaug [Department of Medical Genetics, OUS Ullevaal, Oslo (Norway)] [Department of Medical Genetics, OUS Ullevaal, Oslo (Norway); Alsner, Jan; Overgaard, Jens [Department of Experimental Clinical Oncology, Ahus University Hospital (Norway)] [Department of Experimental Clinical Oncology, Ahus University Hospital (Norway); Borresen-Dale, Anne-Lise [Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo (Norway) [Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo (Norway); K. G. Jebsen Breast cancer centre, Institute for Clinical Medicine, University of Oslo, Oslo (Norway); Fosså, Sophie D. [K. G. Jebsen Breast cancer centre, Institute for Clinical Medicine, University of Oslo, Oslo (Norway) [K. G. Jebsen Breast cancer centre, Institute for Clinical Medicine, University of Oslo, Oslo (Norway); National Resource Centre for Late Effects after Cancer Treatment, OUS Radiumhospitalet, Oslo (Norway); Kristensen, Vessela N. [Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo (Norway) [Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo (Norway); K. G. Jebsen Breast cancer centre, Institute for Clinical Medicine, University of Oslo, Oslo (Norway); Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Ahus University Hospital (Norway)

    2013-07-15T23:59:59.000Z

    Purpose: The aim of the study was to identify noninvasive markers of treatment-induced side effects. Reactive oxygen species (ROS) are generated after irradiation, and genetic variation in genes related to ROS metabolism might influence the level of radiation-induced adverse effects (AEs). Methods and Materials: 92 breast cancer (BC) survivors previously treated with hypofractionated radiation therapy were assessed for the AEs subcutaneous atrophy and fibrosis, costal fractures, lung fibrosis, pleural thickening, and telangiectasias (median follow-up time 17.1 years). Single-nucleotide polymorphisms (SNPs) in 203 genes were analyzed for association to AE grade. SNPs associated with subcutaneous fibrosis were validated in an independent BC survivor material (n=283). The influence of the studied genetic variation on messenger ribonucleic acid (mRNA) expression level of 18 genes previously associated with fibrosis was assessed in fibroblast cell lines from BC patients. Results: Subcutaneous fibrosis and atrophy had the highest correlation (r=0.76) of all assessed AEs. The nonsynonymous SNP rs1139793 in TXNRD2 was associated with grade of subcutaneous fibrosis, the reference T-allele being more prevalent in the group experiencing severe levels of fibrosis. This was confirmed in another sample cohort of 283 BC survivors, and rs1139793 was found significantly associated with mRNA expression level of TXNRD2 in blood. Genetic variation in 24 ROS-related genes, including EGFR, CENPE, APEX1, and GSTP1, was associated with mRNA expression of 14 genes previously linked to fibrosis (P?.005). Conclusion: Development of subcutaneous fibrosis can be associated with genetic variation in the mitochondrial enzyme TXNRD2, critically involved in removal of ROS, and maintenance of the intracellular redox balance.

  18. Silver Clear Nylon Dressing is Effective in Preventing Radiation-Induced Dermatitis in Patients With Lower Gastrointestinal Cancer: Results From a Phase III Study

    SciTech Connect (OSTI)

    Niazi, Tamim M. [Segal Cancer Centre, Department of Radiation Oncology, Jewish General Hospital, McGill University (Canada)] [Segal Cancer Centre, Department of Radiation Oncology, Jewish General Hospital, McGill University (Canada); Vuong, Te, E-mail: tvuong@jgh.mcgill.ca [Segal Cancer Centre, Department of Radiation Oncology, Jewish General Hospital, McGill University (Canada)] [Segal Cancer Centre, Department of Radiation Oncology, Jewish General Hospital, McGill University (Canada); Azoulay, Laurant [Department of Epidemiology, Jewish General Hospital, McGill University (Canada)] [Department of Epidemiology, Jewish General Hospital, McGill University (Canada); Marijnen, Corrie [Department of Clinical Oncology, Leiden University Medical Center, Amsterdam (Netherlands)] [Department of Clinical Oncology, Leiden University Medical Center, Amsterdam (Netherlands); Bujko, Kryzstof [Department of Radiotherapy, The Maria Sklodowska-Curie Memorial Cancer Centre, Warsaw (Poland)] [Department of Radiotherapy, The Maria Sklodowska-Curie Memorial Cancer Centre, Warsaw (Poland); Nasr, Elie [Department of Radiation Oncology, Hotel-Dieu de France Hospital (Lebanon)] [Department of Radiation Oncology, Hotel-Dieu de France Hospital (Lebanon); Lambert, Christine; Duclos, Marie; Faria, Sergio; David, Marc [Department of Radiation Oncology, Montreal-General-Hospital, McGill University, Montreal (Canada)] [Department of Radiation Oncology, Montreal-General-Hospital, McGill University, Montreal (Canada); Cummings, Bernard [Department of Radiation Oncology, Princess Margaret Hospital, University of Toronto (Canada)] [Department of Radiation Oncology, Princess Margaret Hospital, University of Toronto (Canada)

    2012-11-01T23:59:59.000Z

    Purpose: For patients with anal canal and advanced rectal cancer, chemoradiation therapy is a curative modality or an important adjunct to surgery. Nearly all patients treated with chemoradiation experience some degree of radiation-induced dermatitis (RID). Prevention and effective treatment of RID, therefore, is of considerable clinical relevance. The present phase III randomized trial compared the efficacy of silver clear nylon dressing (SCND) with that of standard skin care for these patients. Methods and Materials: A total of 42 rectal or anal canal cancer patients were randomized to either a SCND or standard skin care group. SCND was applied from Day 1 of radiation therapy (RT) until 2 weeks after treatment completion. In the control arm, sulfadiazine cream was applied at the time of skin dermatitis. Printed digital photographs taken 2 weeks prior to, on the last day, and two weeks after the treatment completion were scored by 10 blinded readers, who used the common toxicity scoring system for skin dermatitis. Results: The radiation dose ranged from 50.4 to 59.4 Gy, and there were no differences between the 2 groups. On the last day of RT, when the most severe RID occurs, the mean dermatitis score was 2.53 (standard deviation [SD], 1.17) for the standard and 1.67 (SD, 1.2; P=.01) for the SCND arm. At 2 weeks after RT, the difference was 0.39 points in favor of SCND (P=.39). There was considerable intraclass correlation among the 10 observers. Conclusions: Silver clear nylon dressing is effective in reducing RID in patients with lower gastrointestinal cancer treated with combined chemotherapy and radiation treatment.

  19. Two-Beam Instability in Electron Cooling

    SciTech Connect (OSTI)

    Burov, Alexey V.; /Fermilab

    2006-04-01T23:59:59.000Z

    The drift motion of cooling electrons makes them able to respond to transverse perturbations of a cooled ion beam. This response may lead to dipole or quadrupole transverse instabilities at specific longitudinal wave numbers. While the dipole instabilities can be suppressed by a combination of the Landau damping, machine impedance, and the active damper, the quadrupole and higher order modes can lead to either emittance growth, or a lifetime degradation, or both. The growth rates of these instabilities are strongly determined by the machine x-y coupling. Thus, tuning out of the coupling resonance and/or reduction of the machine coupling can be an efficient remedy for these instabilities.

  20. Genomic analysis of mouse tumorigenesis

    E-Print Network [OSTI]

    Tam, Mandy Chi-Mun

    2006-01-01T23:59:59.000Z

    The availability of the human and mouse genome sequences has spurred a growing interest in analyzing mouse models of human cancer using genomic techniques. Comparative genomic studies on mouse and human tumors can be ...

  1. FUNCTIONAL GENOMICS Program of Study

    E-Print Network [OSTI]

    Thomas, Andrew

    FUNCTIONAL GENOMICS Program of Study Research Areas Students Applying Correspondence Graduate Genomics. Students receive training in the biological, physical and computational sciences through of primary institutional affiliation. The Functional Genomics program is administered through the Graduate

  2. Enhancer Identification through Comparative Genomics

    E-Print Network [OSTI]

    Visel, Axel; Bristow, James; Pennacchio, Len A.

    2006-01-01T23:59:59.000Z

    through Comparative Genomics Axel Visel, James Bristow andWalnut Creek, CA 94598 USA. Genomics Division, MS 84-171,Len A. Pennacchio, Genomics Division, One Cyclotron Road, MS

  3. The Future of Microbial Genomics

    SciTech Connect (OSTI)

    Kyrpides, Nikos [Genome Biology group at the DOE Joint Genome Institute

    2010-06-02T23:59:59.000Z

    Nikos Kyrpides, head of the Genome Biology group at the DOE Joint Genome Institute discusses current challenges in the field of microbial genomics on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  4. Ergoregion instability: The hydrodynamic vortex

    E-Print Network [OSTI]

    Leandro A. Oliveira; Vitor Cardoso; Luís C. B. Crispino

    2014-05-16T23:59:59.000Z

    Four-dimensional, asymptotically flat spacetimes with an ergoregion but no horizon have been shown to be linearly unstable against a superradiant-triggered mechanism. This result has wide implications in the search for astrophysically viable alternatives to black holes, but also in the understanding of black holes and Hawking evaporation. Here we investigate this instability in detail for a particular setup which can be realized in the laboratory: the {\\it hydrodynamic vortex}, an effective geometry for sound waves, with ergoregion and without an event horizon.

  5. Coherent instabilities in random lasers

    SciTech Connect (OSTI)

    Andreasen, Jonathan; Sebbah, Patrick; Vanneste, Christian [Laboratoire de Physique de la Matiere Condensee, CNRS UMR 6622, Universite de Nice-Sophia Antipolis, Parc Valrose, F-06108, Nice Cedex 02 (France)

    2011-08-15T23:59:59.000Z

    A numerical study is presented of random lasers as a function of the pumping rate above the threshold for lasing. Depending on the leakiness of the system resonances, which is typically larger in random lasers compared to conventional lasers, we observe that the stationary lasing regime becomes unstable above a second threshold. Coherent instabilities are observed as self pulsation at a single frequency of the output intensity, population inversion, as well as the atomic polarization. We find these Rabi oscillations have the same frequency everywhere in the random laser despite the fact that the field intensity strongly depends on the spatial location.

  6. Radiation-induced lung injury

    SciTech Connect (OSTI)

    Rosiello, R.A.; Merrill, W.W. (Yale Univ. Medical Center, New Haven, CT (USA))

    1990-03-01T23:59:59.000Z

    The use of radiation therapy is limited by the occurrence of the potentially fatal clinical syndromes of radiation pneumonitis and fibrosis. Radiation pneumonitis usually becomes clinically apparent from 2 to 6 months after completion of radiation therapy. It is characterized by fever, cough, dyspnea, and alveolar infiltrates on chest roentgenogram and may be difficult to differentiate from infection or recurrent malignancy. The pathogenesis is uncertain, but appears to involve both direct lung tissue toxicity and an inflammatory response. The syndrome may resolve spontaneously or may progress to respiratory failure. Corticosteroids may be effective therapy if started early in the course of the disease. The time course for the development of radiation fibrosis is later than that for radiation pneumonitis. It is usually present by 1 year following irradiation, but may not become clinically apparent until 2 years after radiation therapy. It is characterized by the insidious onset of dyspnea on exertion. It most often is mild, but can progress to chronic respiratory failure. There is no known successful treatment for this condition. 51 references.

  7. Radiation-induced gene responses

    SciTech Connect (OSTI)

    Woloschak, G.E.; Paunesku, T.; Shearin-Jones, P.; Oryhon, J.

    1996-12-31T23:59:59.000Z

    In the process of identifying genes that are differentially regulated in cells exposed to ultraviolet radiation (UV), we identified a transcript that was repressed following the exposure of cells to a combination of UV and salicylate, a known inhibitor of NF-kappaB. Sequencing this band determined that it has identify to lactate dehydrogenase, and Northern blots confirmed the initial expression pattern. Analysis of the sequence of the LDH 5` region established the presence of NF-kappaB, Sp1, and two Ap-2 elements; two partial AP- 1; one partial RE, and two halves of E-UV elements were also found. Electromobility shift assays were then performed for the AP-1, NF- kappaB, and E-UV elements. These experiments revealed that binding to NF-kappaB was induced by UV but repressed with salicylic acid; UV did not affect AP-1 binding, but salicylic acid inhibited it alone or following UV exposure; and E-UV binding was repressed by UV, and salicylic acid had little effect. Since the binding of no single element correlated with the expression pattern of LDH, it is likely that multiple elements govern UV/salicylate-mediated expression.

  8. Evolutionary Genomics of Salmonella enterica Subspecies

    E-Print Network [OSTI]

    2013-01-01T23:59:59.000Z

    M. 2013. Evolutionary genomics of Salmonella entericaEvolutionary Genomics of Salmonella enterica Subspecies

  9. Automated Microbial Genome Annotation

    SciTech Connect (OSTI)

    Land, Miriam [DOE Joint Genome Institute at Oak Ridge National Laboratory

    2009-05-29T23:59:59.000Z

    Miriam Land of the DOE Joint Genome Institute at Oak Ridge National Laboratory gives a talk on the current state and future challenges of moving toward automated microbial genome annotation at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  10. Evolutionary Optimization of Feedback Controllers for Thermoacoustic Instabilities

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Evolutionary Optimization of Feedback Controllers for Thermoacoustic Instabilities Nikolaus Hansen prone to thermoacoustic instabilities which arise due to a feedback loop involving fluctua- tions in acoustic pressure, velocity and heat release. Thermoacoustic instabilities may cause mechanical damage

  11. Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies

    E-Print Network [OSTI]

    2013-01-01T23:59:59.000Z

    annotation and comparative genomics. Database (Oxford) 2009,et al. : Comparative genomics of the core and accessoryComparative genomics of the core and accessory genomes of 48

  12. Linear Gain for the Microbunching Instability in an RF Compressor

    E-Print Network [OSTI]

    Venturini, M.

    2010-01-01T23:59:59.000Z

    Instability in an RF Compressor M. Venturini Lawrencefor investigating this instability in rf compressors. We useapplied to magnetic compressors [2, 3] and derive some

  13. Eukaryotic Genomics Data from the DOE Joint Genome Institute (JGI)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    From the JGI webportal users can choose Eukaryotic genomes from a photo list, access the JGI FTP directories to download data files, use the Tree of Life navigation tool, or choose a genome and go directly to a website specific to that one genome. The individual sites include direct access to download sequence files, BLAST, search, view and navigate the genomic annotations.

  14. Update on Genomic Studies of Algae Paths toward Algal Genomics

    E-Print Network [OSTI]

    Update on Genomic Studies of Algae Paths toward Algal Genomics Arthur R. Grossman* The Carnegie of genomic information that is being used to help researchers understand the gene content of organisms, how the expression of genes. In this introductory manuscript, I discuss select algae and how genomics is impacting

  15. Comparative and Functional Genomics Comp Funct Genom 2003; 4: 239245.

    E-Print Network [OSTI]

    Wurtele, Eve Syrkin

    Comparative and Functional Genomics Comp Funct Genom 2003; 4: 239­245. Published online 1 April://www.botany.iastate.edu/mash/metnetex/metabolicnetex.html) is pub- licly available software in development for analysis of genome-wide RNA, protein and metabolite in the post-genome era is to understand how interactions among molecules in a cell determine its form

  16. Institute for Plant Genomics and Biotechnology GENOMICS AND BIOTECHNOLOGY

    E-Print Network [OSTI]

    Institute for Plant Genomics and Biotechnology GENOMICS AND BIOTECHNOLOGY A multidisciplinary organization, the Institute for Plant Genomics and Biotechnology is a composed of faculty members representing projects at the Institute for Plant Genomics and Biotechnology include the development of transgenic plants

  17. Comparative and Functional Genomics Comp Funct Genom 2003; 4: 3136.

    E-Print Network [OSTI]

    Allen, John F.

    Comparative and Functional Genomics Comp Funct Genom 2003; 4: 31­36. Published online in Wiley and mitochondria contain genomes John F. Allen* Plant Biochemistry, Center for Chemistry and Chemical Engineering that the nucleotide sequences of mitochondrial and chloroplast genomes would provide the answer has proved unfounded

  18. Fuzzy Genome Sequence Assembly for Single and Environmental Genomes

    E-Print Network [OSTI]

    Nicolescu, Monica

    Fuzzy Genome Sequence Assembly for Single and Environmental Genomes Sara Nasser, Adrienne Breland. Traditional methods obtain a microorganism's DNA by culturing it in- dividually. Recent advances in genomics microbial commu- nities are often very complex with tens and hundreds of species. Assembling these genomes

  19. Nonlinear Dynamics of Single Bunch Instability

    SciTech Connect (OSTI)

    Stupakov, G.V.; /SLAC; Breizman, B.N.; Pekker, M.S.; /Texas U.

    2011-09-09T23:59:59.000Z

    A nonlinear equation is derived that governs the evolution of the amplitude of unstable oscillations with account of quantum diffusion effects due to the synchrotron radiation. Numerical solutions to this equation predict a variety of possible scenarios of nonlinear evolution of the instability some of which are in good qualitative agreement with experimental observations. Microwave single bunch instability in circular accelerators has been observed in many machines. The instability usually arises when the number of particles in the bunch exceeds some critical value, Nc, which varies depending on the parameters of the accelerating regime. Recent observations on the SLC damping rings at SLAC with a new low-impedance vacuum chamber revealed new interesting features of the instability. In some cases, after initial exponential growth, the instability eventually saturated at a level that remained constant through the accumulation cycle. In other regimes, relaxation-type oscillations were measured in nonlinear phase of the instability. In many cases, the instability was characterized by a frequency close to the second harmonic of the synchrotron oscillations. Several attempts have been made to address the nonlinear stage of the instability based on either computer simulations or some specific assumptions regarding the structure of the unstable mode. An attempt of a more general consideration of the problem is carried out in this paper. We adopt an approach recently developed in plasma physics for analysis of nonlinear behavior of weakly unstable modes in dynamic systems. Assuming that the growth rate of the instability is much smaller than its frequency, we find a time dependent solution to Vlasov equation and derive an equation for the complex amplitude of the oscillations valid in the nonlinear regime. Numerical solutions to this equation predict a variety of possible scenarios of nonlinear evolution of the instability some of which are in good qualitative agreement with experimental observations.

  20. RADIATIVE RAYLEIGH-TAYLOR INSTABILITIES

    SciTech Connect (OSTI)

    Jacquet, Emmanuel [Laboratoire de Mineralogie et Cosmochimie de Museum (LMCM), CNRS and Museum National d'Histoire Naturelle, UMR 7202, 57 rue Cuvier, 75005 Paris (France); Krumholz, Mark R., E-mail: ejacquet@mnhn.fr, E-mail: krumholz@ucolick.org [Department of Astronomy, University of California, Santa Cruz, CA 95064 (United States)

    2011-04-01T23:59:59.000Z

    We perform analytic linear stability analyses of an interface separating two stratified media threaded by a radiation flux, a configuration relevant in several astrophysical contexts. We develop a general framework for analyzing such systems and obtain exact stability conditions in several limiting cases. In the optically thin, isothermal regime, where the discontinuity is chemical in nature (e.g., at the boundary of a radiation pressure-driven H II region), radiation acts as part of an effective gravitational field, and instability arises if the effective gravity per unit volume toward the interface overcomes that away from it. In the optically thick 'adiabatic' regime where the total (gas plus radiation) specific entropy of a Lagrangian fluid element is conserved, for example at the edge of radiation pressure-driven bubble around a young massive star, we show that radiation acts like a modified equation of state and derive a generalized version of the classical Rayleigh-Taylor stability condition.

  1. Mechanical instability at finite temperature

    E-Print Network [OSTI]

    Xiaoming Mao; Anton Souslov; Carlos I. Mendoza; T. C. Lubensky

    2014-07-08T23:59:59.000Z

    Many physical systems including lattices near structural phase transitions, glasses, jammed solids, and bio-polymer gels have coordination numbers that place them at the edge of mechanical instability. Their properties are determined by an interplay between soft mechanical modes and thermal fluctuations. In this paper we investigate a simple square-lattice model with a $\\phi^4$ potential between next-nearest-neighbor sites whose quadratic coefficient $\\kappa$ can be tuned from positive negative. We show that its zero-temperature ground state for $\\kappa power-law behavior of the shear modulus as a function of temperature. We expect our study to provide a general framework for the study of finite-temperature mechanical and phase behavior of other systems with a large number of floppy modes.

  2. Human Genome Program

    SciTech Connect (OSTI)

    Not Available

    1993-01-01T23:59:59.000Z

    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. The Center for integrative genomics

    E-Print Network [OSTI]

    Kaessmann, Henrik

    The Center for integrative genomics Report 2005­2006 #12;Presentation Director's message 4 Scientific advisory committee 6 Organigram of the CIG 7 research The structure and function of genomes and their evolution alexandrereymond ­ Genome structure and expression 10 henrikKaessmann ­ Evolutionary genomics 12

  4. Genomic definition of species

    SciTech Connect (OSTI)

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01T23:59:59.000Z

    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.

  5. Genomic library construction

    DOE Patents [OSTI]

    Church, George M. (Brookline, MA); Zhang, Kun (San Diego, CA)

    2011-07-26T23:59:59.000Z

    Compositions and methods for amplifying nucleic acid sequences from a single cell are provided. Compositions and methods for constructing a genomic library from a single cell are also provided.

  6. Genomics, Gene Expression and Other Studies in Soybean Rust

    E-Print Network [OSTI]

    Posada-Buitrago, Martha Lucia

    2005-01-01T23:59:59.000Z

    Joint Genome Institute Genomics, Gene Expression and otherRust Martha Lucía Posada-Buitrago Ph.D Genomics DivisionEvolutionary Genomics DOE- Joint Genome Institute Lawrence

  7. Two-stream Instability in Pulsar Magnetospheres

    E-Print Network [OSTI]

    V. V. Usov

    2002-04-24T23:59:59.000Z

    Creation of electron-positron pairs near the pulsar surface and the parameters of plasma in pulsar magnetospheres are discussed. It is argued that the pair creation process is nonstationary, and the pair plasma that flows out from the pulsar environment is strongly nonhomogeneous and gathers into separate clouds. Plasma instabilities in the outflowing plasma are reviewed. The two-stream instability that develops due to strong nonhomogeneity of the outflowing plasma is the most plausible reason for the generation of coherent radio emission of pulsars. The development of the two-stream instability in pulsar magnetospheres is considered.

  8. Nucleomorph genomes: structure, function, origin and evolution

    E-Print Network [OSTI]

    Archibald, John

    Nucleomorph genomes: structure, function, origin and evolution John M. Archibald Summary and four genomes--two nuclear genomes, an endosymbiont- derived plastid genome and a mitochondrial genome derived from the host cell. Like mitochondrial and plastid genomes, the genome of the endosymbiont nucleus

  9. Fueling the Future with Fungal Genomics

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2011-01-01T23:59:59.000Z

    JW. 2010. China's fungal genomics initiative: a whitepaper.and Saccharomycotina. BMC Genomics. 8, 325. Bailly J,Harnessing ectomycorrhizal genomics for ecological insights.

  10. Bioinformatics and Genomics Degree Requirements Booklet

    E-Print Network [OSTI]

    dePamphilis, Claude

    Bioinformatics and Genomics Degree Requirements Booklet Fall 2010 #12;Contents Course Requirements Bioinformatics and Genomics Curriculum -------------------------------------------------------8 General #12;Bioinformatics and Genomics Option (BG

  11. VISTA - computational tools for comparative genomics

    E-Print Network [OSTI]

    Frazer, Kelly A.; Pachter, Lior; Poliakov, Alexander; Rubin, Edward M.; Dubchak, Inna

    2004-01-01T23:59:59.000Z

    tools for comparative genomics Kelly A. Frazer 1 , LiorBerkeley, CA, 94720 Genomics Division, Lawrence Berkeleymultiple comparative genomics tools and provides users with

  12. Instabilities in particle-laden flows

    E-Print Network [OSTI]

    Dupuy, Benjamin, 1981-

    2004-01-01T23:59:59.000Z

    Particles are present in many industrial processes and in nature. Dry granular flows and suspensions have been well studied and present a broad range of problems in terms of rheology and instabilities. In both cases, new ...

  13. Jeans instability in a quantum dusty magnetoplasma

    SciTech Connect (OSTI)

    Salimullah, M. [Department of Physics, GC University, Lahore-54000 (Pakistan); Salam Chair in Physics, GC University, Lahore-54000 (Pakistan); Jamil, M.; Shah, H. A. [Department of Physics, GC University, Lahore-54000 (Pakistan); Murtaza, G. [Salam Chair in Physics, GC University, Lahore-54000 (Pakistan)

    2009-01-15T23:59:59.000Z

    Jeans instability in a homogeneous cold quantum dusty plasma in the presence of the ambient magnetic field and the quantum effect arising through the Bohm potential has been examined using the quantum magnetohydrodynamic model. It is found that the Jeans instability is significantly reduced by the presence of the dust-lower-hybrid wave and the ion quantum effect. The minimum wavenumber for Jeans stability depends clearly on ion quantum effect and the dust-lower-hybrid frequency also.

  14. Energy Gradient Theory of Hydrodynamic Instability

    E-Print Network [OSTI]

    Hua-Shu Dou

    2005-01-29T23:59:59.000Z

    A new universal theory for flow instability and turbulent transition is proposed in this study. Flow instability and turbulence transition have been challenging subjects for fluid dynamics for a century. The critical condition of turbulent transition from theory and experiments differs largely from each other for Poiseuille flows. In this paper, a new mechanism of flow instability and turbulence transition is presented for parallel shear flows and the energy gradient theory of hydrodynamic instability is proposed. It is stated that the total energy gradient in the transverse direction and that in the streamwise direction of the main flow dominate the disturbance amplification or decay. A new dimensionless parameter K for characterizing flow instability is proposed for wall bounded shear flows, which is expressed as the ratio of the energy gradients in the two directions. It is thought that flow instability should first occur at the position of Kmax which may be the most dangerous position. This speculation is confirmed by Nishioka et al's experimental data. Comparison with experimental data for plane Poiseuille flow and pipe Poiseuille flow indicates that the proposed idea is really valid. It is found that the turbulence transition takes place at a critical value of Kmax of about 385 for both plane Poiseuille flow and pipe Poiseuille flow, below which no turbulence will occur regardless the disturbance. More studies show that the theory is also valid for plane Couette flows and Taylor-Couette flows between concentric rotating cylinders.

  15. Computational genomics : mapping, comparison, and annotation of genomes

    E-Print Network [OSTI]

    Batzoglou, Serafim

    2000-01-01T23:59:59.000Z

    The field of genomics provides many challenges to computer scientists and mathematicians. The area of computational genomics has been expanding recently, and the timely application of computer science in this field is ...

  16. Microbial Genomics Data from the DOE Joint Genome Institute (JGI)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    As of March 2008, The Joint Genome Institute has released 296 Prokaryotic microbial sites, with 216 in finished status.

  17. Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux

    E-Print Network [OSTI]

    Hammerton, James

    Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux Erin A. Lynch1 , Morgan G. Eisen1,3,12,13 *, Marc T. Facciotti1,3,14 * 1 Microbiology Graduate Group, University of California We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula

  18. Clinical Microfluidics for Neutrophil Genomics and Proteomics...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Clinical Microfluidics for Neutrophil Genomics and Proteomics. Clinical Microfluidics for Neutrophil Genomics and Proteomics. Abstract: Neutrophils play critical roles in...

  19. Mammalian comparative genomics and epigenomics

    E-Print Network [OSTI]

    Mikkelsen, Tarjei Sigurd, 1978-

    2009-01-01T23:59:59.000Z

    The human genome sequence can be thought of as an instruction manual for our species, written and rewritten over more than a billion of years of evolution. Taking a complete inventory of our genome, dissecting its genes ...

  20. Genomics Division Home

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField8,Dist.Newof EnergyFundingGeneGenome Engineering withfor Genomics

  1. SHORT REVIEW Butterfly genomics eclosing

    E-Print Network [OSTI]

    Beldade, Patrícia

    SHORT REVIEW Butterfly genomics eclosing P Beldade1 , WO McMillan2 and A Papanicolaou3 1 Section to an explosion of genomic data and the emergence of new research avenues. Evolutionary and ecological functional genomics, with its focus on the genes that affect ecological success and adaptation in natural populations

  2. Coherent Instabilities of ILC Damping Ring

    SciTech Connect (OSTI)

    Heifets, S.; Stupakov, G.; Bane, K.; /SLAC

    2006-09-27T23:59:59.000Z

    The paper presents the first attempt to estimates the ILC damping ring impedance and compare thresholds of the classical instabilities for several designs initially proposed for the DR. The work was carried out in the spring of 2006. Since then the choice of the DR is narrowed. Nevertheless, the analysis described may be useful for the next iterations of the beam stability. Overall, the conventional instabilities will have little impact on the ring performance provided the careful design of the ring minimizes the impedance below acceptable level indicated above. The only exception is the transverse CB instability. The longitudinal CB is less demanding. However, even the transverse CB instability would have threshold current above nominal provided the aperture in the wigglers is increased from 8 mm to 16 mm. The microwave instability needs more studies. Nevertheless, we should remember that the ILC DR is different from existing high-current machines at least in two respects: absence of the beam-beam tune spread stabilizing beams in colliders, and unusual strict requirements for low emittance. That may cause new problems such as bunch emittance dilution due to high-frequency wakes (BPMs, grooves), etc. Even if such a possibility exists, it probably universal for all machines and ought be addressed in the design of vacuum components rather than have effect on the choice of the machine design.

