National Library of Energy BETA

Sample records for radiation-induced genomic instability

  1. DNA damage in cells exhibiting radiation-induced genomic instability

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

    Keszenman, Deborah J.; Kolodiuk, Lucia; Baulch, Janet E.

    2015-02-22

    Cells exhibiting radiation induced genomic instability exhibit varied spectra of genetic and chromosomal aberrations. Even so, oxidative stress remains a common theme in the initiation and/or perpetuation of this phenomenon. Isolated oxidatively modified bases, abasic sites, DNA single strand breaks and clustered DNA damage are induced in normal mammalian cultured cells and tissues due to endogenous reactive oxygen species generated during normal cellular metabolism in an aerobic environment. While sparse DNA damage may be easily repaired, clustered DNA damage may lead to persistent cytotoxic or mutagenic events that can lead to genomic instability. In this study, we tested the hypothesismore »that DNA damage signatures characterised by altered levels of endogenous, potentially mutagenic, types of DNA damage and chromosomal breakage are related to radiation-induced genomic instability and persistent oxidative stress phenotypes observed in the chromosomally unstable progeny of irradiated cells. The measurement of oxypurine, oxypyrimidine and abasic site endogenous DNA damage showed differences in non-double-strand breaks (DSB) clusters among the three of the four unstable clones evaluated as compared to genomically stable clones and the parental cell line. These three unstable clones also had increased levels of DSB clusters. The results of this study demonstrate that each unstable cell line has a unique spectrum of persistent damage and lead us to speculate that alterations in DNA damage signaling and repair may be related to the perpetuation of genomic instability.« less

  2. The influence of TRP53 in the dose response of radiation-induced apoptosis, DNA repair and genomic stability in murine haematopoietic cells

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

    Lemon, Jennifer A.; Taylor, Kristina; Verdecchia, Kyle; Phan, Nghi; Boreham, Douglas R.

    2014-01-01

    Apoptotic and DNA damage endpoints are frequently used as surrogate markers of cancer risk, and have been well-studied in the Trp53+/- mouse model. We report the effect of differing Trp53 gene status on the dose response of ionizing radiation exposures (0.01-2 Gy), with the unique perspective of determining if effects of gene status remain at extended time points. Here we report no difference in the dose response for radiation-induced DNA double-strand breaks in bone marrow and genomic instability (MN-RET levels) in peripheral blood, between wild-type (Trp53+/+) and heterozygous (Trp53+/-) mice. The dose response for Trp53+/+ mice showed higher initial levelsmore »of radiation-induced lymphocyte apoptosis relative to Trp53+/- between 0 and 1 Gy. Although this trend was observed up to 12 hours post-irradiation, both genotypes ultimately reached the same level of apoptosis at 14 hours, suggesting the importance of late-onset p53-independent apoptotic responses in this mouse model. Expected radiation-induced G1 cell cycle delay was observed in Trp53+/+ but not Trp53+/-. Although p53 has an important role in cancer risk, we have shown its influence on radiation dose response can be temporally variable. This research highlights the importance of caution when using haematopoietic endpoints as surrogates to extrapolate radiation-induced cancer risk estimation.« less

  3. The influence of TRP53 in the dose response of radiation-induced apoptosis, DNA repair and genomic stability in murine haematopoietic cells

    SciTech Connect (OSTI)

    Lemon, Jennifer A.; Taylor, Kristina; Verdecchia, Kyle; Phan, Nghi; Boreham, Douglas R.

    2014-01-01

    Apoptotic and DNA damage endpoints are frequently used as surrogate markers of cancer risk, and have been well-studied in the Trp53+/- mouse model. We report the effect of differing Trp53 gene status on the dose response of ionizing radiation exposures (0.01-2 Gy), with the unique perspective of determining if effects of gene status remain at extended time points. Here we report no difference in the dose response for radiation-induced DNA double-strand breaks in bone marrow and genomic instability (MN-RET levels) in peripheral blood, between wild-type (Trp53+/+) and heterozygous (Trp53+/-) mice. The dose response for Trp53+/+ mice showed higher initial levels of radiation-induced lymphocyte apoptosis relative to Trp53+/- between 0 and 1 Gy. Although this trend was observed up to 12 hours post-irradiation, both genotypes ultimately reached the same level of apoptosis at 14 hours, suggesting the importance of late-onset p53-independent apoptotic responses in this mouse model. Expected radiation-induced G1 cell cycle delay was observed in Trp53+/+ but not Trp53+/-. Although p53 has an important role in cancer risk, we have shown its influence on radiation dose response can be temporally variable. This research highlights the importance of caution when using haematopoietic endpoints as surrogates to extrapolate radiation-induced cancer risk estimation.

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

    SciTech Connect (OSTI)

    Marchetti, Francesco; Wyrobek, Andrew J.