  3. Instability limits for spontaneous double layer formation

    SciTech Connect (OSTI)

    Carr, J. Jr. [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States) [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States); Department of Physics, Texas Lutheran University, Seguin, Texas 78155 (United States); Galante, M. E.; McCarren, D.; Scime, E. E.; Sears, S.; VanDervort, R. W. [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States)] [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States); Magee, R. M. [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States) [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States); TriAlpha Energy, Inc., Foothill Ranch, California 92610 (United States); Reynolds, E. [Department of Physics and Engineering, West Virginia Wesleyan, Buckhannon, West Virginia 26201 (United States)] [Department of Physics and Engineering, West Virginia Wesleyan, Buckhannon, West Virginia 26201 (United States)

    2013-11-15T23:59:59.000Z

    We present time-resolved measurements that demonstrate that large amplitude electrostatic instabilities appear in pulsed, expanding helicon plasmas at the same time as particularly strong double layers appear in the expansion region. A significant cross-correlation between the electrostatic fluctuations and fluctuations in the number of ions accelerated by the double layer electric field is observed. No correlation is observed between the electrostatic fluctuations and ions that have not passed through the double layer. These measurements confirm that the simultaneous appearance of the electrostatic fluctuations and the double layer is not simple coincidence. In fact, the accelerated ion population is responsible for the growth of the instability. The double layer strength, and therefore, the velocity of the accelerated ions, is limited by the appearance of the electrostatic instability.

  4. Strings, vortex rings, and modes of instability

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Gubser, Steven S.; Nayar, Revant; Parikh, Sarthak

    2015-03-01T23:59:59.000Z

    We treat string propagation and interaction in the presence of a background Neveu–Schwarz three-form field strength, suitable for describing vortex rings in a superfluid or low-viscosity normal fluid. A circular vortex ring exhibits instabilities which have been recognized for many years, but whose precise boundaries we determine for the first time analytically in the small core limit. Two circular vortices colliding head-on exhibit stronger instabilities which cause splitting into many small vortices at late times. We provide an approximate analytic treatment of these instabilities and show that the most unstable wavelength is parametrically larger than a dynamically generated length scalemore »which in many hydrodynamic systems is close to the cutoff. We also summarize how the string construction we discuss can be derived from the Gross–Pitaevskii Lagrangian, and also how it compares to the action for giant gravitons.« less

  5. Bernstein instability driven by thermal ring distribution

    SciTech Connect (OSTI)

    Yoon, Peter H., E-mail: yoonp@umd.edu [Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742 (United States); School of Space Research, Kyung Hee University, Yongin-Si, Gyeonggi-Do 446-701 (Korea, Republic of); Hadi, Fazal; Qamar, Anisa [Institute of Physics and Electronics, University of Peshawar, Peshawar 25000 (Pakistan)

    2014-07-15T23:59:59.000Z

    The classic Bernstein waves may be intimately related to banded emissions detected in laboratory plasmas, terrestrial, and other planetary magnetospheres. However, the customary discussion of the Bernstein wave is based upon isotropic thermal velocity distribution function. In order to understand how such waves can be excited, one needs an emission mechanism, i.e., an instability. In non-relativistic collision-less plasmas, the only known Bernstein wave instability is that associated with a cold perpendicular velocity ring distribution function. However, cold ring distribution is highly idealized. The present Brief Communication generalizes the cold ring distribution model to include thermal spread, so that the Bernstein-ring instability is described by a more realistic electron distribution function, with which the stabilization by thermal spread associated with the ring distribution is demonstrated. The present findings imply that the excitation of Bernstein waves requires a sufficiently high perpendicular velocity gradient associated with the electron distribution function.

  6. Pulsational Instabilities in Accreting White Dwarfs

    E-Print Network [OSTI]

    Phil Arras; Dean M. Townsley; Lars Bildsten

    2006-04-13T23:59:59.000Z

    (Abridged) The Cataclysmic Variable (CV) population harbors a diverse range of donor stars and accreting white dwarfs (WDs). A range of WD masses is expected, from low mass Helium core WDs, to massive WDs which have previously accreted at rates high enough for Hydrogen to burn steadily. Furthermore, a wide range of Helium enrichment is expected in the accreted material depending on the degree to which the donor star is evolved. We investigate the impact of this diversity on the range of effective temperatures ($T_{\\rm eff}$) for which g-modes are unstable. The critical $T_{\\rm eff}$ below which modes are unstable ("blue edge") depends on both surface gravity, $g$, and He abundance, $Y$. The Hydrogen/first Helium ionization instability strip is more sensitive to $g$ than $Y$. We find that (for solar composition envelopes), relative to a fiducial WD mass $0.6 M_\\odot$, the blue edge for a $0.4 M_\\odot$ He core WD shifts downward by $\\approx 1000 {\\rm K}$, while that for a massive $\\approx 1.2 M_\\odot$ WD shifts upward by $\\approx 2000 {\\rm K}$. The second Helium ionization instability strip exhibits strong dependences on both $g$ and $Y$. Surprisingly, increasing $Y$ by only 10% relative to solar creates an instability strip near $15,000 {\\rm K}$. Hence CV's below the period gap with evolved donor stars of $Y\\ga 0.4$ may have an "intermediate" instability strip well outside of the isolated DA and DB variables. This "intermediate" instability strip also occurs for low mass He WD with solar composition envelopes. The lack of pulsations in CV's with $T_{\\rm eff}$ in the pure Hydrogen ZZ Ceti instability strip is also easily explained.

  7. Dissipation induced Instabilities and the Mechanical Laser

    E-Print Network [OSTI]

    Marcel G. Clerc; Jerrold E. Marsden

    2001-03-26T23:59:59.000Z

    We study the 1:1 resonance for perturbed Hamiltonian systems with small dissipative and energy injection terms. These perturbations of the 1:1 resonance exhibit dissipation induced instabilities. This mechanism allow us to show that a slightly pumping optical cavity is unstable when one takes into account the dissipative effects. The Maxwell-Bloch equations are the asymptotic normal form that describe this instability when energy is injected through forcing at zero frequency. We display a simple mechanical system, close to the 1:1 resonance, which is a mechanical analog of the Laser.

  8. Understanding magnetic instability in gapless superconductors

    E-Print Network [OSTI]

    Mei Huang

    2005-09-18T23:59:59.000Z

    Magnetic instability in gapless superconductors still remains as a puzzle. In this article, we point out that the instability might be caused by using BCS theory in mean-field approximation, where the phase fluctuation has been neglected. The mean-field BCS theory describes very well the strongly coherent or rigid superconducting state. With the increase of mismatch between the Fermi surfaces of pairing fermions, the phase fluctuation plays more and more important role, and "soften" the superconductor. The strong phase fluctuation will eventually quantum disorder the superconducting state, and turn the system into a phase-decoherent pseudogap state.

  9. Coral Reef Genomics: Developing tools for functional genomics of coral symbiosis

    E-Print Network [OSTI]

    Schwarz, Jodi; Brokstein, Peter; Manohar, Chitra; Coffroth, Mary Alice; Szmant, Alina; Medina, Monica

    2008-01-01T23:59:59.000Z

    Coral Reef Genomics: Developing toolsfor functional genomics of coral symbiosis Jodi SCHWARZ 1 ,symbiosis functional genomics cDNA microarray ABSTRACT

  10. Navigating protected genomics data with UCSC Genome Browser in a Box.

    E-Print Network [OSTI]

    2014-01-01T23:59:59.000Z

    H. et al. (2013) Integrative Genomics Viewer (IGV):High-performance genomics data visualization andbrowsers for comparative genomics. Bioinformatics. In press.

  11. A physical map of the papaya genome with integrated genetic map and genome sequence

    E-Print Network [OSTI]

    2009-01-01T23:59:59.000Z

    genetic map and genome sequence Qingyi Yu 1 , Eric Tong 1 ,assist whole genome shotgun sequence assembly. Results: Thethe genetic map and genome sequence using BAC end sequences

  12. Longitudinal Instability Studies at the SURF II Storage Ring...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Longitudinal Instability Studies at the SURF II Storage Ring at NIST 1 Longitudinal Instability Studies at the SURF II Storage Ring at NIST K. C. Harkay and N. S. Sereno Advanced...

  13. Coherent instabilities in a semiconductor laser with fast gain recovery

    E-Print Network [OSTI]

    Wang, Christine Y.; Diehl, L.; Gordon, A.; Jirauschek, C.; Kartner, F. X.; Belyanin, Alexey; Bour, D.; Corzine, S.; Hofler, G.; Troccoli, M.; Faist, J.; Capasso, Federico

    2007-01-01T23:59:59.000Z

    We report the observation of a coherent multimode instability in quantum cascade lasers (QCLs), which is driven by the same fundamental mechanism of Rabi oscillations as the elusive Risken-Nummedal-Graham-Haken (RNGH) instability predicted 40 years...

  14. Prediction of Thermoacoustic Instabilities: Numerical Study of Mach number Effects.

    E-Print Network [OSTI]

    Nicoud, Franck

    Prediction of Thermoacoustic Instabilities: Numerical Study of Mach number Effects. K. Wieczorek equations. I. Introduction In the calculation of thermoacoustic instabilities, an assumption lead to significant changes in the evaluation of the thermo-acoustic modes present in the combustion

  15. STREAMWISE AND CROSSFLOW INSTABILITIES ON INCLINED CIRCULAR CYLINDERS

    E-Print Network [OSTI]

    STREAMWISE AND CROSSFLOW INSTABILITIES ON INCLINED CIRCULAR CYLINDERS S. J. Garrett , J. P: Turbine blades, swept cylinder, streamwise & crossflow instabilities Abstract Observations of streamwise and crossflow insta- bilities on swept circular cylinders over a range of inclinations are presented

  16. Interaction of Turing and flow-induced chemical instabilities

    SciTech Connect (OSTI)

    Dawson, S.P. (Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)); Lawniczak, A. (Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario N1G 2W1 (Canada) Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)); Kapral, R. (Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 1A1 (Canada))

    1994-04-01T23:59:59.000Z

    The interaction between the Turing instability and the instability induced by a differential flow is studied in the Selkov model. Both instabilities give rise to the formation of spatial patterns, and for a range of parameter values, these patterns can compete. The effect of anisotropic diffusion on the pattern formation process is investigated. Stripes with different orientations that travel with time and the suppression of patterns due to a competition of both instabilities are observed.

  17. Salt Stress in Desulfovibrio vulgaris Hildenborough: An integrated genomics approach

    E-Print Network [OSTI]

    Mukhopadhyay, Aindrila

    2010-01-01T23:59:59.000Z

    2002. Integrating cancer genomics and proteomics in theWeb site for comparative genomics. Genome Res 15:1015-22.Hildenborough: An integrated genomics approach. Aindrila

  18. Computational methods and analyses in comparative genomics and epigenomics

    E-Print Network [OSTI]

    Peng, Qian

    2012-01-01T23:59:59.000Z

    promise of comparative genomics in mammals. Science, 286,homology relationships. Genomics, Dehal, P. and Boore, J.to plant comparative genomics. Genome Research, 13(5), 999–

  19. acanthamoeba castellanii genome: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and Medicine Websites Summary: Prokaryotic Genomes Eurkaryotic Genomes Chapter 6. Genomics and Gene Identification Weigang Qiu Weigang Qiu Chapter 6. Genomics and Gene...

  20. aeromonas caviae genomic: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and Medicine Websites Summary: Prokaryotic Genomes Eurkaryotic Genomes Chapter 6. Genomics and Gene Identification Weigang Qiu Weigang Qiu Chapter 6. Genomics and Gene...

  1. Process Svstems Enaineerina Instability of Distillation Columns

    E-Print Network [OSTI]

    Skogestad, Sigurd

    Process Svstems Enaineerina , Instability of Distillation Columns Elling W. Jacobsen and Sigurd recognized, distillation columns, operating with reflux and boilup as independent inputs, may have The dynamic behavior of distillation columns has been stud- ied quite extensively over the past decades

  2. Convective Instability of a Boundary Layer with

    E-Print Network [OSTI]

    Conrad, Clint

    proportional to the integral over the depth of the lithosphere of the 19 #12;ratio of thermal buoyancy. Such instabilities are driven by the negative thermal buoyancy of the cold lithosphere and retarded largely for driving convective downwelling. For non-Newtonian viscosity with power law exponent n and temperature

  3. Shear flow instabilities in viscoelastic fluids

    E-Print Network [OSTI]

    Miller, Joel C.

    2006-05-23T23:59:59.000Z

    - stabilities may be desirable: for example in microfluidics it may be necessary 2to mix two fluids together. This is made difficult by the small length scales and resulting low Reynolds number. An instability which mixes the entire flow is needed. Part I...

  4. Wetting and lubricating film instabilities in microchannels

    E-Print Network [OSTI]

    Cubaud, Thomas

    , and silicone oils . Dynamic wetting transitions: a pearl flow thick lubricating film , b spider flow thinWetting and lubricating film instabilities in microchannels Thomas Cubaud Department of Mechanical of partially wetting threads in planar microchannels of height h=100 or 250 m fluids: ethanol, mineral oils

  5. Laboratory experiments on arc deflection and instability

    SciTech Connect (OSTI)

    Zweben, S.; Karasik, M.

    2000-03-21T23:59:59.000Z

    This article describes experiments on arc deflection instability carried out during the past few years at the Princeton University Plasma Physics Laboratory (PPPL). The approach has been that of plasma physicists interested in arcs, but they believe these results may be useful to engineers who are responsible for controlling arc behavior in large electric steel furnaces.

  6. Current-Driven Filament Instabilities in Relativistic Plasmas. Final report

    SciTech Connect (OSTI)

    Chuang Ren

    2013-02-13T23:59:59.000Z

    This grant has supported a study of some fundamental problems in current- and flow-driven instabilities in plasmas and their applications in inertial confinement fusion (ICF) and astrophysics. It addressed current-driven instabilities and their roles in fast ignition, and flow-driven instabilities and their applications in astrophysics.

  7. WHEN DOES FINANCIAL SECTOR (IN)STABILITY INDUCE FINANCIAL REFORMS?

    E-Print Network [OSTI]

    Boyer, Edmond

    WHEN DOES FINANCIAL SECTOR (IN)STABILITY INDUCE FINANCIAL REFORMS? Susie LEE Ingmar SCHUMACHER (in)stability induce financial reforms? Susie Lee1 Ingmar Schumacher2 October 26, 2011 Abstract The article studies whether financial sector (in)stability had an effect on reforms in the fi- nancial sector

  8. AIAA 2003-0771 CROSSFLOW INSTABILITIES THEORY & TECHNOLOGY

    E-Print Network [OSTI]

    #12;AIAA 2003-0771 CROSSFLOW INSTABILITIES ­ THEORY & TECHNOLOGY William S. Saric* and Helen L the years, the crossflow instability has been the primary challenge for Laminar Flow Control (LFC). Favorable pressure gradients used to stabilize streamwise instabilities destabilize crossflow. For years

  9. GIS: a web-based genomics information system for efficiently manipulating and accessing genome physical maps 

    E-Print Network [OSTI]

    Chen, Huaming

    2000-01-01T23:59:59.000Z

    Biological science has entered the genome era. Global genome integrative physical and genetic mapping promises to revolutionize modern genomics research. To facilitate manipulation and applications of the results from genomics research, many...

  10. Population genomics: Whole-genome analysis of polymorphism and divergence in Drosophila simulans

    E-Print Network [OSTI]

    2007-01-01T23:59:59.000Z

    PLoS BIOLOGY Population Genomics: Whole-Genome Analysis ofwww.plosbiology.org Population Genomics of D. simulans Table11 | e310 Population Genomics of D. simulans Table S15. GO

  11. GIS: a web-based genomics information system for efficiently manipulating and accessing genome physical maps

    E-Print Network [OSTI]

    Chen, Huaming

    2000-01-01T23:59:59.000Z

    Biological science has entered the genome era. Global genome integrative physical and genetic mapping promises to revolutionize modern genomics research. To facilitate manipulation and applications of the results from genomics research, many...

  12. POSTDOCTORAL POSITION IN BIOINFORMATICS AND EVOLUTIONARY GENOMICS: Next generation sequencing and analysis of complex polyploid genomes

    E-Print Network [OSTI]

    Rennes, Université de

    POSTDOCTORAL POSITION IN BIOINFORMATICS AND EVOLUTIONARY GENOMICS: Next generation sequencing and analysis of complex polyploid genomes The research group Genome Evolution and Speciation (Team) to work on the analysis of genome and transcriptome sequence data (generated using 454 Roche

  13. Investigation of plasma instabilities relevant toInvestigation of plasma instabilities relevant to inertial confinement fusioninertial confinement fusion

    E-Print Network [OSTI]

    Strathclyde, University of

    . At sufficiently high temperatures a propagating fusion burn wave is ignited, releasing ~70 times the energy it is hoped that their effects can be minimized allowing fusion power to be harnessed to help combat the world's energy crisis. Plasmas InstabilitiesInertial Confinement Instabilities Small instabilities in a plasma

  14. Original article Neisseria Base: a comparative genomics

    E-Print Network [OSTI]

    Jordan, King

    Original article Neisseria Base: a comparative genomics database for Neisseria meningitidis Lee S, septicemia and in some cases pneumonia. Genomic studies hold great promise for N. meningitidis research genomics database and genome browser that houses and displays publicly available N. meningitidis genomes

  15. A Novel Approach for Comparative Genomics

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    A Novel Approach for Comparative Genomics & Annotation Transfer Alban MANCHERON Raluca URICARU Eric is genome comparison good for?" Genome comparison is crucial for genome annotation, regulatory motifs identification, and vaccine design aims at finding genomic regions either specific to or in one

  16. Solar wind kinetic instabilities at small plasma betas

    SciTech Connect (OSTI)

    Ibscher, D., E-mail: ibscher@tp4.rub.de; Schlickeiser, R. [Institut für Theoretische Physik, Lehrstuhl IV: Weltraum- und Astrophysik, Ruhr-Universität Bochum, D-44780 Bochum (Germany)] [Institut für Theoretische Physik, Lehrstuhl IV: Weltraum- und Astrophysik, Ruhr-Universität Bochum, D-44780 Bochum (Germany)

    2014-02-15T23:59:59.000Z

    The ordinary perpendicular mode of drifting bi-Maxwellian plasma particle distributions with and without temperature anisotropy can provide aperiodic instabilities. These instabilities occur if the perpendicular thermal energy is much smaller than the streaming energy. This provides instabilities at small parallel plasma betas ?{sub ?}<1 and temperature anisotropies A?instability, here we compare measurements in the solar wind with the instability provided by this mode.

  17. GenomeView: a next-generation genome browser Thomas Abeel1,2,3,

    E-Print Network [OSTI]

    Gent, Universiteit

    GenomeView: a next-generation genome browser Thomas Abeel1,2,3, *, Thomas Van Parys1,2 , Yvan Saeys GenomeView, a stand-alone genome browser specifically designed to visualize and manipulate a multitude of genomics data. GenomeView enables users to dynamically browse high volumes of aligned short-read data

  18. Yeast Genomic Library Genomic DNA Sau3AI partial digestion

    E-Print Network [OSTI]

    Odorizzi, Greg

    Yeast Genomic Library Concept: Genomic DNA ­ Sau3AI partial digestion Vector DNA ­ BamHI full digestion partial Ligate and transform above products Vector Information: · use centromeric plasmid to avoid of the mcs Preparing Vector: 1) digest 3-4ug of library vector with BamHI for 2-4hrs in a total volume of 20

  19. Genome 361: Fundamentals of Genetics and Genomics Spring 2014 Instructors

    E-Print Network [OSTI]

    Dunham, Maitreya

    testing for inherited diseases, human cloning, stem cell research, and genetically modified foods, to name1 Genome 361: Fundamentals of Genetics and Genomics Spring 2014 Instructors Maitreya Dunham.edu Course overview Genetics is the scientific study of heredity. In the last century, many genetic methods

  20. ORIGINAL PAPER The interdisciplinary engineering knowledge genome

    E-Print Network [OSTI]

    Shai, Offer

    ORIGINAL PAPER The interdisciplinary engineering knowledge genome Yoram Reich · Offer Shai Received, termed the ``Interdisciplinary Engineering Knowledge Genome'', which is an organized collection of system, the Interdisciplinary Engineering Knowledge Genome unifies many engineering disciplines, providing a basis

  1. Trichoderma: the genomics of opportunistic success

    E-Print Network [OSTI]

    Druzhinina, Irina S.

    2011-01-01T23:59:59.000Z

    of a fungal prey. BMC Genomics 10, 567 (2009). This studythe TrichoEST functional genomics approach. Curr. Genet. 51,in Hypocrea jecorina. BMC Genomics. 9, 430 (2008) Mukherjee,

  2. Evolutionary Genomics of Salmonella enterica Subspecies

    E-Print Network [OSTI]

    2013-01-01T23:59:59.000Z

    M. 2002. Evolutionary genomics of Salmonella: genesubsystems technology. BMC Genomics 9:75. 23. Ochman H,Salmonella enterica. BMC Genomics 12:425. PubMed. 29. Falush

  3. Tissue sampling and standards for vertebrate genomics

    E-Print Network [OSTI]

    2012-01-01T23:59:59.000Z

    and standards for vertebrate genomics. GigaScience 2012 1:8.transition to conservation genomics. TIG 2010, 26:177–187.Siemens DH: Ecological genomics––changing perspectives on

  4. Genomics and Systems Biology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of Science (SC) Environmental AssessmentsGeoffrey Campbelllong version)ConfinementGeneralGenomics and

  5. Genome Science/Technologies

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField8,Dist.Newof EnergyFundingGeneGenome Engineering with TALGenome

  6. Genomics and Systems Biology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField8,Dist.Newof EnergyFundingGeneGenome Engineering withfor

  7. A Taste of Algal Genomes from the Joint Genome Institute

    SciTech Connect (OSTI)

    Kuo, Alan; Grigoriev, Igor

    2012-06-17T23:59:59.000Z

    Algae play profound roles in aquatic food chains and the carbon cycle, can impose health and economic costs through toxic blooms, provide models for the study of symbiosis, photosynthesis, and eukaryotic evolution, and are candidate sources for bio-fuels; all of these research areas are part of the mission of DOE's Joint Genome Institute (JGI). To date JGI has sequenced, assembled, annotated, and released to the public the genomes of 18 species and strains of algae, sampling almost all of the major clades of photosynthetic eukaryotes. With more algal genomes currently undergoing analysis, JGI continues its commitment to driving forward basic and applied algal science. Among these ongoing projects are the pan-genome of the dominant coccolithophore Emiliania huxleyi, the interrelationships between the 4 genomes in the nucleomorph-containing Bigelowiella natans and Guillardia theta, and the search for symbiosis genes of lichens.

  8. Human Genome Program Image Gallery (from genomics.energy.gov)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    This collection contains approximately 240 images from the genome programs of DOE's Office of Science. The images are divided into galleries related to biofuels research, systems biology, and basic genomics. Each image has a title, a basic citation, and a credit or source. Most of the images are original graphics created by the Genome Management Information System (GMIS). GMIS images are recognizable by their credit line. Permission to use these graphics is not needed, but please credit the U.S. Department of Energy Genome Programs and provide the website http://genomics.energy.gov. Other images were provided by third parties and not created by the U.S. Department of Energy. Users must contact the person listed in the credit line before using those images. The high-resolution images can be downloaded.

  9. Baroclinic Instability on Hot Extrasolar Planets

    E-Print Network [OSTI]

    Polichtchouk, Inna

    2012-01-01T23:59:59.000Z

    We investigate baroclinic instability in flow conditions relevant to hot extrasolar planets. The instability is important for transporting and mixing heat, as well as for influencing large-scale variability on the planets. Both linear normal mode analysis and non-linear initial value calculations are carried out -- focusing on the freely-evolving, adiabatic situation. Using a high-resolution general circulation model (GCM) which solves the traditional primitive equations, we show that large-scale jets similar to those observed in current GCM simulations of hot extrasolar giant planets are likely to be baroclinically unstable on a timescale of few to few tens of planetary rotations, generating cyclones and anticyclones that drive weather systems. The growth rate and scale of the most unstable mode obtained in the linear analysis are in qualitative, good agreement with the full non-linear calculations. In general, unstable jets evolve differently depending on their signs (eastward or westward), due to the chang...

  10. Front instabilities in evaporatively dewetting nanofluids

    E-Print Network [OSTI]

    I. Vancea; U. Thiele; E. Pauliac-Vaujour; A. Stannard; C. P. Martin; M. O. Blunt; P. J. Moriarty

    2008-06-25T23:59:59.000Z

    Various experimental settings that involve drying solutions or suspensions of nanoparticles -- often called nanofluids -- have recently been used to produce structured nanoparticle layers. In addition to the formation of polygonal networks and spinodal-like patterns, the occurrence of branched structures has been reported. After reviewing the experimental results we use a modified version of the Monte Carlo model first introduced by Rabani et al. [Nature 426, 271 (2003)] to study structure formation in evaporating films of nanoparticle solutions for the case that all structuring is driven by the interplay of evaporating solvent and diffusing nanoparticles. After introducing the model and its general behavior we focus on receding dewetting fronts which are initially straight but develop a transverse fingering instability. We analyze the dependence of the characteristics of the resulting branching patterns on the driving chemical potential, the mobility and concentration of the nanoparticles, and the interaction strength between liquid and nanoparticles. This allows us to understand the underlying instability mechanism.

  11. Nonabelian plasma instabilities in Bjorken expansion

    E-Print Network [OSTI]

    Anton Rebhan

    2008-10-17T23:59:59.000Z

    Plasma instabilities are parametrically the dominant nonequilibrium dynamics of a weakly coupled quark-gluon plasma. In recent years the time evolution of the corresponding collective colour fields has been studied in stationary anisotropic situations. Here I report on recent numerical results on the time evolution of the most unstable modes in a longitudinally expanding plasma as they grow from small rapidity fluctuations to amplitudes where non-Abelian self-interactions become important.

  12. Poverty, Armed Conflict and Financial Instability

    E-Print Network [OSTI]

    Baddeley, Michelle

    flows. Armed conflict does not always contribute to financial instability. Magnusson and Wydick (2001) discuss efficiency of markets in 8 largest African stock markets in comparison with emerging stock markets in South East Asia and Latin America... of strategies is is determined by the relative benefits and costs of reversion to conflict (Collier and Hoeffler, 2004, pp. 8-10). High levels of military spending are associated with increased risk of renewed conflict. 3 POVERTY, CONFLICT AND FINANCIAL...

  13. A high-throughput in vivo micronucleus assay for genome instability screening in mice

    E-Print Network [OSTI]

    Balmus, Gabriel; Karp, Natasha A; Ng, Bee Ling; Jackson, Stephen P; Adams, David J; McIntyre, Rebecca E

    2014-12-31T23:59:59.000Z

    .jackson@gurdon.cam.ac.uk; Ng BL – bln@sanger.ac.uk; Adams DJ – da1@sanger.ac.uk; McIntyre R – rm5@sanger.ac.uk; Primary articles: 20 McIntyre, R.E. et al. Disruption of mouse Cenpj, a regulator of centriole biogenesis, phenocopies Seckel syndrome. PLoS Genet 8, e... into the mouse phenotyping pipeline, we have identified radiation-sensitive mutants, which exhibit increased levels of micronucleated-RET after irradiation but not before. Within this manuscript, 150 we provide additional details on data analysis...

  14. Tearing instability in relativistic magnetically dominated plasmas

    E-Print Network [OSTI]

    S. S. Komissarov; M. Barkov; M. Lyutikov

    2006-06-21T23:59:59.000Z

    Many astrophysical sources of high energy emission, such as black hole magnetospheres, superstrongly magnetized neutron stars (magnetars), and probably relativistic jets in Active Galactic Nuclei and Gamma Ray Bursts involve relativistically magnetically dominated plasma. In such plasma the energy density of magnetic field greatly exceeds the thermal and the rest mass energy density of particles. Therefore the magnetic field is the main reservoir of energy and its dissipation may power the bursting emission from these sources, in close analogy to Solar flares. One of the principal dissipative instabilities that may lead to release of magnetic energy is the tearing instability. In this paper we study, both analytically and numerically, the development of tearing instability in relativistically magnetically-dominated plasma using the framework of resistive magnetodynamics. We confirm and elucidate the previously obtained result on the growth rate of the tearing mode: the shortest growth time is the same as in the case of classical non-relativistic MHD, namely $\\tau =\\sqrt{\\tau_a \\tau_d}$ where $\\tau_a$ is the \\Alfven crossing time and $\\tau_d$ is the resistive time of a current layer.

  15. Genome Sequence Databases (Overview): Sequencing and Assembly

    E-Print Network [OSTI]

    Lapidus, Alla L.

    2009-01-01T23:59:59.000Z

    a graphical tool for sequence finishing. Genome Research 8,Multiplexed genotyping with sequence- tagged molecularX. (1996). An improved sequence assembly program. Genomics

  16. Fueling Future with Algal Genomics

    SciTech Connect (OSTI)

    Grigoriev, Igor

    2012-07-05T23:59:59.000Z

    Algae constitute a major component of fundamental eukaryotic diversity, play profound roles in the carbon cycle, and are prominent candidates for biofuel production. The US Department of Energy Joint Genome Institute (JGI) is leading the world in algal genome sequencing (http://jgi.doe.gov/Algae) and contributes of the algal genome projects worldwide (GOLD database, 2012). The sequenced algal genomes offer catalogs of genes, networks, and pathways. The sequenced first of its kind genomes of a haptophyte E.huxleyii, chlorarachniophyte B.natans, and cryptophyte G.theta fill the gaps in the eukaryotic tree of life and carry unique genes and pathways as well as molecular fossils of secondary endosymbiosis. Natural adaptation to conditions critical for industrial production is encoded in algal genomes, for example, growth of A.anophagefferens at very high cell densities during the harmful algae blooms or a global distribution across diverse environments of E.huxleyii, able to live on sparse nutrients due to its expanded pan-genome. Communications and signaling pathways can be derived from simple symbiotic systems like lichens or complex marine algae metagenomes. Collectively these datasets derived from algal genomics contribute to building a comprehensive parts list essential for algal biofuel development.

  17. Parallel-Flow-Shear Driven Low-Frequency Plasma Instability

    SciTech Connect (OSTI)

    Ishiguro, Seiji [Theory and Computer Simulation Center, National Institute for Fusion Science, Toki-shi, Gifu 509-5292 (Japan); Matsumoto, Noriaki; Kaneko, Toshiro; Hatakeyama, Rikizo [Department of Electronic Engineering, Tohoku University, Sendai 980-8579 (Japan)

    2004-12-01T23:59:59.000Z

    Full three dimensional Particle-in-Cell (PIC) simulations are performed in order to investigate effects of field-aligned (parallel) ion flow shears on low-frequency plasma instabilities. It is shown that the parallel ion flow velocity shear can induce the ion-acoustic instability, even when the ion flow velocity is so small that the instability can not take place. Simulation results are consistent with the analysis based on the local theory.

  18. Rayleigh-Taylor instability in an equal mass plasma

    SciTech Connect (OSTI)

    Adak, Ashish, E-mail: ashish-adak@yahoo.com [Department of Instrumentation Science, Jadavpur University, Kolkata 700 032 (India); Ghosh, Samiran, E-mail: sran-g@yahoo.com [Department of Applied Mathematics, University of Calcutta 92, Acharya Prafulla Chandra Road, Kolkata 700 009 (India); Chakrabarti, Nikhil, E-mail: nikhil.chakrabarti@saha.ac.in [Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700 064 (India)

    2014-09-15T23:59:59.000Z

    The Rayleigh-Taylor (RT) instability in an inhomogeneous pair-ion plasma has been analyzed. Considering two fluid model for two species of ions (positive and negative), we obtain the possibility of the existence of RT instability. The growth rate of the RT instability as usual depends on gravity and density gradient scale length. The results are discussed in context of pair-ion plasma experiments.

  19. Beam-Plasma Instabilities in a 2D Yukawa Lattice

    SciTech Connect (OSTI)

    Kyrkos, S. [Department of Chemistry and Physics, Le Moyne College, Syracuse, New York 13214 (United States); Kalman, G. J. [Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467 (United States); Rosenberg, M. [Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, California 92093 (United States)

    2009-06-05T23:59:59.000Z

    We consider a 2D Yukawa lattice of grains, with a beam of other charged grains moving in the lattice plane. In contrast to Vlasov plasmas, where the electrostatic instability excited by the beam is only longitudinal, here both longitudinal and transverse instabilities of the lattice phonons can develop. We determine and compare the transverse and longitudinal growth rates. The growth rate spectrum in wave number space exhibits remarkable gaps where no instability can develop. Depending on the system parameters, the transverse instability can be selectively excited.

  20. Testing Disk Instability Models for Giant Planet Formation

    E-Print Network [OSTI]

    Alan P. Boss

    2007-04-09T23:59:59.000Z

    Disk instability is an attractive yet controversial means for the rapid formation of giant planets in our solar system and elsewhere. Recent concerns regarding the first adiabatic exponent of molecular hydrogen gas are addressed and shown not to lead to spurious clump formation in the author's disk instability models. A number of disk instability models have been calculated in order to further test the robustness of the mechanism, exploring the effects of changing the pressure equation of state, the vertical temperature profile, and other parameters affecting the temperature distribution. Possible reasons for differences in results obtained by other workers are discussed. Disk instability remains as a plausible formation mechanism for giant planets.

  1. QCD plasma instability and thermalisation at heavy ion collisions

    E-Print Network [OSTI]

    Dietrich Bodeker; Kari Rummukainen

    2007-11-13T23:59:59.000Z

    Under suitable non-equilibrium conditions QCD plasma can develop plasma instabilities, where some modes of the plasma grow exponentially. It has been argued that these instabilities can play a significant role in the thermalisation of the plasma in heavy-ion collision experiments. We study the instability in SU(2) plasmas using the hard thermal loop effective lattice theory, which is suitable for studying real-time evolution of long wavelength modes in the plasma. We observe that under suitable conditions the plasma can indeed develop an instability which can grow to a very large magnitude, necessary for the rapid thermalisation in heavy-ion collisions.

  2. anisotropy instability thresholds: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    these fluctuations are enhanced along the temperature anisotropy thresholds of the mirror, proton oblique firehose, and ion cyclotron instabilities. In addition, the measured...

  3. PPPL extends system for suppressing instabilities to long-pulse...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    instabilities will be vital for future fusion facilities such as ITER, the huge international project under construction in France. The original system developed on...

  4. Two-stream instability with time-dependent drift velocity

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Qin, Hong [PPPL; Davidson, Ronald C. [PPPL

    2014-01-01T23:59:59.000Z

    The classical two-stream instability driven by a constant relative drift velocity between two plasma components is extended to the case with time-dependent drift velocity. A solution method is developed to rigorously define and calculate the instability growth rate for linear perturbations relative to the time-dependent unperturbed two-stream motions. Stability diagrams for the oscillating two-stream instability are presented over a large region of parameter space. It is shown that the growth rate for the classical two-stream instability can be significantly reduced by adding an oscillatory component to the relative drift velocity.

  5. Fast transverse instability in the NSNS Accumulator Ring

    SciTech Connect (OSTI)

    Ruggiero, A.G.; Blaskiewicz, M.

    1997-08-01T23:59:59.000Z

    This paper reports on the results of investigation of possible fast transverse instabilities in the NSNS Accumulator Ring. The instability may be caused by the presence of stripline devices like kicker magnets, the active damper system, and by the RF cavities, and the sharp steps of the vacuum pipe. The instability can be overcome by adopting aluminum as the material of the vacuum pipe.Still the growth time of the instability remains short especially for the mode in proximity of the betatron tune.

  6. Two-stream instability with time-dependent drift velocity

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Qin, Hong; Davidson, Ronald C.

    2014-06-01T23:59:59.000Z

    The classical two-stream instability driven by a constant relative drift velocity between two plasma components is extended to the case with time-dependent drift velocity. A solution method is developed to rigorously define and calculate the instability growth rate for linear perturbations relative to the time-dependent unperturbed two-stream motions. Stability diagrams for the oscillating two-stream instability are presented over a large region of parameter space. It is shown that the growth rate for the classical two-stream instability can be significantly reduced by adding an oscillatory component to the relative drift velocity.

  7. Front instabilities in evaporatively dewetting nanofluids and U. Thiele

    E-Print Network [OSTI]

    Front instabilities in evaporatively dewetting nanofluids I. Vancea and U. Thiele Department of nanoparticles ­ often called nanofluids ­ have recently been used to produce structured nanoparticle layers

  8. Human genome. 1993 Program report

    SciTech Connect (OSTI)

    Not Available

    1994-03-01T23:59:59.000Z

    The purpose of this report is to update the Human Genome 1991-92 Program Report and provide new information on the DOE genome program to researchers, program managers, other government agencies, and the interested public. This FY 1993 supplement includes abstracts of 60 new or renewed projects and listings of 112 continuing and 28 completed projects. These two reports, taken together, present the most complete published view of the DOE Human Genome Program through FY 1993. Research is progressing rapidly toward 15-year goals of mapping and sequencing the DNA of each of the 24 different human chromosomes.

  9. Genomic Aspects of Research Involving Polyploid Plants

    SciTech Connect (OSTI)

    Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Tschaplinski, Timothy J [ORNL; Wullschleger, Stan D [ORNL; Tuskan, Gerald A [ORNL

    2011-01-01T23:59:59.000Z

    Almost all extant plant species have spontaneously doubled their genomes at least once in their evolutionary histories, resulting in polyploidy which provided a rich genomic resource for evolutionary processes. Moreover, superior polyploid clones have been created during the process of crop domestication. Polyploid plants generated by evolutionary processes and/or crop domestication have been the intentional or serendipitous focus of research dealing with the dynamics and consequences of genome evolution. One of the new trends in genomics research is to create synthetic polyploid plants which provide materials for studying the initial genomic changes/responses immediately after polyploid formation. Polyploid plants are also used in functional genomics research to study gene expression in a complex genomic background. In this review, we summarize the recent progress in genomics research involving ancient, young, and synthetic polyploid plants, with a focus on genome size evolution, genomics diversity, genomic rearrangement, genetic and epigenetic changes in duplicated genes, gene discovery, and comparative genomics. Implications on plant sciences including evolution, functional genomics, and plant breeding are presented. It is anticipated that polyploids will be a regular subject of genomics research in the foreseeable future as the rapid advances in DNA sequencing technology create unprecedented opportunities for discovering and monitoring genomic and transcriptomic changes in polyploid plants. The fast accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.

  10. A Statistical Framework for Spatial Comparative Genomics

    E-Print Network [OSTI]

    A Statistical Framework for Spatial Comparative Genomics Rose Hoberman May 2007 CMU-CS-07, or the U.S. Government. #12;Keywords: spatial comparative genomics, comparative genomics, gene clusters, max-gap clusters, gene teams, whole genome duplication, paralogons, synteny, ortholog detection #12

  11. Hindawi Publishing Corporation Comparative and Functional Genomics

    E-Print Network [OSTI]

    Newcastle upon Tyne, University of

    Hindawi Publishing Corporation Comparative and Functional Genomics Volume 2007, Article ID 47304, 7 pages doi:10.1155/2007/47304 Meeting Report eGenomics: Cataloguing Our Complete Genome Collection III, Michigan State University, East Lansing, MI 48824, USA 3 The Institute for Genomic Research, 9712 Medical

  12. Genomics and ornithology Scott V. Edwards

    E-Print Network [OSTI]

    Edwards, Scott

    REVIEW Genomics and ornithology Scott V. Edwards Received: 23 September 2007 / Accepted: 27 Genomics is revolutionizing ornithology in the same ways it is reinvigorating other biological disciplines. In this review, I will highlight applications of genomics and genomics technologies to the study of the ecology

  13. SHORT REVIEW Ecological genomics: understanding gene and

    E-Print Network [OSTI]

    Kaufman, Glennis A.

    SHORT REVIEW Ecological genomics: understanding gene and genome function in the natural environment MC Ungerer, LC Johnson and MA Herman Division of Biology, Ecological Genomics Institute, Kansas State University, Manhattan, KS, USA The field of ecological genomics seeks to understand the genetic mechanisms

  14. 2004 Structural, Function and Evolutionary Genomics

    SciTech Connect (OSTI)

    Douglas L. Brutlag Nancy Ryan Gray

    2005-03-23T23:59:59.000Z

    This Gordon conference will cover the areas of structural, functional and evolutionary genomics. It will take a systematic approach to genomics, examining the evolution of proteins, protein functional sites, protein-protein interactions, regulatory networks, and metabolic networks. Emphasis will be placed on what we can learn from comparative genomics and entire genomes and proteomes.

  15. Assignment of Orthologous Genes via Genome Rearrangement

    E-Print Network [OSTI]

    Lonardi, Stefano

    Assignment of Orthologous Genes via Genome Rearrangement Xin Chen, Jie Zheng, Zheng Fu, Peng Nan of genomes is a fundamental and challenging problem in comparative genomics. Existing methods that assign sequence similarity and evolutionary events at a genome level, where orthologous genes are assumed

  16. Methods in comparative genomics: genome correspondence, gene identification and motif discovery

    E-Print Network [OSTI]

    Kellis, Manolis

    1 Methods in comparative genomics: genome correspondence, gene identification and motif discovery@mit.edu, nickp@genome.wi.mit.edu, bwb@genome.wi.mit.edu, bab@mit.edu, lander@wi.mit.edu (1) MIT/Whitehead Institute Center for Genome Research, 320 Charles St., Cambridge MA 02139 (2) MIT Computer Science

  17. Extreme Genomics By Scouring the Genomes of 50 HIV-Resistant People, Study

    E-Print Network [OSTI]

    Dolbow, John

    Extreme Genomics By Scouring the Genomes of 50 HIV-Resistant People, Study Takes Aim at Rare Gene Genome Variation, and his colleagues think that the complete genome sequences of those fortunate few against the viral strain that usually infects humans. That's because the CCR5 protein is Extreme Genomics

  18. Growth Temperature and Genome Size in Bacteria Are Negatively Correlated, Suggesting Genomic Streamlining

    E-Print Network [OSTI]

    Wagner, Andreas

    Growth Temperature and Genome Size in Bacteria Are Negatively Correlated, Suggesting Genomic.wagner@ieu.uzh.ch; nsabath@gmail.com. Accepted: March 25, 2013 Abstract Prokaryotic genomes are small and compact. Either this feature is caused by neutral evolution or by natural selection favoring small genomes--genome streamlining

  19. The Genome Database Organism-centered listing of available genomic sequence records and projects

    E-Print Network [OSTI]

    Levin, Judith G.

    The Genome Database Organism-centered listing of available genomic sequence records and projects http://www.ncbi.nlm.nih.gov/genome National Center for Biotechnology Information · National Library | NCBI Genome | Last Update August 19, 2013 Contact: info@ncbi.nlm.nih.gov Scope Since 2011, the Genome

  20. Chapter 14: Genome Assembly and Annotation Process Annotation of other genomes

    E-Print Network [OSTI]

    Levin, Judith G.

    Chapter 14: Genome Assembly and Annotation Process Paul Kitts Summary Box 1 Annotation of other genomes NCBI may assemble a genome prior to annotation, add annotations to a genome assembled elsewhere, or simply process an annotated genome to produce RefSeqs and maps for display in Map Viewer (Chapter 20

  1. The Magnetorotational Instability in a Collisionless Plasma

    E-Print Network [OSTI]

    Eliot Quataert; William Dorland; Greg Hammett

    2002-05-28T23:59:59.000Z

    We consider the linear axisymmetric stability of a differentially rotating collisionless plasma in the presence of a weak magnetic field; we restrict our analysis to wavelengths much larger than the proton Larmor radius. This is the kinetic version of the magnetorotational instability explored extensively as mechanism for magnetic field amplification and angular momentum transport in accretion disks. The kinetic calculation is appropriate for hot accretion flows onto compact objects and for the growth of very weak magnetic fields, where the collisional mean free path is larger than the wavelength of the unstable modes. We show that the kinetic instability criterion is the same as in MHD, namely that the angular velocity decrease outwards. However, nearly every mode has a linear kinetic growth rate that differs from its MHD counterpart. The kinetic growth rates also depend explicitly on beta, i.e., on the ratio of the gas pressure to the pressure of the seed magnetic field. For beta ~ 1 the kinetic growth rates are similar to the MHD growth rates while for beta >> 1 they differ significantly. For beta >> 1, the fastest growing mode has a growth rate of sqrt{3} Omega for a Keplerian disk, larger than its MHD counterpart; there are also many modes whose growth rates are negligible, < beta^{-1/2} Omega << Omega. We provide a detailed physical interpretation of these results and show that gas pressure forces, rather than just magnetic forces, are central to the behavior of the magnetorotational instability in a collisionless plasma. We also discuss the astrophysical implications of our analysis.

  2. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    SciTech Connect (OSTI)

    Kuo, Alan; Grigoriev, Igor

    2009-04-17T23:59:59.000Z

    Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

  3. Instabilities in the Nuclear Energy Density Functional

    E-Print Network [OSTI]

    M. Kortelainen; T. Lesinski

    2010-02-05T23:59:59.000Z

    In the field of Energy Density Functionals (EDF) used in nuclear structure and dynamics, one of the unsolved issues is the stability of the functional. Numerical issues aside, some EDFs are unstable with respect to particular perturbations of the nuclear ground-state density. The aim of this contribution is to raise questions about the origin and nature of these instabilities, the techniques used to diagnose and prevent them, and the domain of density functions in which one should expect a nuclear EDF to be stable.

  4. Current Filamentation Instability in Laser Wakefield Accelerators

    SciTech Connect (OSTI)

    Huntington, C. M.; Drake, R. P. [Atmospheric, Oceanic and Space Science, University of Michigan, Ann Arbor, Michigan, 48103 (United States); Thomas, A. G. R.; McGuffey, C.; Matsuoka, T.; Chvykov, V.; Kalintchenko, G.; Yanovsky, V.; Maksimchuk, A.; Krushelnick, K. [Center for Ultrafast Optical Science, University of Michigan, Ann Arbor, Michigan 48109 (United States); Kneip, S.; Najmudin, Z.; Palmer, C. [Blackett Laboratory, Imperial College London, London, SW7 2BZ (United Kingdom); Katsouleas, T. [Platt School of Engineering, Duke University, Durham, North Carolina, 27708 (United States)

    2011-03-11T23:59:59.000Z

    Experiments using an electron beam produced by laser-wakefield acceleration have shown that varying the overall beam-plasma interaction length results in current filamentation at lengths that exceed the laser depletion length in the plasma. Three-dimensional simulations show this to be a combination of hosing, beam erosion, and filamentation of the decelerated beam. This work suggests the ability to perform scaled experiments of astrophysical instabilities. Additionally, understanding the processes involved with electron beam propagation is essential to the development of wakefield accelerator applications.

  5. Plasma planar filament instability and Alfven waves

    E-Print Network [OSTI]

    Garcia de Andrade

    2007-03-05T23:59:59.000Z

    Inhomogeneous plasmas filaments instabilities are investigated by using the techniques of classical differential geometry of curves where Frenet torsion and curvature describe completely the motion of curves. In our case the Frenet frame changes in time and also depends upon the other coordinates taking into account the inhomogeneity of the plasma. The exponential perturbation method so commonly used to describe cosmological perturbatons is applied to magnetohydrodynamic (MHD) plasma equations to find longitudinal modes describing Alfven waves propagation modes describing plasma waves in the medium. Stability is investigated in the imaginary axis of the spectra of complex frequencies ${\\omega}$ or $Im(\\omega)\

  6. Voltage instability: Mechanisms and control strategies

    SciTech Connect (OSTI)

    Vu, K.T. [ABB Transmission Technology Inst., Raleigh, NC (United States). Power Systems Center] [ABB Transmission Technology Inst., Raleigh, NC (United States). Power Systems Center; Liu, C.C. [Univ. of Washington, Seattle, WA (United States)] [Univ. of Washington, Seattle, WA (United States); Taylor, C.W. [Bonneville Power Administration, Portland, OR (United States)] [Bonneville Power Administration, Portland, OR (United States); Jimma, K.M. [Puget Sound Power and Light Co., Bellevue, WA (United States)] [Puget Sound Power and Light Co., Bellevue, WA (United States)

    1995-11-01T23:59:59.000Z

    One of the main objectives in operating an electric power system is to maintain a proper voltage level throughout a system. Failure to do so can lead to equipment damage and blackout. The article discusses the nonlinear aspects of power systems, with emphasis on voltage instability. It provides an overview of the state-of-the-art on the analysis and control of voltage dynamics. Dynamic mechanisms and control strategies are discussed from both theoretical and practical standpoints. The remedial controls implemented in the Puget Sound region of the Pacific Northwest indicate the practical significance of the research area.

  7. Modulational instability in wind-forced waves

    E-Print Network [OSTI]

    Brunetti, Maura

    2014-01-01T23:59:59.000Z

    We consider the wind-forced nonlinear Schroedinger (NLS) equation obtained in the potential flow framework when the Miles growth rate is of the order of the wave steepness. In this case, the form of the wind-forcing terms gives rise to the enhancement of the modulational instability and to a band of positive gain with infinite width. This regime is characterised by the fact that the ratio between wave momentum and norm is not a constant of motion, in contrast to what happens in the standard case where the Miles growth rate is of the order of the steepness squared.

  8. Protein Instability and Lou Gehrig's Disease

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible forPortsmouth/Paducah47,193.70 HgPromisingProtecting yourProtein FlipsProtein Instability

  9. Synthetic Genomics: Options for Governance

    E-Print Network [OSTI]

    Garfinkel, Michele

    2007-10-17T23:59:59.000Z

    Gene and genome synthesis, that is, constructing long stretches of DNA from constituent chemicals, provides scientists with new and unparalleled capabilities both for understanding biology and for using it for beneficial ...

  10. The Center for integrative genomics

    E-Print Network [OSTI]

    Fankhauser, Christian

    , a new advenTure · a new institute with state-of-the-art technologies and facilities · Cutting edge roles for the human herpes simplex virus host cell factor HCF- in controlling genome duplication, transcription factors, a

  11. Electrohydrodynamic instabilities in thin liquid trilayer films

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Roberts, Scott A. [Sandia National Lab., Albuquerque, NM (United States); Kumar, Satish [Univ. of Minnesota, Minneapolis, MN (United States)

    2010-09-12T23:59:59.000Z

    Experiments by Dickey et al. [Langmuir, 22, 4315 (2006)] and Leach et al. [Chaos, 15, 047506 (2005)] show that novel pillar shapes can be generated from electrohydrodynamic instabilities at the interfaces of thin polymer/polymer/air trilayer films. In this paper, we use linear stability analysis to investigate the effect of free charge and ac electric fields on the stability of trilayer systems. Our work is also motivated by our recent theoretical study [J. Fluid Mech., 631, 255 (2009)] which demonstrates how ac electric fields can be used to increase control over the pillar formation process in thin liquid bilayer films. For perfect dielectric films, the effect of an AC electric field can be understood by considering an equivalent DC field. Leaky dielectric films yield pillar configurations that are drastically different from perfect dielectric films, and AC fields can be used to control the location of free charge within the trilayer system. This can alter the pillar instability modes and generate smaller diameter pillars when conductivities are mismatched. The results presented here may be of interest for the creation of complex topographical patterns on polymer coatings and in microelectronics.

  12. Electrohydrodynamic instabilities in thin liquid trilayer films

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Roberts, Scott A.; Kumar, Satish

    2010-01-01T23:59:59.000Z

    Experiments by Dickey and Leach show that novel pillar shapes can be generated from electrohydrodynamic instabilities at the interfaces of thin polymer/polymer/air trilayer films. In this paper, we use linear stability analysis to investigate the effect of free charge and ac electric fields on the stability of trilayer systems. Our work is also motivated by our recent theoretical study which demonstrates how ac electric fields can be used to increase control over the pillar formation process in thin liquid bilayer films. For perfect dielectric films, the effect of an AC electric field can be understood by considering an equivalent DCmore »field. Leaky dielectric films yield pillar configurations that are drastically different from perfect dielectric films, and AC fields can be used to control the location of free charge within the trilayer system. This can alter the pillar instability modes and generate smaller diameter pillars when conductivities are mismatched. The results presented here may be of interest for the creation of complex topographical patterns on polymer coatings and in microelectronics.« less

  13. Beam Dynamics and Instabilities in ELIC Design

    SciTech Connect (OSTI)

    S. Ahmed,B. Yunn,G. Krafft

    2011-09-01T23:59:59.000Z

    In this paper, we report the first study of beam related instabilities in lepton ring of the proposed electron-ion collider beyond the 12 GeV upgrade of CEBAF at Jefferson lab. The design parameters are consistent with PEP-II. Present studies reveal that coupled bunch and two stream instabilities are important issues and we need feedback system. The Medium Energy Electron Ion Collider (MEIC) at Jefferson Lab has been envisioned as future high energy particle accelerator beyond the 12 GeV upgrade of CEBAF. The MEIC will consist of the existing polarized electron source complex with 12 GeV upgrade and a new ion complex with polarized and unpolarized light to medium ions. The conceptual layout is shown in Fig. 1 and the basic parameters in comparison with the similar machines are discussed in Table 1. The maximum permissible collision frequency at 1.5 GHz is dictated by the existing electron machine, allowing the relatively small charge per bunch and large crossing angle resulting in the increased beam stability and high luminosity. In this paper, we present the preliminary study of collective effects for e-ring.

  14. Industry Motivated Advancements of Current Combustion Instability Model: The Conversion of

    E-Print Network [OSTI]

    Flandro, Gary A.

    INSTABILITY CHARACTERISTICS IN GAS TURBINES ...................- 5 - 1.5. COMBUSTION INSTABILITYIndustry Motivated Advancements of Current Combustion Instability Model: The Conversion of Volume to thank Dr. Flandro. His eternal knowledge of Combustion Instability has resonated in this work and his

  15. Genomic neighbourhood and the regulation of gene expression Genomic neighbourhood and transcriptional regulation

    E-Print Network [OSTI]

    Babu, M. Madan

    Genomic neighbourhood and the regulation of gene expression Genomic neighbourhood and transcriptional regulation Subhajyoti De and M. Madan Babu MRC Laboratory of Molecular Biology, Hills Road..................................................................................................................................................................................1 2. Genomic neighbourhood and its influence on gene regulation

  16. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches

    E-Print Network [OSTI]

    Chandonia, John-Marc; Brenner, Steven E.

    2004-01-01T23:59:59.000Z

    SK, Bonanno JB. Structural genomics. Methods Biochem AnalMizuguchi K. Structural genomics: an overview. Prog BiophysSE. A tour of structural genomics. Nat Rev Genet 2001;2(10):

  17. Atomic scale mixing for inertial confinement fusion associated hydro instabilities

    E-Print Network [OSTI]

    New York at Stoney Brook, State University of

    Atomic scale mixing for inertial confinement fusion associated hydro instabilities J. Melvina, , P Alamos, NM 87545, USA Abstract Hydro instabilities have been identified as a potential cause- able. We find numerical convergence for this important quantity, in a purely hydro study, with only

  18. Computation of azimuthal combustion instabilities in an helicopter combustion chamber

    E-Print Network [OSTI]

    Nicoud, Franck

    Computation of azimuthal combustion instabilities in an helicopter combustion chamber C. Sensiau to compute azimuthal combustion instabilities is presented. It requires a thermoacoustic model using a n - formulation for the coupling between acoutics and combustion. The parameters n and are computed from a LES

  19. Electrostatic Interchange Instabilities of a Rotating, High-Temperature Plasma

    E-Print Network [OSTI]

    Mauel, Michael E.

    Electrostatic Interchange Instabilities of a Rotating, High-Temperature Plasma Confined by a Dipole #2 Mach Probe #1 Mach Probe #2 High-field, 0.2 MA-turn Water-cooled Magnet #12;Interchange Modes-sized/global... Fast hot electron interchange instability: drift-resonant transport; Gryokinetics; phase-space holes

  20. Thermal instability caused by plasma-wall interaction

    SciTech Connect (OSTI)

    Marenkov, E. D. [National Research Nuclear University Moscow Engineering Physics Institute (Russian Federation); Krasheninnikov, S. I. [University of California (United States); Pisarev, A. A.; Tsvetkov, I. V. [National Research Nuclear University Moscow Engineering Physics Institute (Russian Federation)

    2012-04-15T23:59:59.000Z

    A one-dimensional model describing recycling of hydrogen isotopes in fusion reactors is proposed. The dispersion relation for thermal instability caused by plasma-wall interaction is derived, and conditions under which it develops are determined. It is shown analytically and numerically that this instability can develop under typical tokamak conditions.

  1. Self-Gravity Driven Instabilities in the ISM

    E-Print Network [OSTI]

    R. M. Hueckstaedt; J. H. Hunter Jr; R. V. E. Lovelace

    2006-03-29T23:59:59.000Z

    In order to understand star formation it is important to understand the dynamics of atomic and molecular clouds in the interstellar medium (ISM). Nonlinear hydrodynamic flows are a key component to the ISM. One route by which nonlinear flows arise is the onset and evolution of interfacial instabilities. Interfacial instabilities act to modify the interface between gas components at different densities and temperatures. Such an interface may be subject to a host of instabilities, including the Rayleigh-Taylor, Kelvin-Helmholtz, and Richtmyer-Meshkov instabilities. Recently, a new density interface instability was identified. This self-gravity interfacial instability (SGI) causes any displacement of the interface to gr ow on roughly a free-fall time scale, even when the perturbation wavelength is much less than the Jeans length. In previous work, we used numerical simulations to confirm the expectations of linear theory and examine the nonlinear evolution of the SGI. We now continue our study by generalizing our initial conditions to allow the acceleration due to self-gravity to be non-zero across the interface. We also consider the behaviour of the SGI for perturbation wavelengths near the Jeans wavelength. We conclude that the action of self-gravity across a density interface may play a significant role in the ISM either by fueling the growth of new instabilities or modifying the evolution of existing instabilities.

  2. Detection of instabilities and transition in milling operation using wavelets

    E-Print Network [OSTI]

    Khurjekar, Parag Padmakar

    2000-01-01T23:59:59.000Z

    and undesirable due to their detrimental effects. Chatter is one such type of instability and is characterized by the violent relative vibration between the workpiece and tool. The objective of this research is to detect the onset of instabilities in milling...

  3. The Nonlinear Downstream Development of Baroclinic Instability Joseph Pedlosky

    E-Print Network [OSTI]

    Pedlosky, Joseph

    The Nonlinear Downstream Development of Baroclinic Instability Joseph Pedlosky Woods Hole The downstream development in both space and time of baroclinic instability is studied in a nonlinear channel as a conceptual model for the development of fluctuations in currents like the Gulf Stream and Kuroshio downstream

  4. Nonlinear instability of elementary stratified flows at large Richardson number

    E-Print Network [OSTI]

    Majda, Andrew J.

    Nonlinear instability of elementary stratified flows at large Richardson number Andrew J. Majdaa 1999 Elementary stably stratified flows with linear instability at all large Richardson numbers have been introduced recently by the authors J. Fluid Mech. 376, 319­350 1998 . These elementary stratified

  5. Genomics of emerging infectious disease: A PLoS collection.

    E-Print Network [OSTI]

    Eisen, Jonathan A; MacCallum, Catriona J

    2009-01-01T23:59:59.000Z

    Origins and evolutionary genomics of the 2009 swine-originan Infectious Diseases Genomics Project predict and preventRavel J (2009) The role of genomics in the identification,

  6. TOPSAN: a collaborative annotation environment for structural genomics.

    E-Print Network [OSTI]

    Weekes, Dana; Krishna, S; Bakolitsa, Constantina; Wilson, Ian A; Godzik, Adam; Wooley, John

    2010-01-01T23:59:59.000Z

    environment for structural genomics Dana Weekes 1† , S Srihigh-throughput structural genomics centers, despite theirbeing determined by structural genomics centers and high-

  7. Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

    E-Print Network [OSTI]

    2011-01-01T23:59:59.000Z

    Potnis et al. : Comparative genomics reveals diversity amongtomato and pepper. BMC Genomics Submit your next manuscriptpv. syringae Potnis et al. BMC Genomics 2011, 12:146 http://

  8. Dissection of Plant Defense Mechanisms Using Chemical and Molecular Genomics

    E-Print Network [OSTI]

    Rodriguez-Salus, Melinda Sue

    2012-01-01T23:59:59.000Z

    of auxins by a chemical genomics approach." Journal ofadvances in chemical genomics." Current Medicinal Chemistrymolecular and chemical genomics." Phytopathology 97(7): S58-

  9. Validation in Genomics: CpG Island Methylation Revisited

    E-Print Network [OSTI]

    Segal, Mark R

    2006-01-01T23:59:59.000Z

    analysis. In: Functional Genomics: Methods and Protocols, M.Segal: Validation in Genomics: CpG Island Methylationpackage and applications to genomics. Bioinformatics and

  10. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    E-Print Network [OSTI]

    Ditty, Jayna L.

    2012-01-01T23:59:59.000Z

    Page Incorporating Genomics and Bioinformatics across the2007) Discovering Genomics, Proteomics, and Bioinformatics,2003) Public access for teaching genomics, proteomics, and

  11. Environmental Genomics Reveals a Single-Species Ecosystem Deep Earth

    E-Print Network [OSTI]

    Arkin, Adam P.

    2014-01-01T23:59:59.000Z

    Environmental Genomics Reveals a Single-Species EcosystemTechnology Program, DOE Joint Genomics Institute, Berkeley,and Environmental Research, Genomics:GTL program through

  12. MicrobesOnline: an integrated portal for comparative functional genomics

    E-Print Network [OSTI]

    Joachimiak, Marcin P.

    2014-01-01T23:59:59.000Z

    comparative functional genomics Marcin P. Joachimiak 1,2 ,for comparative functional genomics of bacteria and archaea.publicly avail- able functional genomics data from published

  13. Microbes Online: an integrated portal for comparative functional genomics

    E-Print Network [OSTI]

    Arkin, Adam P.

    2014-01-01T23:59:59.000Z

    comparative functional genomics of bacteria, archaea, fungifor comparative functional genomics Paramvir S. Dehal 1,2* (and Environmental Research, Genomics:GTL program through

  14. additional structural genome: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    a mitochondrial genome Archibald, John 3 Protein structure prediction and structural genomics CiteSeer Summary: Genome sequencing projects are producing linear amino acid...

  15. ancient human genome: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    permafrost-preserved hair, the genome technologies have initiated an era of personal genomics. Eight human genome sequences have been reported so far Nielsen, Rasmus 3 A large...

  16. analyses genomes comparison: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    %) of coding sequence, the human genome encodes only 3%, while 13 COMPUTATIONAL GENOMICS: MAPPING, COMPARISON, AND ANNOTATION OF GENOMES Biotechnology Websites Summary:...

  17. ancient genome duplication: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    permafrost-preserved hair, the genome technologies have initiated an era of personal genomics. Eight human genome sequences have been reported so far Nielsen, Rasmus 8 Gene &...

  18. Buoyancy Instabilities in a Weakly Collisional Intracluster Medium

    E-Print Network [OSTI]

    Kunz, Matthew W; Reynolds, Christopher S; Stone, James M

    2012-01-01T23:59:59.000Z

    The intracluster medium of galaxy clusters is a weakly collisional, high-beta plasma in which the transport of heat and momentum occurs primarily along magnetic-field lines. Anisotropic heat conduction allows convective instabilities to be driven by temperature gradients of either sign, the magnetothermal instability (MTI) in the outskirts of non-isothermal clusters and the heat-flux buoyancy-driven instability (HBI) in their cooling cores. We employ the Athena MHD code to investigate the nonlinear evolution of these instabilities, self-consistently including the effects of anisotropic viscosity (i.e. Braginskii pressure anisotropy), anisotropic conduction, and radiative cooling. We highlight the importance of the microscale instabilities that inevitably accompany and regulate the pressure anisotropies generated by the HBI and MTI. We find that, in all but the innermost regions of cool-core clusters, anisotropic viscosity significantly impairs the ability of the HBI to reorient magnetic-field lines orthogonal...

  19. Modulational instability of electromagnetic waves in a collisional quantum magnetoplasma

    SciTech Connect (OSTI)

    Niknam, A. R., E-mail: a-niknam@sbu.ac.ir [Laser and Plasma Research Institute, Shahid Beheshti University, G.C., Tehran (Iran, Islamic Republic of); Rastbood, E.; Bafandeh, F.; Khorashadizadeh, S. M., E-mail: smkhorashadi@birjand.ac.ir [Physics Department of Birjand University, Birjand (Iran, Islamic Republic of)

    2014-04-15T23:59:59.000Z

    The modulational instability of right-hand circularly polarized electromagnetic electron cyclotron (CPEM-EC) wave in a magnetized quantum plasma is studied taking into account the collisional effects. Employing quantum hydrodynamic and nonlinear Schrödinger equations, the dispersion relation of modulated CPEM-EC wave in a collisional plasma has been derived. It is found that this wave is unstable in such a plasma system and the growth rate of the associated instability depends on various parameters such as electron Fermi temperature, plasma number density, collision frequency, and modulation wavenumber. It is shown that while the increase of collision frequency leads to increase of the growth rate of instability, especially at large wavenumber limit, the increase of plasma number density results in more stable modulated CPEM-EC wave. It is also found that in contrast to collisionless plasma in which modulational instability is restricted to small wavenumbers, in collisional plasma, the interval of instability occurrence can be extended to a large domain.

  20. Pair Instability Supernovae of Very Massive Population III Stars

    E-Print Network [OSTI]

    Chen, Ke-Jung; Woosley, Stan; Almgren, Ann; Whalen, Daniel

    2014-01-01T23:59:59.000Z

    Numerical studies of primordial star formation suggest that the first stars in the universe may have been very massive. Stellar models indicate that non-rotating Population III stars with initial masses of 140-260 Msun die as highly energetic pair-instability supernovae. We present new two-dimensional simulations of primordial pair-instability supernovae done with the CASTRO code. Our simulations begin at earlier times than previous multidimensional models, at the onset of core collapse, to capture any dynamical instabilities that may be seeded by collapse and explosive burning. Such instabilities could enhance explosive yields by mixing hot ash with fuel, thereby accelerating nuclear burning, and affect the spectra of the supernova by dredging up heavy elements from greater depths in the star at early times. Our grid of models includes both blue supergiants and red supergiants over the range in progenitor mass expected for these events. We find that fluid instabilities driven by oxygen and helium burning ari...

  1. Primary, secondary instabilities and control of the rotating-disk boundary layer

    E-Print Network [OSTI]

    ;Typical 3D boundary layers rotating disk swept wing Common features: · crossflow component near the wall · inflection point · strong inviscid instability · secondary instabilities ; growth and saturation of crossflow

  2. GOLD: The Genomes Online Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Kyrpides, Nikos; Liolios, Dinos; Chen, Amy; Tavernarakis, Nektarios; Hugenholtz, Philip; Markowitz, Victor; Bernal, Alex

    Since its inception in 1997, GOLD has continuously monitored genome sequencing projects worldwide and has provided the community with a unique centralized resource that integrates diverse information related to Archaea, Bacteria, Eukaryotic and more recently Metagenomic sequencing projects. As of September 2007, GOLD recorded 639 completed genome projects. These projects have their complete sequence deposited into the public archival sequence databases such as GenBank EMBL,and DDBJ. From the total of 639 complete and published genome projects as of 9/2007, 527 were bacterial, 47 were archaeal and 65 were eukaryotic. In addition to the complete projects, there were 2158 ongoing sequencing projects. 1328 of those were bacterial, 59 archaeal and 771 eukaryotic projects. Two types of metadata are provided by GOLD: (i) project metadata and (ii) organism/environment metadata. GOLD CARD pages for every project are available from the link of every GOLD_STAMP ID. The information in every one of these pages is organized into three tables: (a) Organism information, (b) Genome project information and (c) External links. [The Genomes On Line Database (GOLD) in 2007: Status of genomic and metagenomic projects and their associated metadata, Konstantinos Liolios, Konstantinos Mavromatis, Nektarios Tavernarakis and Nikos C. Kyrpides, Nucleic Acids Research Advance Access published online on November 2, 2007, Nucleic Acids Research, doi:10.1093/nar/gkm884]

    The basic tables in the GOLD database that can be browsed or searched include the following information:

    • Gold Stamp ID
    • Organism name
    • Domain
    • Links to information sources
    • Size and link to a map, when available
    • Chromosome number, Plas number, and GC content
    • A link for downloading the actual genome data
    • Institution that did the sequencing
    • Funding source
    • Database where information resides
    • Publication status and information

    (Specialized Interface)

  3. Addressing the Omics Data Explosion: a Comprehensive Reference Genome Representation and the Democratization of Comparative Genomics and Immunogenomics

    E-Print Network [OSTI]

    Nguyen, Ngan Kim

    2014-01-01T23:59:59.000Z

    Hubs: Web Accessible Browsers for Compar- ative Genomics 3.1Comparative Genomics Analyses . . . . . . . . . . . . . .browsers for comparative genomics” B.1 E. coli KO11FL 162099

  4. Infrared instability from nonlinear QCD evolution

    E-Print Network [OSTI]

    R. Enberg; R. Peschanski

    2006-01-13T23:59:59.000Z

    Using the Balitsky-Kovchegov (BK) equation as an explicit example, we show that nonlinear QCD evolution leads to an instability in the propagation toward the infrared of the gluon transverse momentum distribution, if one starts with a state with an infrared cut-off. This effect takes the mathematical form of rapidly moving traveling wave solutions of the BK equation, which we investigate by numerical simulations. These traveling wave solutions are different from those governing the transition to saturation, which propagate towards the ultraviolet. The infrared wave speed, formally infinite for the leading order QCD kernel, is determined by higher order corrections. This mechanism could play a role in the rapid decrease of the mean free path in the Color Glass Condensate scenario for heavy ion collisions.

  5. Saturation of the R-mode Instability

    E-Print Network [OSTI]

    Phil Arras; Eanna E. Flanagan; Sharon M. Morsink; A. Katrin Schenk; Saul A. Teukolsky; Ira Wasserman

    2003-02-11T23:59:59.000Z

    Rossby waves (r-modes) in rapidly rotating neutron stars are unstable because of the emission of gravitational radiation. We study saturation of this instability by nonlinear transfer of energy to stellar "inertial" oscillation modes. We present detailed calculations of stellar inertial modes in the WKB limit, their linear damping by bulk and shear viscosity, and the nonlinear coupling forces among these modes. The saturation amplitude is derived in the extreme limits of strong or weak driving by radiation reaction, as compared to the damping rate of low order inertial modes. We find the saturation energy is {\\it extremely small}, at least four orders of magnitude smaller than that found by previous investigators. We discuss the consequences of this result for spin evolution of young neutron stars, and neutron stars being spun up by accretion in Low Mass X-ray Binaries.We also discuss the detection of these gravitational waves by LIGO.

  6. MIX and Instability Growth from Oblique Shock

    SciTech Connect (OSTI)

    Molitoris, J D; Batteux, J D; Garza, R G; Tringe, J W; Souers, P C; Forbes, J W

    2011-07-22T23:59:59.000Z

    We have studied the formation and evolution of shock-induced mix resulting from interface features in a divergent cylindrical geometry. In this research a cylindrical core of high-explosive was detonated to create an oblique shock wave and accelerate the interface. The interfaces studied were between the high-explosive/aluminum, aluminum/plastic, and finally plastic/air. Pre-emplaced surface features added to the aluminum were used to modify this interface. Time sequence radiographic imaging quantified the resulting instability formation from the growth phase to over 60 {micro}s post-detonation. Thus allowing the study of the onset of mix and evolution to turbulence. The plastic used here was porous polyethylene. Radiographic image data are compared with numerical simulations of the experiments.

  7. Dynamics and instability of false vacuum bubbles

    E-Print Network [OSTI]

    Anthony Aguirre; Matthew C. Johnson

    2005-11-22T23:59:59.000Z

    This paper examines the classical dynamics of false vacuum regions embedded in surrounding regions of true vacuum, in the thin-wall limit. The dynamics of all generally relativistically allowed solutions -- most but not all of which have been previously studied -- are derived, enumerated, and interpreted. We comment on the relation of these solutions to possible mechanisms whereby inflating regions may be spawned from non-inflating ones. We then calculate the dynamics of first order deviations from spherical symmetry, finding that many solutions are unstable to such aspherical perturbations. The parameter space in which the perturbations on bound solutions inevitably become nonlinear is mapped. This instability has consequences for the Farhi-Guth-Guven mechanism for baby universe production via quantum tunneling.

  8. Dynamics and instability of false vacuum bubbles

    SciTech Connect (OSTI)

    Aguirre, Anthony; Johnson, Matthew C. [Department of Physics, University of California, Santa Cruz, California 95064 (United States)

    2005-11-15T23:59:59.000Z

    This paper examines the classical dynamics of false-vacuum regions embedded in surrounding regions of true vacuum, in the thin-wall limit. The dynamics of all generally relativistically allowed solutions--most but not all of which have been previously studied--are derived, enumerated, and interpreted. We comment on the relation of these solutions to possible mechanisms whereby inflating regions may be spawned from noninflating ones. We then calculate the dynamics of first-order deviations from spherical symmetry, finding that many solutions are unstable to such aspherical perturbations. The parameter space in which the perturbations on bound solutions inevitably become nonlinear is mapped. This instability has consequences for the Farhi-Guth-Guven mechanism for baby universe production via quantum tunneling.

  9. Front instabilities in evaporatively dewetting nanofluids

    E-Print Network [OSTI]

    Vancea, I; Pauliac-Vaujour, E; Stannard, A; Martín, C P; Blunt, M O; Moriarty, P J

    2008-01-01T23:59:59.000Z

    Various experimental settings that involve drying solutions or suspensions of nanoparticles -- often called nanofluids -- have recently been used to produce structured nanoparticle layers. In addition to the formation of polygonal networks and spinodal-like patterns, the occurrence of branched structures has been reported. After reviewing the experimental results we use a modified version of the Monte Carlo model first introduced by Rabani et al. [Nature 426, 271 (2003)] to study structure formation in evaporating films of nanoparticle solutions for the case that all structuring is driven by the interplay of evaporating solvent and diffusing nanoparticles. After introducing the model and its general behavior we focus on receding dewetting fronts which are initially straight but develop a transverse fingering instability. We analyze the dependence of the characteristics of the resulting branching patterns on the driving chemical potential, the mobility and concentration of the nanoparticles, and the interactio...

  10. Mitigation of radiation induced surface contamination

    DOE Patents [OSTI]

    Klebanoff, Leonard E. (Dublin, CA); Stulen, Richard H. (Livermore, CA)

    2003-01-01T23:59:59.000Z

    A process for mitigating or eliminating contamination and/or degradation of surfaces having common, adventitious atmospheric contaminants adsorbed thereon and exposed to radiation. A gas or a mixture of gases is introduced into the environment of a surface(s) to be protected. The choice of the gaseous species to be introduced (typically a hydrocarbon gas, water vapor, or oxygen or mixtures thereof) is dependent upon the contaminant as well as the ability of the gaseous species to bind to the surface to be protected. When the surface and associated bound species are exposed to radiation reactive species are formed that react with surface contaminants such as carbon or oxide films to form volatile products (e.g., CO, CO.sub.2) which desorb from the surface.

  11. Radiation Induced Nanocrystal Formation in Metallic Glasses 

    E-Print Network [OSTI]

    Carter, Jesse

    2010-01-14T23:59:59.000Z

    simple system consisting of only two elements, several intermetallic compounds can exist, each with their own crystal structure (face-centered cubic, body-centered, etc), and the system gets much more complicated when the number of constituents... of Alloys and Compounds, Vol 431, Q.S. Zhang, W. Zhang, G.Q. Xie, K.S. Nakayama, H. Kimura and A. Inoue, Formation of bulk metallic glass in situ composites in Cu50Zr45Ti5 alloy, Pages 236-240, Copyright 2007, with permission from Elsevier. 16 Fig. 9...

  12. Radiation Induced Nanocrystal Formation in Metallic Glasses

    E-Print Network [OSTI]

    Carter, Jesse

    2010-01-14T23:59:59.000Z

    The irradiation of metallic glasses to induce nanocrystallization was studied in two metallic glass compositions, Cu50Zr45Ti5 and Zr55Cu30Al10Ni5. Atomic mobility was described using a model based on localized excess free volume due to displace...

  13. ; Evolution of genes and genomes on the Drosophila phylogeny

    E-Print Network [OSTI]

    Kellis, Manolis

    ARTICLES ; Evolution of genes and genomes on the Drosophila phylogeny Drosophila 12 Genomes Consortium* Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome

  14. The Genome of the Epsilonproteobacterial Chemolithoautotroph Sulfurimonas dentrificans

    E-Print Network [OSTI]

    Sievert, Stefan M.; USF Genomics Class

    2008-01-01T23:59:59.000Z

    10 , Jörg Simon 11 , and the USF Genomics Class 2, ? Biologyof coverage at the Production Genomics Facility of the Joint

  15. Genome Size Varaiation in D. melanogaster

    E-Print Network [OSTI]

    Alfrejd, Benjamin

    2011-04-26T23:59:59.000Z

    in genome size may account for some of the missing heritability. We measured female genome sizes for 34 Drosophila melanogaster inbred strains that derived from isofemale lines established from a natural population in Raleigh, NC, in addition to a group...

  16. Genome Engineering with TAL Effector Nucleases

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Genome Engineering with TAL Effector Nucleases Print Genome engineering (GE), an emerging discipline in which a DNA sequence is altered at a single position, has a wide variety of...

  17. GWIDD: Genome-wide protein docking database

    E-Print Network [OSTI]

    Kundrotas, Petras J.; Zhu, Zhengwei; Vasker, Ilya A.

    2009-11-09T23:59:59.000Z

    Structural information on interacting proteins is important for understanding life processes at the molecular level. Genome-wide docking database is an integrated resource for structural studies of protein–protein interactions on the genome scale...

  18. Joint Genome Institute's Automation Approach and History

    SciTech Connect (OSTI)

    Roberts, Simon

    2006-07-05T23:59:59.000Z

    Department of Energy/Joint Genome Institute (DOE/JGI) collaborates with DOE national laboratories and community users, to advance genome science in support of the DOE missions of clean bio-energy, carbon cycling, and bioremediation.

  19. On Higuchi Ghosts and Gradient Instabilities in Bimetric Gravity

    E-Print Network [OSTI]

    Könnig, Frank

    2015-01-01T23:59:59.000Z

    We discuss the conditions to satisfy the Higuchi bound and to avoid gradient instabilities in the scalar sector for cosmological solutions in singly coupled bimetric gravity theories. We find that in expanding universes the ratio of the scale factors of the reference and observable metric has to increase at all times. This automatically implies a ghost-free helicity-2 sector and enforces a phantom Dark Energy. Furthermore, the condition for the absence of gradient instabilities in the scalar sector will be analyzed. Finally, we discuss whether cosmological solutions, including exotic evolutions like bouncing cosmologies, can exist, in which both the Higuchi ghost and scalar instabilities are absent at all times.

  20. Tilted accretion discs in cataclysmic variables: tidal instabilities and superhumps

    E-Print Network [OSTI]

    J. R. Murray; P. J. Armitage

    1998-09-10T23:59:59.000Z

    We investigate the growth of tidal instabilities in accretion discs in a binary star potential, using three dimensional numerical simulations. As expected from analytic work, the disc is prone to an eccentric instability provided that it is large enough to extend to the 3:1 resonance. The eccentric disc leads to positive superhumps in the light curve. It has been proposed that negative superhumps might arise from a tilted disc, but we find no evidence that the companion gravitational tilt instability can grow fast enough in a fluid disc to create a measurable inclination. The origin of negative superhumps in the light curves of cataclysmic variables remains a puzzle.

  1. Prediction of core saturation instability at an HVDC converter

    SciTech Connect (OSTI)

    Burton, R.S. [Teshmont Consultants, Inc., Winnipeg, Manitoba (Canada)] [Teshmont Consultants, Inc., Winnipeg, Manitoba (Canada); Fuchshuber, C.F. [Alberta Power Ltd., Edmonton, Alberta (Canada)] [Alberta Power Ltd., Edmonton, Alberta (Canada); Woodford, D.A. [Manitoba HVDC Research Centre, Winnipeg, Manitoba (Canada)] [Manitoba HVDC Research Centre, Winnipeg, Manitoba (Canada); Gole, A.M. [Univ. of Manitoba, Winnipeg, Manitoba (Canada)] [Univ. of Manitoba, Winnipeg, Manitoba (Canada)

    1996-10-01T23:59:59.000Z

    Core saturation instability has occurred on several HVDC schemes resulting from interactions between second harmonic and dc quantities (voltages and currents) on the ac side of the converter and fundamental frequency quantities on the dc side of the converter. The instability can be reinforced by unbalanced saturation of the converter transformers. The paper presents an analytical method which can be used to quickly screen ac and dc system operating conditions to predict where core saturation instability is likely to occur. Analytical results have been confirmed using the digital transients simulation program PSCAD/EMTDC.

  2. Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting

    E-Print Network [OSTI]

    Botstein, David

    Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome Jodi E. Hirschman, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, 5-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University, Washington Road, Princeton

  3. Population genomics20-02-2009 Antnio Rodrigues; Bruno Santos / 59 Population Genomics

    E-Print Network [OSTI]

    Goldschmidt, Christina

    Population genomics20-02-2009 António Rodrigues; Bruno Santos / 59 Population Genomics 1 António Rodrigues (PDBC 2008) Bruno Santos (PDBC 2008) #12;Population genomics20-02-2009 António Rodrigues; Bruno Santos / 59 Contents 2 2 1000 genome project 1 Motivation and Introduction New generation sequencing

  4. Genome Sequence of the Pea Aphid Acyrthosiphon The International Aphid Genomics Consortium"

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Genome Sequence of the Pea Aphid Acyrthosiphon pisum The International Aphid Genomics Consortium we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple

  5. Comparative Sequencing of Plant Genomes: Choices to Make The first sequenced genome of a plant,

    E-Print Network [OSTI]

    Purugganan, Michael D.

    COMMENTARY Comparative Sequencing of Plant Genomes: Choices to Make The first sequenced genome of a plant, Arabidopsis thaliana, was published ,6 years ago (Arabidopsis Genome Initiative, 2000). Since that time, the complete rice genome (Oryza sativa; Goff et al., 2002; Yu et al., 2002; International Rice

  6. From genomics to chemical genomics: new developments in KEGG

    E-Print Network [OSTI]

    Minoru Kanehisa; Susumu Goto; Masahiro Hattori; Kiyoko F. Aoki-kinoshita; Masumi Itoh; Shuichi Kawashima; Toshiaki Katayama; Michihiro Araki; Mika Hirakawa

    2006-01-01T23:59:59.000Z

    The increasing amount of genomic and molecular information is the basis for understanding higherorder biological systems, such as the cell and the 15 organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource

  7. Joint Genome Institute's Automation Approach and History

    E-Print Network [OSTI]

    Roberts, Simon

    2006-01-01T23:59:59.000Z

    Joint Genome Institute’s Automation Approach and Historythroughput environment; – automation does not necessarilyissues “Islands of Automation” – modular instruments with

  8. Transforming Growth Factor ?-1 (TGF-?1) Is a Serum Biomarker of Radiation Induced Fibrosis in Patients Treated With Intracavitary Accelerated Partial Breast Irradiation: Preliminary Results of a Prospective Study

    SciTech Connect (OSTI)

    Boothe, Dustin L. [Weill Cornell Medical College of Cornell University, New York, New York (United States); Coplowitz, Shana [Department of Radiation Oncology, Stich Radiation Center, Weill Cornell Medical College of Cornell University, New York, New York (United States); Greenwood, Eleni [Weill Cornell Medical College of Cornell University, New York, New York (United States); Barney, Christian L. [Department of Radiation Oncology, Ohio State University, Columbus, Ohio (United States); Christos, Paul J. [Division of Biostatistics and Epidemiology, Department of Public Health, Weill Cornell Medical College of Cornell University, New York, New York (United States); Parashar, Bhupesh; Nori, Dattatreyudu; Chao, K. S. Clifford [Department of Radiation Oncology, Stich Radiation Center, Weill Cornell Medical College of Cornell University, New York, New York (United States); Wernicke, A. Gabriella, E-mail: gaw9008@med.cornell.edu [Department of Radiation Oncology, Stich Radiation Center, Weill Cornell Medical College of Cornell University, New York, New York (United States)

    2013-12-01T23:59:59.000Z

    Purpose: To examine a relationship between serum transforming growth factor ? -1 (TGF-?1) values and radiation-induced fibrosis (RIF). Methods and Materials: We conducted a prospective analysis of the development of RIF in 39 women with American Joint Committee on Cancer stage 0-I breast cancer treated with lumpectomy and accelerated partial breast irradiation via intracavitary brachytherapy (IBAPBI). An enzyme-linked immunoassay (Quantikine, R and D, Minneapolis, MN) was used to measure serum TGF-?1 before surgery, before IBAPBI, and during IBAPBI. Blood samples for TGF-?1 were also collected from 15 healthy, nontreated women (controls). The previously validated tissue compliance meter (TCM) was used to objectively assess RIF. Results: The median time to follow-up for 39 patients was 44 months (range, 5-59 months). RIF was graded by the TCM scale as 0, 1, 2, and 3 in 5 of 20 patients (25%), 6 of 20 patients (30%), 5 of 20 patients (25%), and 4 of 20 patients (20%), respectively. The mean serum TGF-?1 values were significantly higher in patients before surgery than in disease-free controls, as follows: all cancer patients (30,201 ± 5889 pg/mL, P=.02); patients with any type of RIF (32,273 ± 5016 pg/mL, P<.0001); and women with moderate to severe RIF (34,462 ± 4713 pg/mL, P<0.0001). Patients with moderate to severe RIF had significantly elevated TGF-?1 levels when compared with those with none to mild RIF before surgery (P=.0014) during IBAPBI (P?0001), and the elevation persisted at 6 months (P?.001), 12 months (P?.001), 18 months (P?.001), and 24 months (P=.12). A receiver operating characteristic (ROC) curve of TGF-?1 values predicting moderate to severe RIF was generated with an area under the curve (AUC){sub ROC} of 0.867 (95% confidence interval 0.700-1.000). The TGF-?1 threshold cutoff was determined to be 31,000 pg/mL, with associated sensitivity and specificity of 77.8% and 90.0%, respectively. Conclusions: TGF-?1 levels correlate with the development of moderate to severe RIF. The pre-IBAPBI mean TGF-?1 levels can serve as an early biomarker for the development of moderate to severe RIF after IBAPBI.

  9. Genome Biology 2004, 6:302 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch

    E-Print Network [OSTI]

    Gent, Universiteit

    Genome Biology 2004, 6, Technologiepark 927, B-9052 Ghent, Belgium. E-mail: Yves.vandepeer@psb.ugent.be Published: 21 December 2004 Genome at http://genomebiology.com/2004/6/1/302 © 2004 BioMed Central Ltd A report on the Plant Genomics European

  10. The Human Genome Project: Sequencing the Future

    E-Print Network [OSTI]

    genome programs--Genomes to Life, the Microbial Genome Program, and the Microbial Cell Project on fossil fuels. The new findings also have the potential to provide tools for enhanced biothreat agent detection and response and for using genetically engineered microbes to clean up toxic wastes in contaminat

  11. Leading Edge Bacterial Genomics and Pathogen Evolution

    E-Print Network [OSTI]

    Mekalanos, John

    Leading Edge Review Bacterial Genomics and Pathogen Evolution David M. Raskin,1 Rekha Seshadri,2 Medical School, Boston, MA 02115, USA 2 The Institute for Genomic Research, 9712 Medical Center Drive.02.002 The availability of hundreds of bacterial genome sequences has altered the study of bacte- rial pathogenesis

  12. INVITED: Comparative Microbial Genomics Giri Narasimhan

    E-Print Network [OSTI]

    Narasimhan, Giri

    INVITED: Comparative Microbial Genomics Giri Narasimhan Bioinformatics Research Group (Bio, comparative genomics holds the keys to decipher and mine this wealth of information. We discuss the diverse ways in which the availability of comparative genomics data allows us to answer more questions

  13. UNL Core for Applied Genomics and Ecology

    E-Print Network [OSTI]

    Farritor, Shane

    UNL Core for Applied Genomics and Ecology Bioinformatics training Roche 454 GS-FLX Registration, Microbiomes, Variant Analysis, Whole Genomes, Transcriptomes Data Analysis and Statistics CAGE database and employer. University of Nebraska-Lincoln*Core for Applied Genomics and Ecology* 323 Filley Hall *Lincoln

  14. One day seminar: Genetics and Genomics of

    E-Print Network [OSTI]

    Brierley, Andrew

    SCHOOL OF MEDICINE One day seminar: Genetics and Genomics of Infectious Diseases Malaria and TB 14th June 2013 University of St Andrews - School of Medicine Pathogen genome research allows exquisite to understanding disease progression. Pathogen genome sequencing is accessible to most. Outputs have broad

  15. Bridging mycorrhizal genomics, metagenomics and forest ecology

    E-Print Network [OSTI]

    Pringle, Anne

    Meetings Bridging mycorrhizal genomics, metagenomics and forest ecology 6th New Phytologist of easily cultured saprotrophic fungi (among the first three published genomes were the models Saccharomyces or biotechnological interest, genomics is now poised to rapidly permeate the fields of fungal ecology and evolution

  16. Prospects & Overviews Evolution of eukaryotic genome

    E-Print Network [OSTI]

    Babu, M. Madan

    , O. dioica has a rapidly evolving, highly compact genome with a divergent intron-exon organization. Additionally, O. dioica lacks the minor spli- ceosome and key DNA repair pathway genes. Even with a compact on various aspects of the global genome architecture and different genomic fea- tures such as intron

  17. Genome Biology 2005, 6:312 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch

    E-Print Network [OSTI]

    Kellis, Manolis

    Genome Biology 2005, 6:312 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch Meeting report Large-scale discovery and validation of functional elements in the human genome-mail: bbernst@fas.harvard.edu. Manolis Kellis. E-mail: manoli@mit.edu Published: 1 March 2005 Genome Biology

  18. Genome Biology 2006, 7:320 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch

    E-Print Network [OSTI]

    Pritham, Ellen J.

    Genome Biology 2006, 7:320 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch Meeting report Mobile DNA: genomes under the influence Cédric Feschotte and Ellen J Pritham Feschotte. Email: cedric@uta.edu Published: 30 June 2006 Genome Biology 2006, 7:320 (doi:10.1186/gb-2006

  19. DATA QUALITY IN GENOME DATABASES (Research Paper)

    E-Print Network [OSTI]

    Weske, Mathias

    DATA QUALITY IN GENOME DATABASES (Research Paper) Heiko Müller Humboldt University Berlin, Germany@dbis.informatik.hu-berlin.de Abstract: Genome databases store data about molecular biological entities such as genes, proteins, diseases is their importance in the process of drug discovery. Genome data is analyzed and interpreted to gain so-called leads

  20. Genome Biology 2007, 8:R34 commentreviewsreportsdepositedresearchrefereedresearchinteractionsinformation

    E-Print Network [OSTI]

    Shneiderman, Ben

    Genome Biology 2007, 8:R34 analytics tool for genome assemblies Michael C Schatz*, Adam M Phillippy*, Ben Shneiderman and Steven L the original work is properly cited. Hawkeye: a visual analytics tool for genome assembliesHawkeye is a new

  1. Computational Approaches Towards Human Genome Annotation

    E-Print Network [OSTI]

    Singh, Jaswinder Pal

    Computational Approaches Towards Human Genome Annotation Mark Gerstein Molecular Biophysics of the human genome. My talk will be concerned with topics within this area, in particular annotating pseudogenes (protein fossils) in the genome. I will discuss a comprehensive pseudogene identification pipeline

  2. Inferring Ancestral Chloroplast Genomes with Inverted Repeat

    E-Print Network [OSTI]

    Tang, Jijun

    Inferring Ancestral Chloroplast Genomes with Inverted Repeat Liying Cui # , Feng Yue + , Claude W 87131 Abstract--- Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, inser­ tions/deletions and gene order

  3. Journal of Marine Research, 69, 5777, 2011 Secondary instability of salt sheets

    E-Print Network [OSTI]

    Smyth, William David

    Journal of Marine Research, 69, 57­77, 2011 Secondary instability of salt sheets by Satoshi Kimura1), the salt-fingering instability is supplanted by the salt-sheet instability. Previous direct numerical simulation (DNS) experiments on salt sheets revealed that flow becomes turbulent via secondary instabilities

  4. Managing the genome data deluge

    SciTech Connect (OSTI)

    Aldhous, P.

    1993-10-22T23:59:59.000Z

    This article describes efforts to integrate all the databases containing sequence information generated by the Human Genome Project. Projects range from putting all the information in one central source, to creating systems for allowing the user to communicate with the different databases in one operation.

  5. Nuclear Organization and Genome Function

    E-Print Network [OSTI]

    Corces, Victor G.

    Nuclear Organization and Genome Function Kevin Van Bortle and Victor G. Corces Department-range interactions and have proposed roles in nuclear organization. In this review, we explore recent findings for the roles of insulators in nuclear organization. 163 Annu.Rev.CellDev.Biol.2012.28:163-187.Downloadedfromwww

  6. CROP & SOIL SCIENCES Quantitative Genomics

    E-Print Network [OSTI]

    Arnold, Jonathan

    CROP & SOIL SCIENCES Quantitative Genomics Committee Membership Dr. Scott Jackson - committee chair Dr. Peng-Wah Chee Department of Crop & Soil Sciences Department of Crop & Soil Sciences University of Horticulture Department of Crop & Soil Sciences University of Georgia University of Georgia 2360 Rainwater Rd

  7. Microfluidic Devices for Genomic Analysis

    E-Print Network [OSTI]

    the puzzle of interactions between proteins is far more complicated than deciphering genomes, due to the lack, and industry. Fractionation of biological molecules, such as nucleic acids and proteins, plays a central role of proteins' equivalent of amplification, fractionation and sequencing techniques. Micro- and nano

  8. Title of dissertation: HYDROMAGNETIC TURBULENT INSTABILITY IN LIQUID SODIUM

    E-Print Network [OSTI]

    Lathrop, Daniel P.

    ABSTRACT Title of dissertation: HYDROMAGNETIC TURBULENT INSTABILITY IN LIQUID SODIUM EXPERIMENTS Daniel R. Sisan, Doctor of Philosophy, 2004 Dissertation directed by: Professor Daniel P. Lathrop Department of Physics This dissertation describes the observation of magnetically-induced instabil- ities

  9. anterior shoulder instability: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ON THE SHOULDER JOINT DURING by individual muscles that contribute to isometric abduction of the upper limb in the coronal plane De Luca, Carlo J. 35 Jeans Instability in...

  10. Investigation of thermal filamentation instability over Gakona, Alaska

    E-Print Network [OSTI]

    Cohen, Joel (Joel A.), S.B. Massachusetts Institute of Technology

    2007-01-01T23:59:59.000Z

    The thermal filamentation instability has been invoked to explain the formation of parallel plate waveguides in mid-latitude ionospheric plasmas during Arecibo, Puerto Rico heating experiments in 1997. The geometry of the ...

  11. Control of transversal instabilities in reaction-diffusion systems

    E-Print Network [OSTI]

    Molnos, Sonja; Totz, Jan Frederik; Engel, Harald

    2015-01-01T23:59:59.000Z

    In two-dimensional reaction-diffusion systems, local curvature perturbations in the shape of traveling waves are typically damped out and disappear in the course of time. If, however, the inhibitor diffuses much faster than the activator, transversal instabilities can arise, leading from flat to folded, spatio-temporally modulated wave shapes and to spreading spiral turbulence. For experimentally relevant parameter values, the photosensitive Belousov-Zhabotinsky reaction (PBZR) does not exhibit transversal wave instabilities. Here, we propose a mechanism to artificially induce these instabilities via a wave shape dependent spatio-temporal feedback loop, and study the emerging wave patterns. In numerical simulations with the modified Oregonator model for the PBZR using experimentally realistic parameter values we demonstrate the feasibility of this control scheme. Conversely, in a piecewise-linear version of the FitzHugh-Nagumo model transversal instabilities and spiral turbulence in the uncontrolled system ar...

  12. Magnetorotational instability in cool cores of galaxy clusters

    E-Print Network [OSTI]

    Nipoti, C; Ettori, S; Bianconi, M

    2015-01-01T23:59:59.000Z

    Clusters of galaxies are embedded in halos of optically thin, gravitationally stratified, weakly magnetized plasma at the system's virial temperature. Due to radiative cooling and anisotropic heat conduction, such intracluster medium (ICM) is subject to local instabilities, which are combinations of the thermal, magnetothermal and heat-flux-driven buoyancy instabilities. If the ICM rotates significantly, its stability properties are substantially modified and, in particular, also the magnetorotational instability (MRI) can play an important role. We study simple models of rotating cool-core clusters and we demonstrate that the MRI can be the dominant instability over significant portions of the clusters, with possible implications for the dynamics and evolution of the cool cores. Our results give further motivation for measuring the rotation of the ICM with future X-ray missions such as ASTRO-H and ATHENA.

  13. Activation of conductive pathways via deformation-induced instabilities

    E-Print Network [OSTI]

    Ni, Xinchen

    2014-01-01T23:59:59.000Z

    Inspired by the pattern transformation of periodic elastomeric cellular structures, the purpose of this work is to exploit this unique ability to activate conductive via deformation-induced instabilities. Two microstructural ...

  14. acoustic decay instability: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    examples have short orbital times so the unstable growth time can be small. L. E. Montenegro; C. Yuan; B. G. Elmegreen 1999-03-26 9 Curvature and Acoustic Instabilities in...

  15. Magnetorotational instability in plasmas with mobile dust grains

    SciTech Connect (OSTI)

    Ren Haijun [CAS Key Laboratory of Basic Plasma Physics, Department of Modern Physics, University of Science and Technology of China, Hefei 230026 (China); Cao Jintao [Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Li Ding [CAS Key Laboratory of Basic Plasma Physics, Department of Modern Physics, University of Science and Technology of China, Hefei 230026 (China); Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Chu, Paul K. [Department of Physics and Materials Science, City University of Hong Kong, Tat Chee Avenue, Kowloon (Hong Kong)

    2013-03-15T23:59:59.000Z

    The magnetorotational instability of dusty plasmas is investigated using the multi-fluid model and the general dispersion relation is derived based on local approximation. The dust grains are found to play an important role in the dispersion relation in the low-frequency mode and exhibit destabilizing effects on the plasma. Both the instability criterion and growth rate are affected significantly by the dust and when the dust is heavy enough to be unperturbed, the reduced dispersion relations are obtained. The instability criteria show that the dust grains have stabilizing effects on the instability when the rotation frequency decreases outwards and conversely lead to destabilizing effects when the rotation frequency increases outwards. The results are relevant to accession and protoplanetary disks.

  16. Physics-based flame dynamics modeling and thermoacoustic instability mitigation

    E-Print Network [OSTI]

    Altay, Hurrem Murat

    2009-01-01T23:59:59.000Z

    The objectives of this work are (i) to investigate the coupled unsteady heat release mechanisms responsible for thermoacoustic instabilities under different flame anchoring configurations, (ii) to develop reduced-order ...

  17. Transverse electron-scale instability in relativistic shear flows

    E-Print Network [OSTI]

    Alves, E P; Fonseca, R A; Silva, L O

    2015-01-01T23:59:59.000Z

    Electron-scale surface waves are shown to be unstable in the transverse plane of a shear flow in an initially unmagnetized plasma, unlike in the (magneto)hydrodynamics case. It is found that these unstable modes have a higher growth rate than the closely related electron-scale Kelvin-Helmholtz instability in relativistic shears. Multidimensional particle-in-cell simulations verify the analytic results and further reveal the emergence of mushroom-like electron density structures in the nonlinear phase of the instability, similar to those observed in the Rayleigh Taylor instability despite the great disparity in scales and different underlying physics. Macroscopic ($\\gg c/\\omega_{pe}$) fields are shown to be generated by these microscopic shear instabilities, which are relevant for particle acceleration, radiation emission and to seed MHD processes at long time-scales.

  18. On the ordinary mode instability for low beta plasmas

    SciTech Connect (OSTI)

    Hadi, F.; Qamar, A. [Institute of Physics and Electronics, University of Peshawar, Peshawar (Pakistan); Bashir, M. F. [Department of Physics, G. C. University, Lahore (Pakistan); Salam Chair in Physics, G. C. University, Lahore (Pakistan); Yoon, P. H. [Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742-2431 (United States); School of Space Research, Kyung Hee University, Yongin (Korea, Republic of); Schlickeiser, R. [Institut für Theoretische Physik, Lehrstuhl IV: Weltraum- and Astrophysik, Ruhr-Universität, Bochum (Germany)

    2014-05-15T23:59:59.000Z

    The purely growing ordinary (O) mode instability, first discussed by Davidson and Wu [Phys. Fluids 13, 1407 (1970)], has recently received renewed attention owing to its potential applicability to the solar wind plasma. In a series of papers, Ibscher, Schlickeiser, and their colleagues [Phys. Plasmas 19, 072116 (2012); ibid. 20, 012103 (2013); ibid. 20, 042121 (2013); ibid. 21, 022110 (2014)] revisited the O mode instability and extended it to the low-beta plasma regime by considering a counter-streaming bi-Maxwellian model. However, the O-mode instability is, thus, far discussed only on the basis of the marginal stability condition rather than actual numerical solutions of the dispersion relation. The present paper revisits the O-mode instability by considering the actual complex roots. The marginal stability condition as a function of the (electron) temperature anisotropy and beta naturally emerges in such a scheme.

  19. Influence of flavor oscillations on neutrino beam instabilities

    SciTech Connect (OSTI)

    Mendonça, J. T., E-mail: titomend@ist.utl.pt [Instituto de Física, Universidade de São Paulo, 05508-090 São Paulo SP (Brazil); Haas, F. [Instituto de Física, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre RS (Brazil); Bret, A. [ETSI Industriales, Universidad de Castilla-La Mancha, 13071 Ciudad Real, Spain and Instituto de Investigaciones Energeticas y Aplicaciones Industriales, Campus Universitario de Ciudad Real, 13071 Ciudad Real (Spain)

    2014-09-15T23:59:59.000Z

    We consider the collective neutrino plasma interactions and study the electron plasma instabilities produced by a nearly mono-energetic neutrino beam in a plasma. We describe the mutual interaction between neutrino flavor oscillations and electron plasma waves. We show that the neutrino flavor oscillations are not only perturbed by electron plasmas waves but also contribute to the dispersion relation and the growth rates of neutrino beam instabilities.

  20. Finite-size instabilities in nuclear energy density functionals

    SciTech Connect (OSTI)

    Hellemans, V.; Heenen, P.-H.; Bender, M. [Universite Libre de Bruxelles, PNTPM, CP229, 1050 Bruxelles (Belgium); Univ. Bordeaux, CENBG, UMR5797, F-33170 Gradignan (France) and CNRS/IN2P3, CENBG, UMR5797, F-33170 Gradignan (France)

    2012-10-20T23:59:59.000Z

    The systematic lack of convergence of self-consistent mean-field calculations with certain parameterizations of the Skyrme energy density functional has been attributed to the appearance of finite-size instabilities. In this contribution, we investigate what happens at the instability associated with the C{sub 0}{sup {Delta}s}s{sub 0} Dot-Operator {Delta}s{sub 0} term in a high-spin state of the superdeformed band in {sup 194}Hg.

  1. Influence of flavor oscillations on neutrino beam instabilities

    E-Print Network [OSTI]

    Mendonça, José Tito; Bret, Antoine

    2014-01-01T23:59:59.000Z

    We consider the collective neutrino plasma interactions, and study the electron plasma instabilities produced by a nearly mono-energetic neutrino beam in a plasma. We describe the mutual influence of neutrino flavor oscillations and electron plasma waves. We show that the neutrino flavor oscillations are not only perturbed by electron plasmas waves, but also contribute to the dispersion relation and the growth rates of neutrino beam instabilities.

  2. Suppression of Rayleigh Taylor instability in strongly coupled plasmas

    SciTech Connect (OSTI)

    Das, Amita; Kaw, Predhiman [Institute for Plasma Research, Bhat, Gandhinagar 382428 (India)

    2014-06-15T23:59:59.000Z

    The Rayleigh Taylor instability in a strongly coupled plasma medium has been investigated using the equations of generalized hydrodynamics. It is demonstrated that the visco-elasticity of the strongly coupled medium due to strong inter particle correlations leads to a suppression of the Rayleigh Taylor instability unless certain threshold conditions are met. The relevance of these results to experiments on laser compression of matter to high densities including those related to inertial confinement fusion using lasers has also been shown.

  3. Flow instability and critical heat flux in a ribbed annulus

    SciTech Connect (OSTI)

    Yang, B.W.; Dougherty, T.; Fighetti, C.; Kokolis, S.; Reddy, G.D. [Columbia Univ., New York, NY (United States); McAssey, E.V. Jr. [Villanova Univ., PA (United States); Coutts, A. [Westinghouse Savannah River Co., Aiken, SC (United States)

    1993-11-01T23:59:59.000Z

    An experimental program has been conducted to determine the onset of flow instability point in a heated annulus which is divided into four sub channels by non-conducting ribs. The onset of flow instability is identified by the minimum point in the pressure drop-velocity curve. Comparison with a ribless annulus show that the presence of ribs increases the minimum point velocity. In addition, data are presented which show that under certain conditions premature CHF can be induced by the ribs.

  4. Instability issues for the ESS linac and rings

    SciTech Connect (OSTI)

    Rees, G. H. [Rutherford Appleton Laboratory, CLRC (United Kingdom)

    1999-12-03T23:59:59.000Z

    Comments are made on beam instability issues in the ESS linac and rings. The topics of interest in the linac are halo generation in the absence and presence of machine imperfections, and also the stability of the momentum ramping of the output beam. In the case of the rings, the main concern is for fast coherent transverse instabilities due to the combined effect of coupled electron-proton oscillations and interaction with the wall impedances.

  5. Effect of shrink fits on threshold speeds of rotordynamic instability

    E-Print Network [OSTI]

    Mir, MD. Mofazzal Hossain

    2001-01-01T23:59:59.000Z

    . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 CHAPTER IV TEST APPARATUS . . . . 13 CHAPTER V RESULTS AND DISCUSSION . . . 17 17 30 42 42 47 5. 1 Rap Test. . 5. 2 Running Test 5. 3 Modeling and the Prcdiction of Threshold Speed of Instability.... . . . . . . . . . . . , . . . . . . . . . . . 5. 3. 1 Matching the Base Case. 5. 3. 2 Gunter's Prediction Using C, q 5. 3. 3 Modeling and Prediction of the Threshold Speed Using the XLTRC Code. . . . 51 5. 4 Prediction of the Onset Speed of Instability for a Tight Inteiference Fit...

  6. Strange Attractors Characterizing the Osmotic Instability

    E-Print Network [OSTI]

    Stephan I. Tzenov

    2014-06-04T23:59:59.000Z

    In the present paper a simple dynamical model for computing the osmotically driven fluid flow in a variety of complex, non equilibrium situations is derived from first principles. Using the Oberbeck-Boussinesq approximation, the basic equations describing the process of forward osmosis have been obtained. It has been shown that these equations are very similar to the ones used to model the free Rayleigh-Benard convection. The difference is that while in the case of thermal convection the volume expansion is driven by the coefficient of thermal expansion, the key role for the osmotic instability is played by the coefficient of isothermal compressibility. In addition, it has been shown that the osmotic process represents a propagation of standing waves with time-dependent amplitudes and phase velocity, which equals the current velocity of the solvent passing through the semi-permeable membrane. The evolution of the amplitudes of the osmotic waves is exactly following the dynamics of a strange attractor of Lorenz type with corresponding control parameters.

  7. The (In)Stability of Planetary Systems

    E-Print Network [OSTI]

    Rory Barnes; Thomas Quinn

    2004-01-09T23:59:59.000Z

    We present results of numerical simulations which examine the dynamical stability of known planetary systems, a star with two or more planets. First we vary the initial conditions of each system based on observational data. We then determine regions of phase space which produce stable planetary configurations. For each system we perform 1000 ~1 million year integrations. We examine upsilon And, HD83443, GJ876, HD82943, 47UMa, HD168443, and the solar system (SS). We find that the resonant systems, 2 planets in a first order mean motion resonance, (HD82943 and GJ876) have very narrow zones of stability. The interacting systems, not in first order resonance, but able to perturb each other (upsilon And, 47UMa, and SS) have broad regions of stability. The separated systems, 2 planets beyond 10:1 resonance, (we only examine HD83443 and HD168443) are fully stable. Furthermore we find that the best fits to the interacting and resonant systems place them very close to unstable regions. The boundary in phase space between stability and instability depends strongly on the eccentricities, and (if applicable) the proximity of the system to perfect resonance. In addition to million year integrations, we also examined stability on ~100 million year timescales. For each system we ran ~10 long term simulations, and find that the Keplerian fits to these systems all contain configurations which may be regular on this timescale.

  8. The ecoresponsive genome of Daphnia pulex

    SciTech Connect (OSTI)

    Colbourne, John K.; Pfrender, Michael E.; Gilbert, Donald; Thomas, W. Kelley; Tucker, Abraham; Oakley, Todd H.; Tokishita, Shinichi; Aerts, Andrea; Arnold, Georg J.; Basu, Malay Kumar; Bauer, Darren J.; Caceres, Carla E.; Carmel, Liran; Casola, Claudio; Choi, Jeong-Hyeon; Detter, John C.; Dong, Qunfeng; Dusheyko, Serge; Eads, Brian D.; Frohlich, Thomas; Geiler-Samerotte, Kerry A.; Gerlach, Daniel; Hatcher, Phil; Jogdeo, Sanjuro; Krijgsveld, Jeroen; Kriventseva, Evgenia V; Kültz, Dietmar; Laforsch, Christian; Lindquist, Erika; Lopez, Jacqueline; Manak, Robert; Muller, Jean; Pangilinan, Jasmyn; Patwardhan, Rupali P.; Pitluck, Samuel; Pritham, Ellen J.; Rechtsteiner, Andreas; Rho, Mina; Rogozin, Igor B.; Sakarya, Onur; Salamov, Asaf; Schaack, Sarah; Shapiro, Harris; Shiga, Yasuhiro; Skalitzky, Courtney; Smith, Zachary; Souvorov, Alexander; Sung, Way; Tang, Zuojian; Tsuchiya, Dai; Tu, Hank; Vos, Harmjan; Wang, Mei; Wolf, Yuri I.; Yamagata, Hideo; Yamada, Takuji; Ye, Yuzhen; Shaw, Joseph R.; Andrews, Justen; Crease, Teresa J.; Tang, Haixu; Lucas, Susan M.; Robertson, Hugh M.; Bork, Peer; Koonin, Eugene V.; Zdobnov, Evgeny M.; Grigoriev, Igor V.; Lynch, Michael; Boore, Jeffrey L.

    2011-02-04T23:59:59.000Z

    This document provides supporting material related to the sequencing of the ecoresponsive genome of Daphnia pulex. This material includes information on materials and methods and supporting text, as well as supplemental figures, tables, and references. The coverage of materials and methods addresses genome sequence, assembly, and mapping to chromosomes, gene inventory, attributes of a compact genome, the origin and preservation of Daphnia pulex genes, implications of Daphnia's genome structure, evolutionary diversification of duplicated genes, functional significance of expanded gene families, and ecoresponsive genes. Supporting text covers chromosome studies, gene homology among Daphnia genomes, micro-RNA and transposable elements and the 46 Daphnia pulex opsins. 36 figures, 50 tables, 183 references.

  9. Particle Acceleration in Relativistic Jets due to Weibel Instability

    E-Print Network [OSTI]

    K. -I. Nishikawa; P. Hardee; G. Richardson; R. Preece; H. Sol; G. J. Fishman

    2003-06-04T23:59:59.000Z

    Shock acceleration is an ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, two-streaming instability, and the Weibel instability) created in the shocks are responsible for particle (electron, positron, and ion) acceleration. Using a 3-D relativistic electromagnetic particle (REMP) code, we have investigated particle acceleration associated with a relativistic jet front propagating through an ambient plasma with and without initial magnetic fields. We find only small differences in the results between no ambient and weak ambient magnetic fields. Simulations show that the Weibel instability created in the collisionless shock front accelerates particles perpendicular and parallel to the jet propagation direction. While some Fermi acceleration may occur at the jet front, the majority of electron acceleration takes place behind the jet front and cannot be characterized as Fermi acceleration. The simulation results show that this instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields, which contribute to the electron's transverse deflection behind the jet head. The ``jitter'' radiation (Medvedev 2000) from deflected electrons has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants.

  10. E-Print Network 3.0 - applying whole-genome studies Sample Search...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    (Lec 19) Picture Copyright: AccessExcellence @ the National Museum of Health Summary: Genomics Comparison of whole genomes. - Whole genome sequencing - Whole genome annotation &...

  11. 10. international mouse genome conference

    SciTech Connect (OSTI)

    Meisler, M.H.

    1996-12-31T23:59:59.000Z

    Ten years after hosting the First International Mammalian Genome Conference in Paris in 1986, Dr. Jean-Louis Guenet presided over the Tenth Conference at the Pasteur Institute, October 7--10, 1996. The 1986 conference was a satellite to the Human Gene Mapping Workshop and had approximately 50 attendees. The 1996 meeting was attended by 300 scientists from around the world. In the interim, the number of mapped loci in the mouse increased from 1,000 to over 20,000. This report contains a listing of the program and its participants, and two articles that review the meeting and the role of the laboratory mouse in the Human Genome project. More than 200 papers were presented at the conference covering the following topics: International mouse chromosome committee meetings; Mutant generation and identification; Physical and genetic maps; New technology and resources; Chromatin structure and gene regulation; Rate and hamster genetic maps; Informatics and databases; and Quantitative trait analysis.

  12. Genome Improvement at JGI-HAGSC

    SciTech Connect (OSTI)

    Grimwood, Jane: Schmutz, Jeremy, J.: Myers, Richard, M.

    2012-03-03T23:59:59.000Z

    Since the completion of the sequencing of the human genome, the JGI has rapidly expanded its scientific goals in several DOE mission-relevant areas. At the JGI-HAGSC, we have kept pace with this rapid expansion of projects with our focus on assessing, assembling, improving and finishing eukaryotic whole genome shotgun (WGS) projects for which the shotgun sequence is generated at the Production Genomic Facility (JGI-PGF). We follow this by combining the draft WGS with genomic resources generated at JGI-HAGSC or in collaborator laboratories (including BAC end sequences, genetic maps and FLcDNA sequences) to produce an improved draft sequence. For eukaryotic genomes important to the DOE mission, we then add further information from directed experiments to produce reference genomic sequences that are publicly available for any scientific researcher. Also, we have continued our program for producing BAC-based finished sequence, both for adding information to JGI genome projects and for small BAC-based sequencing projects proposed through any of the JGI sequencing programs. We have now built our computational expertise in WGS assembly and analysis and have moved eukaryotic genome assembly from the JGI-PGF to JGI-HAGSC. We have concentrated our assembly development work on large plant genomes and complex fungal and algal genomes.

  13. Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

    E-Print Network [OSTI]

    2011-01-01T23:59:59.000Z

    the soybean whole genome sequence. BMC Genomics 2010, 11:38.SNPs without a reference sequence. BMC Bioinformatics 2010,identification of repetitive sequences in plants. Nucleic

  14. Cassava Genomics: can genomic technology benefit smallholder farmers in Africa? (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Rounsley, Steve [University of Arizona

    2014-03-20T23:59:59.000Z

    Steve Rounsley of the University of Arizona speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  15. Initial sequencing and comparative analysis of the mouse genome

    E-Print Network [OSTI]

    Eddy, Sean

    Initial sequencing and comparative analysis of the mouse genome Mouse Genome Sequencing Consortium ........................................................................................................................................................................................................................... The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial

  16. Instability localized at the inner surface of an imploding spherical shell

    SciTech Connect (OSTI)

    Han, S.J.

    1983-01-01T23:59:59.000Z

    It is shown that in an imploding spherical shell the surface instabilities are of two different types. The first, which occurs at the outer surfaces, is the Rayleigh-Taylor instability. The second instability occurs at the inner surface. This latter instability is not as disruptive as R-T modes, but it has three basic properties which differ considerably from those of the R-T instability: (1) it is oscillatory at early times; (2) it grows faster in the long wavelength modes; (3) it depends on the equation of state. It is further shown that this new instability is driven by amplified sound waves in the shell.

  17. Keynote Presentation: Genome Beat (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Zimmer, Carl [New York Times

    2013-01-22T23:59:59.000Z

    Carl Zimmer, a reporter for the New York Times, speaks on "The Genome Beat," the opening keynote presentation at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

  18. Genome Announcement1 Draft genome sequence of the electricity producing3

    E-Print Network [OSTI]

    Hazen, Terry

    1 Genome Announcement1 2 Draft genome sequence of the electricity producing3 Thermincola potens of insoluble electron acceptors by model Gram-negative64 bacteria such as Geobacter or Shewanella species (4

  19. Keynote Presentation: Genome Beat (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Zimmer, Carl [New York Times] [New York Times

    2012-03-20T23:59:59.000Z

    Carl Zimmer, a reporter for the New York Times, speaks on "The Genome Beat," the opening keynote presentation at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

  20. Analyzing gigahertz bunch length instabilities with a digital signal processor

    SciTech Connect (OSTI)

    Stege, R.E. Jr.; Krejcik, P.; Minty, M.G.

    1992-11-01T23:59:59.000Z

    A bunch length instability, nicknamed the ``sawtooth``, because of its transient behavior, has been observed at high current running in the Stanford Linear Collider (SLC) electron damping ring. The incompatibility of this instability with successful SLC naming prompted its study using a high bandwidth real-time spectrum analyzer, the Tektronix 3052 digital signal processor (DSP) system. This device has been used to study energy ramping in storage rings but this is the first time it has been used to study transient instability phenomena. It is a particularly valuable tool for use in understanding non-linear, multiple frequency phenomena. The frequency range of this device has been extended through the use of radio frequency (RF) down converters. This paper describes the measurement setup and presents some of the results.

  1. Analyzing gigahertz bunch length instabilities with a digital signal processor

    SciTech Connect (OSTI)

    Stege, R.E. Jr.; Krejcik, P.; Minty, M.G.

    1992-11-01T23:59:59.000Z

    A bunch length instability, nicknamed the sawtooth'', because of its transient behavior, has been observed at high current running in the Stanford Linear Collider (SLC) electron damping ring. The incompatibility of this instability with successful SLC naming prompted its study using a high bandwidth real-time spectrum analyzer, the Tektronix 3052 digital signal processor (DSP) system. This device has been used to study energy ramping in storage rings but this is the first time it has been used to study transient instability phenomena. It is a particularly valuable tool for use in understanding non-linear, multiple frequency phenomena. The frequency range of this device has been extended through the use of radio frequency (RF) down converters. This paper describes the measurement setup and presents some of the results.

  2. Stability of sunspots to convective motions. I. Adiabatic instability

    SciTech Connect (OSTI)

    Moreno-Insertis, F.; Spruit, H.C. (Instituto de Astrofisica de Canarias, La Laguna (Spain); Max-Planck-Institut fuer Physik und Astrophysik, Garching (Germany, F.R.))

    1989-07-01T23:59:59.000Z

    For determining the adiabatic stability of a uniform vertical field in an arbitrary stratification it is sufficient to consider the limit of infinitesimal horizontal wavelength. It is shown how the behavior of the instability can be estimated qualitatively from the dependence of the equipartition field strength on depth. Modes are calculated numerically for analytic stratification models and for a detailed sunspot stratification, including the effects of partial ionization. It is concluded that for the observed field strengths of umbrae the stratification is indeed unstable, with a growth time of about 18 minutes. The unstable eigenfunctions have a maximum at about 2300 km below the surface of the umbra and are about 3900 km deep. Deeper layers may also be unstable depending on unknown details of the stratification. A connection between fluting instability and convective instability is noted. 37 refs.

  3. Diatom Genomics (2009 JGI User Meeting)

    ScienceCinema (OSTI)

    Ambrust, Ginger

    2011-04-25T23:59:59.000Z

    Ginger Armbrust from the University of Washington spoke about diatom genomics on March 26, 2009 at the DOE JGI User Meeting

  4. One Bacterial Cell, One Complete Genome

    E-Print Network [OSTI]

    Woyke, Tanja

    2010-01-01T23:59:59.000Z

    displacement amplification (MDA). Sanger-based finishingour single cell genome and exclude MDA-derived artifacts, wedisplacement amplification (MDA) [4,14], enabling random

  5. GENOMIC RESOURCES NOTE Genomic Resources Notes accepted 1 February 201331 March

    E-Print Network [OSTI]

    Rieseberg, Loren

    GENOMIC RESOURCES NOTE Genomic Resources Notes accepted 1 February 2013­31 March 2013 GENOMIC RESOURCES DEVELOPMENT CONSORTIUM,1 MATTHEW G. KING,2 SE´ BASTIEN RENAUT,3 LOREN H. RIESEBERG2,4 and HEATHER C. ROWE3 1 Molecular Ecology Resources Editorial Office, 6270 University Blvd, Vancouver, BC V6T 1Z4

  6. Genomic Responses to the Loss of LRPPRC MITOCHONDRIAL AND NUCLEAR GENOMIC RESPONSES TO LOSS OF LRPPRC

    E-Print Network [OSTI]

    Mootha, Vamsi K.

    of Systems Biology, Harvard Medical School, Boston, MA 02446 USA Running head: Genomic Responses to the LossGenomic Responses to the Loss of LRPPRC 1 MITOCHONDRIAL AND NUCLEAR GENOMIC RESPONSES TO LOSS with the loss of LRPPRC. Using this strategy, we discovered a specific role for LRPPRC in the expression of all

  7. Status of Plasma Electron Hose Instability Studies in FACET

    SciTech Connect (OSTI)

    Adli, Erik; /U. Oslo; England, Robert Joel; Frederico, Joel; Hogan, Mark; Li, Selina Zhao; Litos, Michael Dennis; Nosochkov, Yuri; /SLAC; An, Weiming; Mori, Warren; /UCLA

    2011-12-13T23:59:59.000Z

    In the FACET plasma-wakefield acceleration experiment a dense 23 GeV electron beam will interact with lithium and cesium plasmas, leading to plasma ion-channel formation. The interaction between the electron beam and the plasma sheath-electrons may lead to a fast growing electron hose instability. By using optics dispersion knobs to induce a controlled z-x tilt along the beam entering the plasma, we investigate the transverse behavior of the beam in the plasma as function of the tilt. We seek to quantify limits on the instability in order to further explore potential limitations on future plasma wakefield accelerators due to the electron hose instability. The FACET plasma-wakefield experiment at SLAC will study beam driven plasma wakefield acceleration. A dense 23 GeV electron beam will interact with lithium or cesium plasma, leading to plasma ion-channel formation. The interaction between the electron beam and the plasma sheath-electrons drives the electron hose instability, as first studied by Whittum. While Ref. [2] indicates the possibility of a large instability growth rate for typical beam and plasma parameters, other studies including have shown that several physical effects may mitigate the hosing growth rate substantially. So far there has been no quantitative benchmarking of experimentally observed hosing in previous experiments. At FACET we aim to perform such benchmarking by for example inducing a controlled z-x tilt along the beamentering the plasma, and observing the transverse behavior of the beam in the plasma as function. The long-term objective of these studies is to quantify potential limitations on future plasma wakefield accelerators due to the electron hose instability.

  8. Chapter 27 -- Breast Cancer Genomics, Section VI, Pathology and Biological Markers of Invasive Breast Cancer

    SciTech Connect (OSTI)

    Spellman, Paul T.; Heiser, Laura; Gray, Joe W.

    2009-06-18T23:59:59.000Z

    Breast cancer is predominantly a disease of the genome with cancers arising and progressing through accumulation of aberrations that alter the genome - by changing DNA sequence, copy number, and structure in ways that that contribute to diverse aspects of cancer pathophysiology. Classic examples of genomic events that contribute to breast cancer pathophysiology include inherited mutations in BRCA1, BRCA2, TP53, and CHK2 that contribute to the initiation of breast cancer, amplification of ERBB2 (formerly HER2) and mutations of elements of the PI3-kinase pathway that activate aspects of epidermal growth factor receptor (EGFR) signaling and deletion of CDKN2A/B that contributes to cell cycle deregulation and genome instability. It is now apparent that accumulation of these aberrations is a time-dependent process that accelerates with age. Although American women living to an age of 85 have a 1 in 8 chance of developing breast cancer, the incidence of cancer in women younger than 30 years is uncommon. This is consistent with a multistep cancer progression model whereby mutation and selection drive the tumor's development, analogous to traditional Darwinian evolution. In the case of cancer, the driving events are changes in sequence, copy number, and structure of DNA and alterations in chromatin structure or other epigenetic marks. Our understanding of the genetic, genomic, and epigenomic events that influence the development and progression of breast cancer is increasing at a remarkable rate through application of powerful analysis tools that enable genome-wide analysis of DNA sequence and structure, copy number, allelic loss, and epigenomic modification. Application of these techniques to elucidation of the nature and timing of these events is enriching our understanding of mechanisms that increase breast cancer susceptibility, enable tumor initiation and progression to metastatic disease, and determine therapeutic response or resistance. These studies also reveal the molecular differences between cancer and normal that may be exploited to therapeutic benefit or that provide targets for molecular assays that may enable early cancer detection, and predict individual disease progression or response to treatment. This chapter reviews current and future directions in genome analysis and summarizes studies that provide insights into breast cancer pathophysiology or that suggest strategies to improve breast cancer management.

  9. Universality of the Plastic Instability in Strained Amorphous Solids

    E-Print Network [OSTI]

    Ratul Dasgupta; Smarajit Karmakar; Itamar Procaccia

    2011-11-03T23:59:59.000Z

    By comparing the response to external strains in metallic glasses and in Lenard-Jones glasses we find a quantitative universality of the fundamental plastic instabilities in the athermal, quasistatic limit. Microscopically these two types of glasses are as different as one can imagine, the latter being determined by binary interactions, whereas the former by multiple interactions due to the effect of the electron gas that cannot be disregarded. In spite of this enormous difference the plastic instability is the same saddle-node bifurcation. As a result the statistics of stress and energy drops in the elasto-plastic steady state are universal, sharing the same system-size exponents.

  10. Acoustic stabilization of electric arc instabilities in nontransferred plasma torches

    SciTech Connect (OSTI)

    Rat, V.; Coudert, J. F. [CNRS, University of Limoges, SPTCS UMR6638, 123 Avenue A. Thomas, 87060 Limoges Cedex (France)

    2010-03-08T23:59:59.000Z

    Electric arc instabilities in dc plasma torches lead to nonhomogeneous treatments of nanosized solid particles or liquids injected within thermal plasma jets. This paper shows that an additional acoustic resonator mounted on the cathode cavity allows reaching a significant damping of these instabilities, particularly the Helmholtz mode of arc oscillations. The acoustic resonator is coupled with the Helmholtz resonator of the plasma torch limiting the amplitude of arc voltage variations. It is also highlighted that this damping is dependent on friction effects in the acoustic resonator.

  11. Nuclear-Coupled Flow Instabilities and Their Effects on Dryout

    SciTech Connect (OSTI)

    M. Ishii; X. Sunn; S. Kuran

    2004-09-27T23:59:59.000Z

    Nuclear-coupled flow/power oscillations in boiling water reactors (BWRs) are investigated experimentally and analytically. A detailed literature survey is performed to identify and classify instabilities in two-phase flow systems. The classification and the identification of the leading physical mechanisms of the two-phase flow instabilities are important to propose appropriate analytical models and scaling criteria for simulation. For the purpose of scaling and the analysis of the nonlinear aspects of the coupled flow/power oscillations, an extensive analytical modeling strategy is developed and used to derive both frequency and time domain analysis tools.

  12. Solar wind driven dust acoustic instability with Lorentzian kappa distribution

    SciTech Connect (OSTI)

    Arshad, Kashif [National Center for Physics (NCP), Quaid-i-Azam University Campus, Shahdra Valley Road, Islamabad 44000 (Pakistan) [National Center for Physics (NCP), Quaid-i-Azam University Campus, Shahdra Valley Road, Islamabad 44000 (Pakistan); Pakistan Institute of Engineering and Applied Sciences, P.O. Nilore, Islamabad and University of Wah, Wah Cantt 47040 (Pakistan); Ehsan, Zahida, E-mail: Ehsan.zahida@gmail.com [National Center for Physics (NCP), Quaid-i-Azam University Campus, Shahdra Valley Road, Islamabad 44000 (Pakistan) [National Center for Physics (NCP), Quaid-i-Azam University Campus, Shahdra Valley Road, Islamabad 44000 (Pakistan); Universita degli Studi del Molise, 86090 Pesche - IS (Italy); INFN Sezione di Napoli, 80126 Napoli (Italy); Department of Physics, COMSATS Institute of Information Technology (CIIT), Defence Road, Off Raiwind Road, Lahore 86090 (Pakistan); Khan, S. A. [National Center for Physics (NCP), Quaid-i-Azam University Campus, Shahdra Valley Road, Islamabad 44000 (Pakistan)] [National Center for Physics (NCP), Quaid-i-Azam University Campus, Shahdra Valley Road, Islamabad 44000 (Pakistan); Mahmood, S. [Theoretical Plasma Physics Division, PINSTEC, PO Box Nilore, Islamabad 44000 (Pakistan)] [Theoretical Plasma Physics Division, PINSTEC, PO Box Nilore, Islamabad 44000 (Pakistan)

    2014-02-15T23:59:59.000Z

    In a three species electron-ion-dust plasma following a generalized non-Maxwellian distribution function (Lorentzian or kappa), it is shown that a kinetic instability of dust-acoustic mode exists. The instability threshold is affected when such (quasineutral) plasma permeates through another static plasma. Such case is of interest when the solar wind is streaming through the cometary plasma in the presence of interstellar dust. In the limits of phase velocity of the waves larger and smaller than the thermal velocity of dust particles, the dispersion properties and growth rate of dust-acoustic mode are investigated analytically with validation via numerical analysis.

  13. Genome sequence of the Brown Norway rat yields insights into

    E-Print Network [OSTI]

    Pachter, Lior

    Genome sequence of the Brown Norway rat yields insights into mammalian evolution Rat Genome Norway (BN) rat strain. The sequence represents a high-quality `draft' covering over 90% of the genome

  14. ORIGINAL ARTICLE Comparative genomics of two newly isolated

    E-Print Network [OSTI]

    Alvarez-Cohen, Lisa

    ORIGINAL ARTICLE Comparative genomics of two newly isolated Dehalococcoides strains of Microbiology, Cornell University, Ithaca, NY, USA Comparative genomics of Dehalococcoides strains and an enrichment were performed using a microarray targeting genes from all available sequenced genomes

  15. Evolutionary Genomics of Life in (and from) the Sea

    E-Print Network [OSTI]

    Boore, Jeffrey L.

    2009-01-01T23:59:59.000Z

    291: 1304-1351. Table 1. Genomics information on the webLBNL-59356 Evolutionary Genomics of Life in (and from) thean engine for comparative genomics. The six largest centers

  16. Comparative genomics reveals evidence of marine adaptation in Salinispora species.

    E-Print Network [OSTI]

    Penn, Kevin; Jensen, Paul R

    2012-01-01T23:59:59.000Z

    Orcutt B, et al: Ecological genomics of marine roseobacters.1037-1042. Penn and Jensen BMC Genomics 2012, 13:86 http://and Jensen: Comparative genomics reveals evidence of marine

  17. Defining Genome Project Standards in a New Era of Sequencing

    SciTech Connect (OSTI)

    Chain, Patrick [DOE-JGI

    2009-05-27T23:59:59.000Z

    Patrick Chain of the DOE Joint Genome Institute gives a talk on behalf of the International Genome Sequencing Standards Consortium on the need for intermediate genome classifications between "draft" and "finished"

  18. Structural Genomics of Minimal Organisms: Pipeline and Results

    E-Print Network [OSTI]

    Kim, Sung-Hou

    2008-01-01T23:59:59.000Z

    of recombinant proteins. J. Struct. Funct. Genomics 5:69-74.proteins. J. Struct. Funct. Genomics 5:69-74. Oganesyan,Structural Genomics of Minimal Organisms: Pipeline and

  19. UV Decontamination of MDA Reagents for Single Cell Genomics

    E-Print Network [OSTI]

    Lee, Janey

    2011-01-01T23:59:59.000Z

    Reagents for Single Cell Genomics Janey Lee 1* , Damon TigheReagents for Single Cell Genomics Janey Lee 1 , Damon TigheAbstract Single cell genomics, the amplification and

  20. Phytozome: A Comparative Platform for Green Plant Genomics

    E-Print Network [OSTI]

    Goodstein, David M.

    2012-01-01T23:59:59.000Z

    a growing plant comparative genomics resource. Nucleic AcidsL.A. (2011) The Sol Genomics Network (solgenomics.net):for comparative plant genomics. Nucleic Acids Res, 36, D959-

  1. The Impact of Structural Genomics: Expectations and Outcomes

    E-Print Network [OSTI]

    Chandonia, John-Marc; Brenner, Steven E.

    2005-01-01T23:59:59.000Z

    Choi et al. , J Struct Funct Genomics 4, 31-4 (2003). H. M.Center for Structural Genomics, sequence families of unknownMCSG) Northeast Structural Genomics Consortium, Novel folds

  2. Target Selection and Deselection at the Berkeley Structural Genomics Center

    E-Print Network [OSTI]

    Chandonia, John-Marc; Kim, Sung-Hou; Brenner, Steven E.

    2005-01-01T23:59:59.000Z

    gene-set concept. Annu Rev Genomics Hum Genet 2000;1:99-116.SE. A tour of structural genomics. Nat Rev Genet 2001;2(10):M, Wang LK. Structural genomics: a pipeline for providing

  3. The common ground of genomics and systems biology

    E-Print Network [OSTI]

    Conesa, Ana; Mortazavi, Ali

    2014-01-01T23:59:59.000Z

    8/S2. Authors’ details Genomics of Gene Expression Lab,systems biology. Annu Rev. Genomics Hum. Genet 2001, 2:343-projection strategies. Genomics 2008, 92(6):373-83. 31.

  4. asian diploid genome: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    coverage, and guided by the reference genome, we used uniquely mapped for personal genomics. The completion of a highly refined, encyclopaedic human genome sequence1,2 was a...

  5. Genomic Sciences | Clean Energy | ORNL

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField8,Dist.Newof EnergyFundingGeneGenome Engineering with

  6. Transforming Wave Propagation in Layered Media via Instability-Induced Interfacial Wrinkling

    E-Print Network [OSTI]

    Rudykh, Stephan

    The ability to control wave propagation in highly deformable layered media with elastic instability-induced wrinkling of interfacial layers is presented. The onset of a wrinkling instability in initially straight interfacial ...

  7. Numerical Modeling of Cased-hole Instability in High Pressure and High Temperature Wells 

    E-Print Network [OSTI]

    Shen, Zheng 1983-

    2012-11-12T23:59:59.000Z

    of cemented sections in High Pressure High Temperature (HPHT) wells. The existing analysis shows that, in the perforation zones, casing/cement is subject to instability, particularly in the presence of cavities. This dissertation focuses on the instability...

  8. Nonsnaking doubly diffusive convectons and the twist instability Cdric Beaume, Edgar Knobloch, and Alain Bergeon

    E-Print Network [OSTI]

    Knobloch, Edgar

    Nonsnaking doubly diffusive convectons and the twist instability Cédric Beaume, Edgar Knobloch diffusive convectons and the twist instability C´edric Beaume,1,a) Edgar Knobloch,1,b) and Alain Bergeon2,c

  9. Crossflow instability in rotor-stator flows with throughflow , M.-P. Chauve

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Crossflow instability in rotor-stator flows with throughflow S. Poncet , M.-P. Chauve We study. As the axial velocity profiles exhibit inflexion points, this instability is of crossflow type. From

  10. Hydrodynamics and heat transfer during flow boiling instabilities in a single microchannel

    E-Print Network [OSTI]

    Aussillous, Pascale

    Hydrodynamics and heat transfer during flow boiling instabilities in a single microchannel July 2008 Keywords: Boiling Microchannels Visualisation Flow boiling instabilities Heat transfer a b intensification heat removal. Flow boiling heat transfer in microchannel geometry and the associated flow

  11. Filamentation instability of current-driven dust ion-acoustic waves in a collisional dusty plasma

    SciTech Connect (OSTI)

    Niknam, A. R. [Laser and Plasma Research Institute, Shahid Beheshti University, G.C., Tehran 19839-63113 (Iran, Islamic Republic of); Haghtalab, T.; Khorashadizadeh, S. M. [Physics Department, Birjand University, Birjand 97179-63384 (Iran, Islamic Republic of)

    2011-11-15T23:59:59.000Z

    A theoretical investigation has been made of the dust ion-acoustic filamentation instability in an unmagnetized current-driven dusty plasma by using the Lorentz transformation formulas. The effect of collision between the charged particles with neutrals and their thermal motion on this instability is considered. Developing the filamentation instability of the current-driven dust ion-acoustic wave allows us to determine the period and the establishment time of the filamentation structure and threshold for instability development.

  12. Comparative genomics analysis of Liberibacter species to elucidate pathogenesis and culturability

    E-Print Network [OSTI]

    Leonard, Michael T.; Fagen, Jennie R.; McCullough, Connor M.; Davis-Richardson, Austin G.; Davis, Michael J.; Triplett, Eric W.

    2014-01-01T23:59:59.000Z

    Vol. 1 (2014) Comparative genomics analysis of Liberibacterof citrus, comparative genomics of this strain with other

  13. SciTech Connect: Achievements of structural genomics

    Office of Scientific and Technical Information (OSTI)

    Achievements of structural genomics Citation Details In-Document Search Title: Achievements of structural genomics You are accessing a document from the Department of Energy's...

  14. SciTech Connect: Multiplex automated genome engineering

    Office of Scientific and Technical Information (OSTI)

    Multiplex automated genome engineering Citation Details In-Document Search Title: Multiplex automated genome engineering You are accessing a document from the Department of...

  15. Combining Functional and Structural Genomics to Sample the Essential...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Functional and Structural Genomics to Sample the Essential Burkholderia Structome. Combining Functional and Structural Genomics to Sample the Essential Burkholderia Structome....

  16. The Seattle Structure Genomics Center for Infectious Disease...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Seattle Structure Genomics Center for Infectious Disease (SSGCID). The Seattle Structure Genomics Center for Infectious Disease (SSGCID). Abstract: The NIAID-funded Seattle...

  17. DOE JGI Whole Genome Shotgun Sequencing, part 1

    ScienceCinema (OSTI)

    Miranda Harmon-Smith

    2010-09-01T23:59:59.000Z

    A Howard Hughes Medical Institute (HHMI) video production describing the Whole Genome Shotgun Sequencing process at the US Department of Energy's Joint Genome Institute (JGI).

  18. DOE JGI Whole Genome Shotgun Sequencing, part 3

    ScienceCinema (OSTI)

    Miranda Harmon-Smith

    2010-09-01T23:59:59.000Z

    A Howard Hughes Medical Institute (HHMI) video production describing the Whole Genome Shotgun Sequencing process at the US Department of Energy's Joint Genome Institute (JGI).

  19. DOE JGI Whole Genome Shotgun Sequencing, part 2

    ScienceCinema (OSTI)

    Miranda Harmon-Smith

    2010-09-01T23:59:59.000Z

    A Howard Hughes Medical Institute (HHMI) video production describing the Whole Genome Shotgun Sequencing process at the US Department of Energy's Joint Genome Institute (JGI).

  20. Comparative Omics-Driven Genome Annotation Refinement: Application...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Abstract: Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being...

  1. analysis incorporating genomic: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Theses and Dissertations Summary: ??Genome sequence analysis is central to todays genomics research, and sequence alignment and Single-Nucleotide Polymorphism (SNP) detection...

  2. atlantic salmon genome: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    maps of the Atlantic salmon (Salmo salar) genome derived from RAD sequencing BMC Genomics 2014, 15 Millar, Andrew J. 2 Sex Determination in Tasmanian Atlantic Salmon. Open...

  3. acyrthosiphon pisum genome: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2008-01-01 3 Genome Sequence of the Pea Aphid Acyrthosiphon The International Aphid Genomics Consortium" Physics Websites Summary: by anyone for any lawful purpose. Funding: Work...

  4. aspergillus genome database: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and avoid outdated data. Heiko Mller 11 Integrative database analysis in structural genomics CiteSeer Summary: Abstract (2 sentences) An important aspect of structural genomics...

  5. accelerated genome evolution: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Theses and Dissertations Summary: ??Genome sequence analysis is central to todays genomics research, and sequence alignment and Single-Nucleotide Polymorphism (SNP) detection...

  6. aphid genome absence: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topic Index 1 Genome Sequence of the Pea Aphid Acyrthosiphon The International Aphid Genomics Consortium" Physics Websites Summary: by anyone for any lawful purpose. Funding: Work...

  7. accurate structural genome: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    door de promotor: unknown authors 8 Protein structure prediction and structural genomics CiteSeer Summary: Genome sequencing projects are producing linear amino acid...

  8. af146527 genomic repeat: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    of Repeats, Signatures, and Patterns in Genomic Sequences Michael Robinson of genomics, proteomics, and many other "-omics," vast quantities of information are generated...

  9. artificial genome model: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Dimension Slatton, Clint 5 Genomic computing: explanatory modelling for functional genomics Richard J. Gilbert Computer Technologies and Information Sciences Websites Summary:...

  10. Uses of antimicrobial genes from microbial genome

    DOE Patents [OSTI]

    Sorek, Rotem; Rubin, Edward M.

    2013-08-20T23:59:59.000Z

    We describe a method for mining microbial genomes to discover antimicrobial genes and proteins having broad spectrum of activity. Also described are antimicrobial genes and their expression products from various microbial genomes that were found using this method. The products of such genes can be used as antimicrobial agents or as tools for molecular biology.

  11. Genome of Geobacter sulfurreducens: Metal Reduction

    E-Print Network [OSTI]

    Lovley, Derek

    and in the generation of electricity. G. sulfurreducens, a member of the - Proteobacteria and of the family GeobacterGenome of Geobacter sulfurreducens: Metal Reduction in Subsurface Environments B. A. Methe´,1 * K. Utterback,1 S. E. Van Aken,1 D. R. Lovley,2 C. M. Fraser1 The complete genome sequence of Geobacter

  12. Meeting report The changing face of genomics

    E-Print Network [OSTI]

    Kellis, Manolis

    , Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02138. MIT Computer Science the new challenges in genomics, particularly in the areas of gene regulation, cell dynamics, and genome evolution. (1) Regulation: Systematic discovery of all regulatory elements Given the primary sequence

  13. Genome Biology 2003, 4:R43 commentreviewsreportsdepositedresearchrefereedresearchinteractionsinformation

    E-Print Network [OSTI]

    Kellis, Manolis

    , Massachusetts Institute of Technology, Cambridge, MA 02139, USA. §Whitehead/MIT Center for Genome Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. ¶Department of Genome conserved word pairs associated with gene-expression changes in yeastsTranscriptional regulation

  14. Computational Identification of Operons in Microbial Genomes

    E-Print Network [OSTI]

    computational pipeline is proposed to find potential operons in microbial genomes. The algorithm relies activities and regulation, it is encouraged by selection. By group regu- lation of certain highly expressed expenditure. In most bacterial genomes, func- tionally coupled gene clusters are often regulated under

  15. Fungal biology: compiling genomes and exploiting them

    SciTech Connect (OSTI)

    Labbe, Jessy L [ORNL; Uehling, Jessie K [ORNL; Payen, Thibaut [INRA; Plett, Jonathan [University of Western Sydney, Australia

    2014-01-01T23:59:59.000Z

    The last 10 years have seen the cost of sequencing complete genomes decrease at an incredible speed. This has led to an increase in the number of genomes sequenced in all the fungal tree of life as well as a wide variety of plant genomes. The increase in sequencing has permitted us to study the evolution of organisms on a genomic scale. A number of talks during the conference discussed the importance of transposable elements (TEs) that are present in almost all species of fungi. These TEs represent an especially large percentage of genomic space in fungi that interact with plants. Thierry Rouxel (INRA, Nancy, France) showed the link between speciation in the Leptosphaeria complex and the expansion of TE families. For example in the Leptosphaeria complex, one species associated with oilseed rape has experienced a recent and massive burst of movement by a few TE families. The alterations caused by these TEs took place in discrete regions of the genome leading to shuffling of the genomic landscape and the appearance of genes specific to the species, such as effectors useful for the interactions with a particular plant (Rouxel et al., 2011). Other presentations showed the importance of TEs in affecting genome organization. For example, in Amanita different species appear to have been invaded by different TE families (Veneault-Fourrey & Martin, 2011).

  16. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

    SciTech Connect (OSTI)

    Hu, Tina T.; Pattyn, Pedro; Bakker, Erica G.; Cao, Jun; Cheng, Jan-Fang; Clark, Richard M.; Fahlgren, Noah; Fawcett, Jeffrey A.; Grimwood, Jane; Gundlach, Heidrun; Haberer, Georg; Hollister, Jesse D.; Ossowski, Stephan; Ottilar, Robert P.; Salamov, Asaf A.; Schneeberger, Korbinian; Spannagl, Manuel; Wang, Xi; Yang, Liang; Nasrallah, Mikhail E.; Bergelson, Joy; Carrington, James C.; Gaut, Brandon S.; Schmutz, Jeremy; Mayer, Klaus F. X.; Van de Peer, Yves; Grigoriev, Igor V.; Nordborg, Magnus; Weigel, Detlef; Guo, Ya-Long

    2011-04-29T23:59:59.000Z

    In our manuscript, we present a high-quality genome sequence of the Arabidopsis thaliana relative, Arabidopsis lyrata, produced by dideoxy sequencing. We have performed the usual types of genome analysis (gene annotation, dN/dS studies etc. etc.), but this is relegated to the Supporting Information. Instead, we focus on what was a major motivation for sequencing this genome, namely to understand how A. thaliana lost half its genome in a few million years and lived to tell the tale. The rather surprising conclusion is that there is not a single genomic feature that accounts for the reduced genome, but that every aspect centromeres, intergenic regions, transposable elements, gene family number is affected through hundreds of thousands of cuts. This strongly suggests that overall genome size in itself is what has been under selection, a suggestion that is strongly supported by our demonstration (using population genetics data from A. thaliana) that new deletions seem to be driven to fixation.

  17. Pinch instabilities in Taylor-Couette flow Dima Shalybkov*

    E-Print Network [OSTI]

    Pinch instabilities in Taylor-Couette flow Dima Shalybkov* A.F. Ioffe Institute for Physics and Technology, 194021 St. Petersburg, Russia Received 6 April 2005; published 19 January 2006 The linear. The destabilizing role of the azimuthal magnetic field is also well known in the plasma theory of pinch stabil- ity

  18. ACTIVE INSTABILITY CONTROL EFFECTIVENESS IN A LIQUID FUELED COMBUSTOR

    E-Print Network [OSTI]

    Lieuwen, Timothy C.

    ACTIVE INSTABILITY CONTROL EFFECTIVENESS IN A LIQUID FUELED COMBUSTOR ADAM COKER YEDIDIA NEUMEIER-fueled combustor that were performed to improve understanding of the factors limiting control performance. A set varied. They show that the combustor's nominal dynamics (i.e., without Received 23 March 2005; accepted 7

  19. Development/Plasticity/Repair Oculomotor Instabilities in Zebrafish Mutant belladonna

    E-Print Network [OSTI]

    Liu, Shih-Chii

    . Both OKR reversal and SO depend on vision and are contrast sensitive. We built a quantitative model optokinetic response; congenital nystagmus; oculomotor instability; achiasmatic; retinal ganglion cell axons by injecting li- pophilic tracer dyes revealed that all larvae with reversed OKR were achiasmatic (Rick et al

  20. Aliveness: Perceived Instability from a Passive Haptic Texture Rendering System

    E-Print Network [OSTI]

    Tan, Hong Z.

    Aliveness: Perceived Instability from a Passive Haptic Texture Rendering System Seungmoon Choi interacting with virtual textures rendered with a force-feedback haptic interface. Our work is aimed during our previous psychophysical experiments performed using a popular texture rendering method (spring

  1. Surfzone eddies in strong alongshore currents: Forced or Instabilities?

    E-Print Network [OSTI]

    Frandsen, Jannette B.

    Surfzone eddies in strong alongshore currents: Forced or Instabilities? Falk Feddersen Associate by surfzone 2D turbulent eddies, which have length-scales > the water depth. Our group's results regarding surfzone eddy-induced mixing learned from dye, drifter, theory, and modeling will be reviewed - however

  2. Modulational instability and solitons in nonlocal media with competing nonlinearities

    SciTech Connect (OSTI)

    Esbensen, B. K.; Bache, M.; Bang, O. [DTU Fotonik, Department of Photonics Engineering, Technical University of Denmark, DK-2800 Kgs. Lyngby (Denmark); Wlotzka, A. [Department of Physics, Institut fuer Theoretische Festkoerperphysik, University of Karlsruhe, D-76128 Karlsruhe (Germany); Krolikowski, W. [Laser Physics Centre, Research School of Physics and Engineering, Australian National University, Canberra, Australian Capital Territory 0200 (Australia)

    2011-11-15T23:59:59.000Z

    We investigate analytically and numerically propagation and spatial localization of light in nonlocal media with competing nonlinearities. In particular, we discuss conditions for the modulational instability of plane waves and formation of spatial solitons. We show that the competing focusing and defocusing nonlinearities enable coexistence of dark or bright spatial solitons in the same medium by varying the intensity of the beam.

  3. Adverse Tunnelling Conditions Arising from Slope Instabilities A Case History

    E-Print Network [OSTI]

    of the Hindustan-Tibet-Highway by a rock fall (LEFT). Rock slide at the dam site blocking the Satluj River (RIGHT) has been under con- struction. The project includes a 60.5 m high concrete gravity dam, an underground-side slopes. SURFACE INSTABILITIES Due to foliation parallel sliding planes and cross cutting orthogonal joint

  4. High Beta Observations of the Hot Electron Interchange Instability

    E-Print Network [OSTI]

    High Beta Observations of the Hot Electron Interchange Instability E.E. Ortiz, M.E. Mauel, D observed in high-beta plasma created in the Levitated Dipole Experiment (LDX). We have previously of anisotropic high beta equilibrium · Measuring Electrostatic Fluctuations · Hot Electron Interchange (HEI

  5. Buoyant melting instabilities beneath extending lithosphere: 1. Numerical models

    E-Print Network [OSTI]

    Tackley, Paul J.

    Buoyant melting instabilities beneath extending lithosphere: 1. Numerical models John W. Hernlund,1,2 Paul J. Tackley,1,3 and David J. Stevenson4 Received 18 November 2006; revised 18 October 2007 diffusely extending lithosphere is studied using numerical convection models covering a wide range

  6. PROGRESS IN EXPERIMENTAL STUDY OF CURRENT FILAMENTATION INSTABILITY*

    E-Print Network [OSTI]

    Brookhaven National Laboratory

    . Simulations were conducted with the particle-in-cell code QuickPIC for e- beam and plasma parameters of the instability. Preliminary results from phase one will be presented along with the progress and diagnostic the compression and ignition of the fuel pellet is accomplished in a single process. The ability to separate ICF

  7. Control of transversal instabilities in reaction-diffusion systems

    E-Print Network [OSTI]

    Sonja Molnos; Jakob Löber; Jan Frederik Totz; Harald Engel

    2015-01-15T23:59:59.000Z

    In two-dimensional reaction-diffusion systems, local curvature perturbations in the shape of traveling waves are typically damped out and disappear in the course of time. If, however, the inhibitor diffuses much faster than the activator, transversal instabilities can arise, leading from flat to folded, spatio-temporally modulated wave shapes and to spreading spiral turbulence. For experimentally relevant parameter values, the photosensitive Belousov-Zhabotinsky reaction (PBZR) does not exhibit transversal wave instabilities. Here, we propose a mechanism to artificially induce these instabilities via a wave shape dependent spatio-temporal feedback loop, and study the emerging wave patterns. In numerical simulations with the modified Oregonator model for the PBZR using experimentally realistic parameter values we demonstrate the feasibility of this control scheme. Conversely, in a piecewise-linear version of the FitzHugh-Nagumo model transversal instabilities and spiral turbulence in the uncontrolled system are shown to be suppressed in the presence of control, thereby stabilising flat wave propagation.

  8. Control and Protection Cooperation Strategy for Voltage Instability

    E-Print Network [OSTI]

    Chen, Zhe

    to be transmitted in the weak linked system. On the other hand, the backup protection relays on the transmissionControl and Protection Cooperation Strategy for Voltage Instability Zhou Liu Aalborg University zli are caused by unexpected backup relay operations due to low voltage or overload state caused by post fault

  9. Turing instability in reaction-diffusion systems with nonlinear diffusion

    SciTech Connect (OSTI)

    Zemskov, E. P., E-mail: zemskov@ccas.ru [Russian Academy of Sciences, Dorodnicyn Computing Center (Russian Federation)

    2013-10-15T23:59:59.000Z

    The Turing instability is studied in two-component reaction-diffusion systems with nonlinear diffusion terms, and the regions in parametric space where Turing patterns can form are determined. The boundaries between super- and subcritical bifurcations are found. Calculations are performed for one-dimensional brusselator and oregonator models.

  10. Effects of ionization on the collisional streaming instability

    SciTech Connect (OSTI)

    Petrovic, D.; Vranjes, J.; Poedts, S. [Center for Plasma Astrophysics, Katholieke Universiteit (KU) Leuven, Celestijnenlaan 200B, 3000 Leuven (Belgium) and Institute of Physics, P.O. Box 57, 11001 Belgrade (Serbia and Montenegro); Center for Plasma Astrophysics, Katholieke Universiteit (KU) Leuven, Celestijnenlaan 200B, 3000 Leuven (Belgium)

    2005-11-15T23:59:59.000Z

    The influence of inelastic collisions on the collisional streaming instability is studied. The dispersion equation of the system is derived in the regime of strongly magnetized electrons and magnetized ions. The linear stability of the system is investigated. The numerical results are applied to a laboratory argon plasma.

  11. Alfvénic instabilities driven by runaways in fusion plasmas

    SciTech Connect (OSTI)

    Fülöp, T. [Department of Applied Physics, Chalmers University of Technology, Göteborg (Sweden); Newton, S. [Euratom/CCFE Fusion Association, Culham Science Centre, Abingdon, Oxfordshire OX14 3DB (United Kingdom)

    2014-08-15T23:59:59.000Z

    Runaway particles can be produced in plasmas with large electric fields. Here, we address the possibility that such runaway ions and electrons excite Alfvénic instabilities. The magnetic perturbation induced by these modes can enhance the loss of runaways. This may have important implications for the runaway electron beam formation in tokamak disruptions.

  12. Combining Pattern Instability and Shape-Memory Hysteresis for Phononic

    E-Print Network [OSTI]

    Combining Pattern Instability and Shape-Memory Hysteresis for Phononic Switching Ji-Hyun Jang Received April 10, 2009 ABSTRACT We report a fully reversible and robust shape-memory effect in a two simulations correctly capture the three steps of the shape-memory cycle observed experimentally. Structures

  13. Kinematics of Nonlinearly Interacting MHD Instabilities in a Plasma

    SciTech Connect (OSTI)

    Hansen, Alexander K.

    2000-07-01T23:59:59.000Z

    Plasmas play host to a wide variety of instabilities. For example, tearing instabilities use finite plasma resistivity to exploit the free energy provided by plasma currents parallel to the magnetic field to alter the magnetic topology of the plasma through a process known as reconnection. These instabilities frequently make themselves known in magnetic confinement experiments such as tokamaks and reversed field pinches (RFPs). In RFP plasmas, in fact, several tearing instabilities (modes) are simultaneously active, and are of large amplitude. Theory predicts that in addition to interacting linearly with magnetic perturbations from outside the plasma, such as field errors or as resistive wall, the modes in the RFP can interact nonlinearly with each other through a three-wave interaction. In the current work investigations of both the linear (external) and nonlinear contributions to the kinematics of the tearing modes in the Madison Symmetric Torus (MST) RFP are reported Theory predicts that tearing modes will respond only to magnetic perturbations that are spatially resonant with them, and was supported by experimental work done on tokamak devices. The results in this work verified that the theory is still applicable to the RFP, in spite of its more complicated magnetic mode structure, involving perturbations of a single poloidal mode number.

  14. TAE SATURATION OF ALPHA PARTICLE DRIVEN INSTABILITY IN TFTR

    E-Print Network [OSTI]

    instabilities the evolution of the wave energy, WE (for Alfven-like waves, the wave energy is nearly equally comparable to the mode width and even to the radius and when the ensemble of particles has a broad energy divided between perturbed magnetic energy and wave kinetic energy so that WE = R d3rBB=4, where B

  15. RADIO EMISSION FROM INSTABILITIES IN SPACE PLASMAS: MARGINAL STABILITY,

    E-Print Network [OSTI]

    Melrose, Don

    I t RADIO EMISSION FROM INSTABILITIES IN SPACE PLASMAS: MARGINAL STABILITY, 4TOCHASTIC GROWTH emission, hich is an indirect emission process first discussed by Ginaburg and Zhe/eznyakoe, 9581, and electron cyclotron maser emission (ECME), which is a direct emission ess first discussed in the presently

  16. Three dimensional axisymmetric simulations of fluid instabilities in curved geometry

    E-Print Network [OSTI]

    Zhang, Yongmin

    refracts through the interface between two materials. Such an instability was predicted theoretically + g1 (6) 2 #12;( E)t +( Ev0)r +( Ev1)z +(pv0)r +(pv1)z = ; 1 r Ev0 ; 1 rpv0 + (g0v0 +g1v1): (7

  17. The influence of internal friction on rotordynamic instability 

    E-Print Network [OSTI]

    Srinivasan, Anand

    2004-09-30T23:59:59.000Z

    Internal friction has been known to be a cause of whirl instability in built-up rotors since the early 1900's. This internal damping tends to make the rotor whirl at shaft speeds greater than a critical speed, the whirl speed usually being equal...

  18. Effect of shrink fits on threshold speeds of rotordynamic instability 

    E-Print Network [OSTI]

    Al-Baz, Khalid A

    2001-01-01T23:59:59.000Z

    The purpose of this thesis is to study the effect of shrink fits on the threshold speeds of rotor instability. Shrink or press fit components in built-up rotors are known sources of internal friction damping. The internal friction damping increases...

  19. Evolution of shock instability in granular gases with viscoelastic collisions

    E-Print Network [OSTI]

    Nick Sirmas; Matei Radulescu

    2014-09-04T23:59:59.000Z

    Shocks in granular media have been shown to develop instabilities. We address the role that early stages of shock development have on this type of instability. We look at the evolution of shock waves driven by a piston in a dilute system of smooth inelastic disks, using both discrete-particle and continuum modelling. To mimic a realistic granular gas, viscoelastic collisions are approximated with an impact velocity threshold $u^*$ needed for inelastic collisions to occur. We show that behaviour of the shock evolution is dependent on the ratio of piston velocity to impact velocity threshold $u_p/u^*$, and the coefficient of restitution $\\varepsilon$. For $u_p/u^*=2.0$, we recover shock evolution behaving similar to that observed in purely inelastic media. This is characterized by a short period where the shock front pulls towards the piston before attaining a developed structure. No pullback is seen for $u_p/u^*=1.0$. Results show the onset of instability for these stronger shocks during this evolving stage. These results suggest that the early stages of shock evolution play an important role in the shock instability.

  20. Strategic Control of Transverse Jet Shear Layer Instabilities J. Davitian,

    E-Print Network [OSTI]

    M'Closkey, Robert T.

    jet in crossflow or transverse jet. Jet nozzles that are flush as well as elevated with respect indicate that the jet's shear layer transitions to global instability when the jet-to-crossflow velocity THE transverse jet or jet in crossflow (JICF) is a flowfield with widespread applications in energy

  1. Analysis of Instability in an Industrial Ammonia Reactor

    E-Print Network [OSTI]

    Skogestad, Sigurd

    Analysis of Instability in an Industrial Ammonia Reactor John C. Morud and Sigurd Skogestad Dept point for this study was an incident in an industrial plant, where the ammonia synthesis reactor became used to analyze the stability, but a more care@1 analysis for this reactor system reveals

  2. FARLEY-BUNEMAN INSTABILITY IN THE SOLAR CHROMOSPHERE

    SciTech Connect (OSTI)

    Gogoberidze, G.; Voitenko, Y.; Poedts, S.; Goossens, M. [CPA/K.U.Leuven, Celestijnenlaan 200B, 3001 Leuven (Belgium)

    2009-11-20T23:59:59.000Z

    The Farley-Buneman instability (FBI) is studied in the partially ionized plasma of the solar chromosphere taking into account the finite magnetization of the ions and Coulomb collisions. We obtain the threshold value for the relative velocity between ions and electrons necessary for the instability to develop. It is shown that Coulomb collisions play a destabilizing role in the sense that they enable the instability even in the regions where the ion magnetization is larger than unity. By applying these results to chromospheric conditions, we show that the FBI cannot be responsible for the quasi-steady heating of the solar chromosphere. However, we do not exclude the instability development locally in the presence of strong cross-field currents and/or strong small-scale magnetic fields. In such cases, FBI should produce locally small-scale, approx0.1-3 m, density irregularities in the solar chromosphere. These irregularities can cause scintillations of radio waves with similar wave lengths and provide a tool for remote chromospheric sensing.

  3. FLUCTUATIONS NEAR THE CONVECTIVE INSTABILITY IN A CHOLESTERIC LIQUID CRYSTAL

    E-Print Network [OSTI]

    Boyer, Edmond

    . For sufficiently strong heating, it is pos- sible for the buoyancy force to overcome the vis- cous shear forces convective pour une certaine valeur critique. A cause du couplage de modes induit par la force extérieure, la, drives the system into convective instability. It is found that, because of the mode coupling induced

  4. Instabilities in Molecular Dynamics Integrators used in Hybrid Monte Carlo Simulations

    E-Print Network [OSTI]

    B. Joo; UKQCD Collaboration

    2001-10-11T23:59:59.000Z

    We discuss an instability in the leapfrog integration algorithm, widely used in current Hybrid Monte Carlo (HMC) simulations of lattice QCD. We demonstrate the instability in the simple harmonic oscillator (SHO) system where it is manifest. We demonstrate the instability in HMC simulations of lattic QCD with dynamical Wilson-Clover fermions and discuss implications for future simulations of lattice QCD.

  5. Crossflow instability of finite Bdewadt flows: Transients and spiral waves Juan M. Lopez,1,a

    E-Print Network [OSTI]

    Lopez, John M.

    Crossflow instability of finite Bödewadt flows: Transients and spiral waves Juan M. Lopez,1,a is not robust, suffering crossflow instability to multiarmed spiral waves via a supercritical Hopf bifurcation as a canonical three- dimensional flow which exemplifies the crossflow instability.1­4 In this flow

  6. Genomic definition of species. Revision 2

    SciTech Connect (OSTI)

    Crkvenjakov, R.; Drmanac, R.

    1993-03-01T23:59:59.000Z

    A genome is the sum total of the DNA sequences in the cells of an individual organism. The common usage that species possess genomes comes naturally to biochemists, who have shown that all protein and nucleic acid molecules are at the same time species- and individual-specific, with minor individual variations being superimposed on a consensus sequence that is constant for a species. By extension, this property is attributed to the common features of DNA in the chromosomes of members of a given species and is called species genome. Our proposal for the definition of a biological species is as follows: A species comprises a group of actual and potential biological organisms built according to a unique genome program that is recorded, and at least in part expressed, in the structures of their genomic nucleic acid molecule(s), having intragroup sequence differences which can be fully interconverted in the process of organismal reproduction.

  7. Proteogenomics : applications of mass spectrometry at the interface of genomics and proteomics

    E-Print Network [OSTI]

    Castellana, Natalie

    2012-01-01T23:59:59.000Z

    of proteomics and genomics to unravel the specificities ofetry and comparative genomics to analyze multiple genomes,”genome,” Comp. Funct. Genomics, vol. 3, no. 3, pp. 244–253,

  8. Genome Structure Gallery from the Mycobacterium Tuberculosis Structual Genomics Consortium

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The TB Structural Genomics Consortium works with the structures of proteins from M. tuberculosis, analyzing these structures in the context of functional information that currently exists and that the Consortium generates. The database of linked structural and functional information constructed from this project will form a lasting basis for understanding M. tuberculosis pathogenesis and for structure-based drug design. The Consortium's structural and functional information is publicly available. The Structures Gallery makes more than 650 total structures available by PDB identifier. Some of these are not consortium targets, but all are viewable in 3D color and can be manipulated in various ways by Jmol, an open-source Java viewer for chemical structures in 3D from http://www.jmol.org/

  9. Genome resequencing in Populus: Revealing large-scale genome variation and implications on specialized-trait genomics

    SciTech Connect (OSTI)

    Muchero, Wellington [ORNL] [ORNL; Labbe, Jessy L [ORNL] [ORNL; Priya, Ranjan [University of Tennessee, Knoxville (UTK)] [University of Tennessee, Knoxville (UTK); DiFazio, Steven P [West Virginia University, Morgantown] [West Virginia University, Morgantown; Tuskan, Gerald A [ORNL] [ORNL

    2014-01-01T23:59:59.000Z

    To date, Populus ranks among a few plant species with a complete genome sequence and other highly developed genomic resources. With the first genome sequence among all tree species, Populus has been adopted as a suitable model organism for genomic studies in trees. However, far from being just a model species, Populus is a key renewable economic resource that plays a significant role in providing raw materials for the biofuel and pulp and paper industries. Therefore, aside from leading frontiers of basic tree molecular biology and ecological research, Populus leads frontiers in addressing global economic challenges related to fuel and fiber production. The latter fact suggests that research aimed at improving quality and quantity of Populus as a raw material will likely drive the pursuit of more targeted and deeper research in order to unlock the economic potential tied in molecular biology processes that drive this tree species. Advances in genome sequence-driven technologies, such as resequencing individual genotypes, which in turn facilitates large scale SNP discovery and identification of large scale polymorphisms are key determinants of future success in these initiatives. In this treatise we discuss implications of genome sequence-enable technologies on Populus genomic and genetic studies of complex and specialized-traits.

  10. Genome-Wide siRNA-Based Functional Genomics of Pigmentation Identifies Novel Genes and Pathways That Impact Melanogenesis in Human Cells

    E-Print Network [OSTI]

    2008-01-01T23:59:59.000Z

    siRNA-Based Functional Genomics of Pigmentation Identifiespoorly understood. Functional genomics based on RNA-mediatedof RNAi-based functional genomics to identify novel genes,

  11. Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts

    E-Print Network [OSTI]

    2006-01-01T23:59:59.000Z

    pI), CP000063 (plasmid AYWB-pII), CP000064 (plasmid AYWB-the other two plasmids (AYWB-pII and AYWB-pIV) were uniquebetween pII03 and ssb of AYWB-pII is similar to genes pI04,

  12. Genome Sequence Databases (Overview): Sequencing and Assembly

    SciTech Connect (OSTI)

    Lapidus, Alla L.

    2009-01-01T23:59:59.000Z

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  13. Taming of Modulation Instability by Spatio-Temporal Modulation of the Potential

    E-Print Network [OSTI]

    Kumar, S; Botey, M; Staliunas, K

    2015-01-01T23:59:59.000Z

    Spontaneous pattern formation in a variety of spatially extended nonlinear system always occurs through a modulation instability: homogeneous state of the system becomes unstable with respect to growing modulation modes. Therefore, the manipulation of the modulation instability is of primary importance in controlling and manipulating the character of spatial patterns initiated by that instability. We show that the spatio-temporal periodic modulation of the potential of the spatially extended system results in a modification of its pattern forming instability. Depending on the modulation character the instability can be partially suppressed, can change its spectrum (for instance the long wave instability can transform into short wave instability), can split into two, or can be completely eliminated. The latter result is of especial practical interest, as can be used to stabilize the intrinsically unstable system. The result bears general character, as it is shown here on a universal model of Complex Ginzburg-L...

  14. Automatic annotation of organellar genomes with DOGMA

    SciTech Connect (OSTI)

    Wyman, Stacia; Jansen, Robert K.; Boore, Jeffrey L.

    2004-06-01T23:59:59.000Z

    Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of extra-nuclear organellar (chloroplast and animal mitochondrial) genomes. It is a web-based package that allows the use of comparative BLAST searches to identify and annotate genes in a genome. DOGMA presents a list of putative genes to the user in a graphical format for viewing and editing. Annotations are stored on our password-protected server. Complete annotations can be extracted for direct submission to GenBank. Furthermore, intergenic regions of specified length can be extracted, as well the nucleotide sequences and amino acid sequences of the genes.

  15. An Integrated Program in Microbial Genome Sequencing and Analysis

    SciTech Connect (OSTI)

    Claire M. Fraser, Ph.D.; J.E. Eisen, Ph.D.; W. Nierman, Ph.D.; K. Nelson, Ph.D.; H. Tettelin, Ph.D.; J. Heidelberg, Ph.D.; O. White, Ph.D.; B. Methe, Ph.D.; N. El-Sayed, Ph.D.; S. Gill, Ph.D.; S. Peterson, Ph.D.; J. Quackenbush, Ph.D.; T. Read, Ph.D.

    2005-11-30T23:59:59.000Z

    Under this award, numerous genome sequences were generated, analyzed, published and made publicly available.

  16. THE CAMPAIGN FOR UC SANTA CRUZ THE GENOMICS

    E-Print Network [OSTI]

    California at Santa Cruz, University of

    THE CAMPAIGN FOR UC SANTA CRUZ THE GENOMICS INSTITUTE #12;OVERVIEW The UC Santa Cruz Genomics Institute provides the framework for the next great leap in the science of genomics. ensured it would genomic science and speed the benefits of discoveries that improve and save lives. Cancer, autoimmune

  17. Target selection and current status of structural genomics for the

    E-Print Network [OSTI]

    Babu, M. Madan

    33 Target selection and current status of structural genomics for the completed microbial genomes 3.2 Structural status of completed microbial genomes in the PDB................ 3.3 Metabolic pathways as targets for structural genomics.......................... 3.3.1 Glycolytic pathway

  18. Functional Genomics: It's All How You Read It

    E-Print Network [OSTI]

    Boguski, Mark S.

    Functional Genomics: It's All How You Read It Philip Hieter and Mark Boguski "Functional genomics to functional genomics? An informal poll of colleagues indicates that the term is widely used, but has many genomics websites that have sprung up over the last 12 months clearly demonstrates that interpretations

  19. Phylogenetics of modern birds in the era of genomics

    E-Print Network [OSTI]

    Edwards, Scott

    Review Phylogenetics of modern birds in the era of genomics Scott V. Edwards*, W. Bryan Jennings and maturation of the genomics era, the completion of the chicken genome and a suite of technologies that promise genomics strategies, including adoption of objective quality scores for sequence data, analysis

  20. APPLIED GENOMICS TECHNOLOGY CENTER www.agtc.med.wayne.edu

    E-Print Network [OSTI]

    Berdichevsky, Victor

    APPLIED GENOMICS TECHNOLOGY CENTER www.agtc.med.wayne.edu CURRENT SERVICES CONTACT INFORMATION Dr. Susan J. Land, Ph.D. Laboratory Director ABOUT THE FACILITY The Applied Genomics Technology Center (AGTC-of-the-art, fee-for-service genomics center that provides a wide range of genomic technologies to the medical

  1. Comparing Bacterial Genomes by Searching their Common Intervals

    E-Print Network [OSTI]

    Fertin, Guillaume

    Comparing Bacterial Genomes by Searching their Common Intervals S´ebastien Angibaud, Damien. Comparing bacterial genomes implies the use of a dedicated measure. It relies on comparing circular genomes genomes that takes into account duplications. Its application on a concrete case, comparing E. coli and V

  2. Initial sequencing and analysis of the human genome

    E-Print Network [OSTI]

    Eddy, Sean

    Initial sequencing and analysis of the human genome International Human Genome Sequencing. ............................................................................................................................................................................................................................................................................ The human genome holds an extraordinary trove of information about human development, physiology, medicine a draft sequence of the human genome. We also present an initial analysis of the data, describing some

  3. Genome Organization and Gene Expression Shape the Transposable Element Distribution

    E-Print Network [OSTI]

    Alvarez, Nadir

    Genome Organization and Gene Expression Shape the Transposable Element Distribution The distribution of transposable elements (TEs) in a genome reflects a balance between insertion rate and selection shaping the organization of genomes. Past research has shown that TEs tend to accumulate in genomic

  4. is a Bioinformatics Scientist at the Institute for Genomic

    E-Print Network [OSTI]

    Salzberg, Steven

    Mihai Pop is a Bioinformatics Scientist at the Institute for Genomic Research. He earned his PhD in Computer Science from Johns Hopkins University in 2000. His research interests include genome assembly and comparative genomics. Adam Phillippy is a Bioinformatics Software Engineer at The Institute for Genomic

  5. Genome-wide mapping and analysis of mammalian promoters

    E-Print Network [OSTI]

    Barrera, Leah Ortiz-Luis

    2007-01-01T23:59:59.000Z

    ed. Bioinformatics and Computational Biology Solutions usingfor computational biology and bioinformatics. Genome Biol

  6. Mapping the Human Reference Genome's Missing Sequence by Three-Way Admixture in Latino Genomes

    E-Print Network [OSTI]

    McCarroll, Steve

    ARTICLE Mapping the Human Reference Genome's Missing Sequence by Three-Way Admixture in Latino Genomes Giulio Genovese,1,2,3,* Robert E. Handsaker,2,3 Heng Li,2,3 Eimear E. Kenny,4,5,6,7,8 and Steven A. McCarroll1,2,3,* A principal obstacle to completing maps and analyses of the human genome involves

  7. Resonant Dampers for Parametric Instabilities in Gravitational Wave Detectors

    E-Print Network [OSTI]

    Gras, Slawek; Barsotti, Lisa; Evans, Matthew

    2015-01-01T23:59:59.000Z

    Advanced gravitational wave interferometric detectors will operate at their design sensitivity with nearly 1MW of laser power stored in the arm cavities. Such large power may lead to the uncontrolled growth of acoustic modes in the test masses due to the transfer of optical energy to the mechanical modes of the arm cavity mirrors. These parametric instabilities have the potential of significantly compromising the detector performance and control. Here we present the design of "acoustic mode dampers" that use the piezoelectric effect to reduce the coupling of optical to mechanical energy. Experimental measurements carried on an Advanced LIGO-like test mass shown a 10-fold reduction in the amplitude of several mechanical modes, thus suggesting that this technique can greatly mitigate the impact of parametric instabilities in advanced detectors.

  8. Instability-driven electromagnetic fields in coronal plasmas

    SciTech Connect (OSTI)

    Manuel, M. J.-E.; Li, C. K.; Séguin, F. H.; Sinenian, N.; Frenje, J. A.; Casey, D. T.; Petrasso, R. D. [Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)] [Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Hager, J. D.; Betti, R.; Hu, S. X.; Delettrez, J.; Meyerhofer, D. D. [Laboratory for Laser Energetics, University of Rochester, Rochester, New York, 14623 (United States)] [Laboratory for Laser Energetics, University of Rochester, Rochester, New York, 14623 (United States)

    2013-05-15T23:59:59.000Z

    Filamentary electromagnetic fields previously observed in the coronae of laser-driven spherical targets [F. H. Séguin et al., Phys. Plasma. 19, 012701 (2012)] have been further investigated in laser-irradiated plastic foils. Face-on proton-radiography provides an axial view of these filaments and shows coherent cellular structure regardless of initial foil-surface conditions. The observed cellular fields are shown to have an approximately constant scale size of ?210 ?m throughout the plasma evolution. A discussion of possible field-generation mechanisms is provided and it is demonstrated that the likely source of the cellular field structure is the magnetothermal instability. Using predicted temperature and density profiles, the fastest growing modes of this instability were found to be slowly varying in time and consistent with the observed cellular size.

  9. Instability-driven electromagnetic fields in coronal plasmas

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Manuel, M. J.-E.; Li, C. K.; Seguin, F. H.; Sinenian, N.; Frenje, J. A.; Casey, D. T.; Petrasso, R. D.; Hager, J. D.; Betti, R.; Hu, S. X.; Delettrez, J.; Meyerhofer, D. D.

    2013-01-01T23:59:59.000Z

    Filamentary electromagnetic fields previously observed in the coronae of laser-driven spherical targets [F. H. S#2;eguin et al., Phys. Plasma. 19, 012701 (2012)] have been further investigated in laser irradiated plastic foils. Face-on proton-radiography provides an axial view of these filaments and shows coherent cellular structure regardless of initial foil-surface conditions. The observed cellular fields are shown to have an approximately constant scale size of #2;210 lm throughout the plasma evolution. A discussion of possible field-generation mechanisms is provided and it is demonstrated that the likely source of the cellular field structure is the magnetothermal instability. Using predicted temperature and density profiles, the fastest growing modes of this instability were found to be slowly varying in time and consistent with the observed cellular size.

  10. Excitation of flow instabilities due to nonlinear scale invariance

    SciTech Connect (OSTI)

    Prasad Datta, Dhurjati, E-mail: dp-datta@yahoo.com [Department of Mathematics, University of North Bengal, Siliguri, West Bengal 734013 (India); Sen, Sudip [National Institute of Aerospace (NASA-LaRC), 100 Exploration Way, Hampton, Virginia 23666 (United States); College of William and Mary, Williamsburg, Virginia 23187 (United States)

    2014-05-15T23:59:59.000Z

    A novel route to instabilities and turbulence in fluid and plasma flows is presented in kinetic Vlasov-Maxwell model. New kind of flow instabilities is shown to arise due to the availability of new kinetic energy sources which are absent in conventional treatments. The present approach is based on a scale invariant nonlinear analytic formalism developed to address irregular motions on a chaotic attractor or in turbulence in a more coherent manner. We have studied two specific applications of this turbulence generating mechanism. The warm plasma Langmuir wave dispersion relation is shown to become unstable in the presence of these multifractal measures. In the second application, these multifractal measures are shown to induce naturally non-Gaussian, i.e., a stretched, Gaussian distribution and anomalous transport for tracer particles from the turbulent advection-diffusion transport equation in a Vlasov plasma flow.

  11. Supercritical Coulomb center and excitonic instability in graphene

    E-Print Network [OSTI]

    O. V. Gamayun; E. V. Gorbar; V. P. Gusynin

    2009-10-31T23:59:59.000Z

    It is well known that there are resonant states with complex energy for the supercritical Coulomb impurity in graphene. We show that opening of a quasiparticle gap decreases the imaginary part of energy, |ImE|, of these states and stabilizes the system. For gapless quasiparticles with strong Coulomb interaction in graphene, we solve the Bethe-Salpeter equation for the electron - hole bound state and show that it has a tachyonic solution for strong enough coupling \\alpha=e^2/\\kappa\\hbar v_F leading to instability of the system. In the random-phase approximation, the critical coupling is estimated to be \\alpha_c =1.62 and is an analogue of the critical charge in the Coulomb center problem. We argue that the excitonic instability should be resolved through the formation of an excitonic condensate and gap generation in the quasiparticle spectrum.

  12. Stabilization of beam-weibel instability by equilibrium density ripples

    SciTech Connect (OSTI)

    Mishra, S. K., E-mail: nishfeb@gmail.com; Kaw, Predhiman; Das, A.; Sengupta, S. [Institute for Plasma Research (IPR), Gandhinagar 382428 (India)] [Institute for Plasma Research (IPR), Gandhinagar 382428 (India); Ravindra Kumar, G. [Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005 (India)] [Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005 (India)

    2014-01-15T23:59:59.000Z

    In this paper, we present an approach to achieve suppression/complete stabilization of the transverse electromagnetic beam Weibel instability in counter streaming electron beams by modifying the background plasma with an equilibrium density ripple, shorter than the skin depth; this weakening is more pronounced when thermal effects are included. On the basis of a linear two stream fluid model, it is shown that the growth rate of transverse electromagnetic instabilities can be reduced to zero value provided certain threshold values for ripple parameters are exceeded. We point out the relevance of the work to recent experimental investigations on sustained (long length) collimation of fast electron beams and integral beam transport for laser induced fast ignition schemes, where beam divergence is suppressed with the assistance of carbon nano-tubes.

  13. Spacing of Kepler Planets: Sculpting by Dynamical Instability

    E-Print Network [OSTI]

    Pu, Bonan

    2015-01-01T23:59:59.000Z

    We study the orbital architecture of multi-planet systems detected by the \\Kepler transit mission using N-body simulations, focussing on the orbital spacing between adjacent planets in systems showing four or more transiting planets. We find that the observed spacings are tightly clustered around $12$ mutual Hill radii, when transit geometry and sensitivity limits are accounted for. In comparison, dynamical integrations reveal that the minimum spacing required for systems of similar masses to survive dynamical instability for as long as a billion years is, $\\sim 10$ if all orbits are circular and coplanar, and $\\sim 12$ if planetary orbits have eccentricities $\\sim 0.02$ (a value suggested by studies of planet transit-time-variations). This apparent coincidence, between the observed spacing and the theoretical stability threshold, leads us to propose that typical planetary systems were formed with even tighter spacing, but most, except for the widest ones, have undergone dynamical instability, and are pared d...

  14. Instability of superconducting state in Josephson tunnel junctions

    SciTech Connect (OSTI)

    Nevirkovets, I.P.; Rudenko, =.M.

    1984-02-01T23:59:59.000Z

    Experiments on low-resistance Josephson Sn--I--Sn tunnel junctions have shown the superconductor to exhibit an instability that manifests itself on the current--voltage characteristic (IVC) in the form of a jumplike decrease of the voltage when it reaches a value 2..delta../e. When a weak magnetic field H is applied parallel to the junction plane and suppresses the nonstationary Josephson effect, the negative-slope IVC section vanishes. The H-dependent instability-current component, as well as the dc component of the Josephson current near 2..delta../e, can be approximated by a function of H/sup -2/. The singularity observed is attributed to the presence of a maximum of the superconducting component, due to the Riedel singularity, at V = 2..delta../e.

  15. Instability-driven electromagnetic fields in coronal plasmas

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Manuel, M. J.-E.; Li, C. K.; Seguin, F. H.; Sinenian, N.; Frenje, J. A.; Casey, D. T.; Petrasso, R. D.; Hager, J. D.; Betti, R.; Hu, S. X.; et al

    2013-01-01T23:59:59.000Z

    Filamentary electromagnetic fields previously observed in the coronae of laser-driven spherical targets [F. H. S#2;eguin et al., Phys. Plasma. 19, 012701 (2012)] have been further investigated in laser irradiated plastic foils. Face-on proton-radiography provides an axial view of these filaments and shows coherent cellular structure regardless of initial foil-surface conditions. The observed cellular fields are shown to have an approximately constant scale size of #2;210 lm throughout the plasma evolution. A discussion of possible field-generation mechanisms is provided and it is demonstrated that the likely source of the cellular field structure is the magnetothermal instability. Using predicted temperature and densitymore »profiles, the fastest growing modes of this instability were found to be slowly varying in time and consistent with the observed cellular size.« less

  16. Turing Instabilities and Patterns Near a Hopf Bifurcation

    E-Print Network [OSTI]

    Rui Dilao

    2005-02-24T23:59:59.000Z

    We derive a necessary and sufficient condition for Turing instabilities to occur in two-component systems of reaction-diffusion equations with Neumann boundary conditions. We apply this condition to reaction-diffusion systems built from vector fields with one fixed point and a supercritical Hopf bifurcation. For the Brusselator and the Ginzburg-Landau reaction-diffusion equations, we obtain the bifurcation diagrams associated with the transition between time periodic solutions and asymptotically stable solutions (Turing patterns). In two-component systems of reaction-diffusion equations, we show that the existence of Turing instabilities is neither necessary nor sufficient for the existence of Turing pattern type solutions. Turing patterns can exist on both sides of the Hopf bifurcation associated to the local vector field, and, depending on the initial conditions, time periodic and stable solutions can coexist.

  17. Nonsnaking doubly diffusive convectons and the twist instability

    SciTech Connect (OSTI)

    Beaume, Cédric, E-mail: ced.beaume@gmail.com; Knobloch, Edgar, E-mail: knobloch@berkeley.edu [Department of Physics, University of California, Berkeley, California 94720 (United States)] [Department of Physics, University of California, Berkeley, California 94720 (United States); Bergeon, Alain, E-mail: alain.bergeon@imft.fr [Université de Toulouse, INPT, UPS, IMFT (Institut de Mécanique des Fluides de Toulouse), Allée Camille Soula, F-31400 Toulouse, France and CNRS, IMFT, F-31400 Toulouse (France)] [Université de Toulouse, INPT, UPS, IMFT (Institut de Mécanique des Fluides de Toulouse), Allée Camille Soula, F-31400 Toulouse, France and CNRS, IMFT, F-31400 Toulouse (France)

    2013-11-15T23:59:59.000Z

    Doubly diffusive convection in a three-dimensional horizontally extended domain with a square cross section in the vertical is considered. The fluid motion is driven by horizontal temperature and concentration differences in the transverse direction. When the buoyancy ratio N = ?1 and the Rayleigh number is increased the conduction state loses stability to a subcritical, almost two-dimensional roll structure localized in the longitudinal direction. This structure exhibits abrupt growth in length near a particular value of the Rayleigh number but does not snake. Prior to this filling transition the structure becomes unstable to a secondary twist instability generating a pair of stationary, spatially localized zigzag states. In contrast to the primary branch these states snake as they grow in extent and eventually fill the whole domain. The origin of the twist instability and the properties of the resulting localized structures are investigated for both periodic and no-slip boundary conditions in the extended direction.

  18. Transverse Mode Coupling Instability with chromaticity and space charge

    SciTech Connect (OSTI)

    Balbekov, V. [Fermi National Accelerator Laboratory, Batavia, IL (United States)

    2014-10-29T23:59:59.000Z

    Transverse mode coupling instability is considered in the paper at different bunch and wake shapes. Exact solution for “hollow” bunch is arrived at and used to develop a proper technique for more realistic distributions. The three-modes approach is proposed for arbitrary bunch with chromaticity included. It is shown that the TMCI threshold and rate depend only slightly on the bunch model used being rather sensitive to the wake shape. Resistive wall wake is considered in detail, and a comparison of the TMCI and collective mode instability with this wake is performed. Space charge tune shift of arbitrary value is included in the consideration providing a firm bridge between the known cases of absent and dominating space charge

  19. Theory and calculations of synchrotron instabilities and feedback-mechanism

    SciTech Connect (OSTI)

    Meijssen, T.E.M.

    1981-08-12T23:59:59.000Z

    The properties of the phenomenon synchrotron radiation are given with general theory on the basic processes and betatron and synchrotron oscillations. A more extended theoretical view at transverse instabilities and the influence of a damping feedback system are discussed. The longitudinal case is covered. For the calculations on the longitudinal case with M equally spaced pointbunches, with N electrons each, in the storage ring, the parasitic modes of the radio-frequency cavity were measured. A description of this is given. The values of damping rates of the longitudinal feedback system found, are as expected, but too low to damp the longitudinal instabilities calculated. This might be caused by the input data. The calculated growth rates are very sensitive to changes in frequency and width of the parasitic modes, which were measured under conditions differing slightly from the operating conditions.

  20. Collaborative Research: Instability and transport of laser beam in plasma

    SciTech Connect (OSTI)

    Rose, Harvey Arnold [New Mexico Consortium; Lushnikov, Pavel [University of New Mexico

    2014-11-18T23:59:59.000Z

    Our goal was to determine the onset of laser light scattering due to plasma wave instabilities. Such scatter is usually regarded as deleterious since laser beam strength is thereby diminished. While this kind of laser-plasma-instability (LPI) has long been understood for the case of coherent laser light, the theory of LPI onset for a laser beam with degraded coherence is recent. Such a laser beam fills plasma with a mottled intensity distribution, which has large fluctuations. The key question is: do the exceptionally large fluctuations control LPI onset or is it controlled by the relatively quiescent background laser intensity? We have answered this question. This is significant because LPI onset power in the former case is typically small compared to that of the latter. In addition, if large laser intensity fluctuations control LPI onset, then nonlinear effects become significant for less powerful laser beams than otherwise estimated.

  1. Laplace-Fourier analysis and instabilities of a gainy slab

    E-Print Network [OSTI]

    Hågenvik, Hans Olaf

    2015-01-01T23:59:59.000Z

    The idealization of monochromatic plane waves leads to considerable simplifications in the analysis of electromagnetic systems. However, for active systems this idealization may be dangerous due to the presence of growing waves. Here we consider a gainy slab, and use a realistic incident beam, which is both causal and has finite width. This clarifies some apparent paradoxes arising from earlier analyses of this setup. In general it turns out to be necessary to involve complex frequencies $\\omega$ and/or complex transversal wavenumbers $k_x$. Simultaneously real $\\omega$ and $k_x$ cannot describe amplified waves in a slab which is infinite in the transversal direction. We also show that the only possibility to have an absolute instability for a finite width beam, is if a normally incident plane wave would experience an instability.

  2. Superconducting instabilities of R-charged black branes

    E-Print Network [OSTI]

    Simon A. Gentle; Benjamin Withers

    2012-07-12T23:59:59.000Z

    We explore superconducting instabilities of black branes in SO(6) gauged supergravity at finite temperature and finite R-charge densities. We compute the critical temperatures for homogeneous neutral and superconducting instabilities in a truncation of 20 scalars and 15 gauge fields as a function of the chemical potentials conjugate to the three U(1) charges in SO(6). We find that despite the imbalance provided by multiple chemical potentials there is always at least one superconducting black brane branch, emerging at a temperature where the normal phase is locally thermodynamically stable. We emphasise that the three-equal charge solution, Reissner-Nordstrom, is subdominant to a thermodynamically unstable black brane at sufficiently low temperatures --- a feature which is hidden in an equal charge truncation.

  3. 1st Genomics-Bioinformatics Day on "Comparative Genomics" April 24th 2003 in the Medawar Building in the

    E-Print Network [OSTI]

    Goldschmidt, Christina

    1st Genomics-Bioinformatics Day on "Comparative Genomics" April 24th 2003 in the Medawar Building. There is a need, however, for researchers interested in genomics and bioinformatics to meet, so Jotun Hein, Richard Mott and Chris Ponting have organised the first Genomics/Bioinformatics day. It is our intention

  4. The Plant Genome [A Supplement to Crop Science] March 2008 No. 1 S-27 Genomic Origins of Potato

    E-Print Network [OSTI]

    Spooner, David

    The Plant Genome [A Supplement to Crop Science] March 2008 No. 1 S-27 Genomic Origins of Potato., and Shelley H. Jansky Abstract Chromosome pairing relationships within cultivated potato (Solanum tuberosum we reexamine potato genome hypotheses with the first phylogenetic analysis of all major genomes

  5. Accelerating Biofuel Feedstock Crop Improvement with Miscanthus Genomics (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Swaminathan, Kankshita [Energy Biosciences Institute

    2014-03-20T23:59:59.000Z

    Kankshita Swaminathan of the Energy Biosciences Institute speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  6. Genome Analyses and Supplement Data from the International Populus Genome Consortium (IPGC)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    International Populus Genome Consortium (IPGC)

    The sequencing of the first tree genome, that of Populus, was a project initiated by the Office of Biological and Environmental Research in DOE’s Office of Science. The International Populus Genome Consortium (IPGC) was formed to help develop and guide post-sequence activities. The IPGC website, hosted at the Oak Ridge National Laboratory, provides draft sequence data as it is made available from DOE Joint Genome Institute, genome analyses for Populus, lists of related publications and resources, and the science plan. The data are available at http://www.ornl.gov/sci/ipgc/ssr_resource.htm.

  7. Facilities and Equipment for Genomics/Comparative Functional Genomics at New York University

    SciTech Connect (OSTI)

    Lennie, Peter

    2006-06-29T23:59:59.000Z

    This award was for partial support for the renovation of space to house research laboratories and moveable scientific equipment for genomics/functional geonomics at New York University.

  8. Geometric Phase in Vacuum Instability:APPLICATIONS in Quantum Cosmology

    E-Print Network [OSTI]

    D. P. Datta

    1993-06-24T23:59:59.000Z

    Three different methods viz. i) a perturbative analysis of the Schr\\"odinger equation ii) abstract differential geometric method and iii) a semiclassical reduction of the Wheeler-Dewitt equation, relating Pancharatnam phase to vacuum instability are discussed. An improved semiclassical reduction is also shown to yield the correct zeroth order semicalssical Einstein equations with backreaction. This constitutes an extension of our earlier discussions on the topic

  9. Gradient instabilities of electromagnetic waves in Hall thruster plasma

    SciTech Connect (OSTI)

    Tomilin, Dmitry [Department of Electrophysics, Keldysh Research Centre, Moscow 125438 (Russian Federation)

    2013-04-15T23:59:59.000Z

    This paper presents a linear analysis of gradient plasma instabilities in Hall thrusters. The study obtains and analyzes the dispersion equation of high-frequency electromagnetic waves based on the two-fluid model of a cold plasma. The regions of parameters corresponding to unstable high frequency modes are determined and the dependence of the increments and intrinsic frequencies on plasma parameters is obtained. The obtained results agree with those of previously published studies.

  10. lincRNAs: Genomics, Evolution, and Mechanisms

    E-Print Network [OSTI]

    Ulitsky, Igor

    Long intervening noncoding RNAs (lincRNAs) are transcribed from thousands of loci in mammalian genomes and might play widespread roles in gene regulation and other cellular processes. This Review outlines the emerging ...

  11. First international E. coli genome meeting

    SciTech Connect (OSTI)

    Not Available

    1992-01-01T23:59:59.000Z

    This volume is a collection of abstracts of oral presentations and poster sessions of studies reported at the First International E. Coli Genome Meeting, held September 10-14, 1992 at the University of Wisconsin.

  12. First international E. coli genome meeting

    SciTech Connect (OSTI)

    Not Available

    1992-12-31T23:59:59.000Z

    This volume is a collection of abstracts of oral presentations and poster sessions of studies reported at the First International E. Coli Genome Meeting, held September 10-14, 1992 at the University of Wisconsin.

  13. Comparative genomics and bioenergetics Jose Castresana *

    E-Print Network [OSTI]

    Castresana, Jose

    Review Comparative genomics and bioenergetics Jose Castresana * European Molecular Biology conclusions about the phylogenetic distribution and evolution of bioenergetic pathways to be drawn conservation used by prokaryotes. In addition, a thorough phylogenetic analysis of other bioenergetic protein

  14. Webinar December 2: Materials Genome Initiative

    Broader source: Energy.gov [DOE]

    The Energy Department will present a live webinar entitled "Materials Genome Initiative" on Tuesday, December 2, from 12:00 to 1:00 p.m. Eastern Standard Time.

  15. Next-generation information systems for genomics 

    E-Print Network [OSTI]

    Mungall, Christopher

    2011-06-27T23:59:59.000Z

    The advent of next-generation sequencing technologies is transforming biology by enabling individual researchers to sequence the genomes of individual organisms or cells on a massive scale. In order to realize the ...

  16. DOE Joint Genome Institute 2008 Progress Report

    E-Print Network [OSTI]

    Gilbert, David

    2009-01-01T23:59:59.000Z

    Genomics of cellulosic biofuels. Nature, 454 (7206):841-845,2008 Termite Bellies and Biofuels (Published in Smithsonian,in the quest for viable biofuels. An estimated 10,000 marine

  17. Computational regulatory genomics : motifs, networks, and dynamics

    E-Print Network [OSTI]

    Kheradpour, Pouya

    2012-01-01T23:59:59.000Z

    Gene regulation, the process responsible for taking a static genome and producing the diversity and complexity of life, is largely mediated through the sequence specific binding of regulators. The short, degenerate nature ...

  18. Prokaryotic Genomes from Microbes Online Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Alm, Eric J.; Huang, Katherine H.; Price, Morgan N.; Koche, Richard P.; Keller, Keith; Dubchak, Inna L.; Arkin, Adam P.

    To describe the potential functions of genes, MicrobesOnline includes protein family analyses (from InterPro and COG), metabolic maps (from KEGG), links to research papers (from UniProt and PubMed), and operon predictions for every genome. To examine each gene's evolutionary history, MicrobesOnline includes precomputed phylogenetic trees for all the gene families. It displays gene trees with genomic context or it compares the gene tree to the species tree. The tools provided with MicrobesOnline allow users to: compute customized motifs, sequence alignments, and phylogenetic trees change expression patterns in metabolic maps annotate genes in various ways The database contains more than 430 genomes. A browse tree tool and a genome browser are available, along with specialized search capabilities. (Specialized Interface)

  19. Justice and the Human Genome Project

    SciTech Connect (OSTI)

    Murphy, T.F.; Lappe, M. [eds.] [eds.

    1992-12-31T23:59:59.000Z

    Most of the essays gathered in this volume were first presented at a conference, Justice and the Human Genome, in Chicago in early November, 1991. The goal of the, conference was to consider questions of justice as they are and will be raised by the Human Genome Project. To achieve its goal of identifying and elucidating the challenges of justice inherent in genomic research and its social applications the conference drew together in one forum members from academia, medicine, and industry with interests divergent as rate-setting for insurance, the care of newborns, and the history of ethics. The essays in this volume address a number of theoretical and practical concerns relative to the meaning of genomic research.

  20. Justice and the Human Genome Project

    SciTech Connect (OSTI)

    Murphy, T.F.; Lappe, M. (eds.)

    1992-01-01T23:59:59.000Z

    Most of the essays gathered in this volume were first presented at a conference, Justice and the Human Genome, in Chicago in early November, 1991. The goal of the, conference was to consider questions of justice as they are and will be raised by the Human Genome Project. To achieve its goal of identifying and elucidating the challenges of justice inherent in genomic research and its social applications the conference drew together in one forum members from academia, medicine, and industry with interests divergent as rate-setting for insurance, the care of newborns, and the history of ethics. The essays in this volume address a number of theoretical and practical concerns relative to the meaning of genomic research.