    2009-01-18

    Exposure to ionizing radiation and other environmental agents can affect the genomic integrity of germ cells and induce adverse health effects in the progeny. Efficient DNA repair during gametogenesis and the early embryonic cycles after fertilization is critical for preventing transmission of DNA damage to the progeny and relies on maternal factors stored in the egg before fertilization. The ability of the maternal repair machinery to repair DNA damage in both parental genomes in the fertilizing egg is especially crucial for the fertilizing male genome that has not experienced a DNA repair-competent cellular environment for several weeks prior to fertilization. During the DNA repair-deficient period of spermatogenesis, DNA lesions may accumulate in sperm and be carried into the egg where, if not properly repaired, could result in the formation of heritable chromosomal aberrations or mutations and associated birth defects. Studies with female mice deficient in specific DNA repair genes have shown that: (i) cell cycle checkpoints are activated in the fertilized egg by DNA damage carried by the sperm; and (ii) the maternal genotype plays a major role in determining the efficiency of repairing genomic lesions in the fertilizing sperm and directly affect the risk for abnormal reproductive outcomes. There is also growing evidence that implicates DNA damage carried by the fertilizing gamete as a mediator of postfertilization processes that contribute to genomic instability in subsequent generations. Transgenerational genomic instability most likely involves epigenetic mechanisms or error-prone DNA repair processes in the early embryo. Maternal and embryonic DNA repair processes during the early phases of mammalian embryonic development can have far reaching consequences for the genomic integrity and health of subsequent generations.

  5. 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.; Garner, F.A.

    1996-12-01

    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.

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

    SciTech Connect (OSTI)

    Engelward, Bevin P

    2009-09-16

    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.

  7. Detection and Repair of Ionizing Radiation-Induced DNA Double Strand Breaks: New Developments in Nonhomologous End Joining

    SciTech Connect (OSTI)

    Wang, Chen [Departments of Biochemistry and Molecular Biology and Oncology, and Southern Alberta Cancer Research Institute, University of Calgary, Calgary (Canada)] [Departments of Biochemistry and Molecular Biology and Oncology, and Southern Alberta Cancer Research Institute, University of Calgary, Calgary (Canada); Lees-Miller, Susan P., E-mail: leesmill@ucalgary.ca [Departments of Biochemistry and Molecular Biology and Oncology, and Southern Alberta Cancer Research Institute, University of Calgary, Calgary (Canada)

    2013-07-01

    DNA damage can occur as a result of endogenous metabolic reactions and replication stress or from exogenous sources such as radiation therapy and chemotherapy. DNA double strand breaks are the most cytotoxic form of DNA damage, and defects in their repair can result in genome instability, a hallmark of cancer. The major pathway for the repair of ionizing radiation-induced DSBs in human cells is nonhomologous end joining. Here we review recent advances on the mechanism of nonhomologous end joining, as well as new findings on its component proteins and regulation.

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

    SciTech Connect (OSTI)

    Schild, David; Wiese, Claudia

    2009-10-15

    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.

  9. Low Dose Radiation-Induced Genome and Epigenome Instability Symposium and Epigenetic Mechanisms, DNA Repair, and Chromatin Symposium at the EMS 2008 Annual Meeting - October 2008

    SciTech Connect (OSTI)

    Morgan, William F.; Kovalchuk, Olga; Dolinoy, Dana C.; Dubrova, Yuri E.; Coleman, Matthew A.; Schär, Primo; Pogribny, Igor; Hendzel, Michael

    2010-02-19

    The Low Dose Radiation Symposium thoughtfully addressed ionizing radiation non-mutational but transmissable alterations in surviving cells. Deregulation of epigenetic processes has been strongly implicated in carcinogenesis, and there is increasing realization that a significant fraction of non-targeted and adaptive mechanisms in response to ionizing radiation are likely to be epigenetic in nature. Much remains to be learned about how chromatin and epigenetic regulators affect responses to low doses of radiation, and how low dose radiation impacts other epigenetic processes. The Epigenetic Mechanisms Symposium focused on on epigenetic mechanisms and their interplay with DNA repair and chromatin changes. Addressing the fact that the most well understood mediators of epigenetic regulation are histone modifications and DNA methylation. Low levels of radiation can lead to changes in the methylation status of certain gene promoters and the expression of DNA methyltransferases, However, epigenetic regulation can also involve changes in higher order chromosome structure.

  10. Radiation-induced mechanical property changes in filled rubber...

    Office of Scientific and Technical Information (OSTI)

    Radiation-induced mechanical property changes in filled rubber Citation Details In-Document Search Title: Radiation-induced mechanical property changes in filled rubber In a recent...

  11. 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 ...

  12. 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.

    2006-02-17

    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.

  13. Computer-aided detection of radiation-induced cerebral microbleeds on susceptibility-weighted MR images

    E-Print Network [OSTI]

    2013-01-01

    ynicl Computer-aided detection of radiation-induced cerebraladvantageous for the detection of radiation-induced CMBs,radiation-induced CMBs with low contrast is a further factor that complicates their detection.

  14. 17 August 2000 FEL 2000 1 Radiation Induced by Relativistic

    E-Print Network [OSTI]

    17 August 2000 FEL 2000 1 Radiation Induced by Relativistic Beams Passing Over a Diffraction 2000 FEL 2000 2 Outline · Spontaneous Smith-Purcell radiation (SPR) can be intense. · Data from the ATF. #12;17 August 2000 FEL 2000 3 Smith-Purcell radiation q v b Dispersion relation: l n c vl cos 1 cosn

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

    E-Print Network [OSTI]

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

    2014-01-01

    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 ...

  16. Radiation-induced decomposition of explosives under extreme conditions

    SciTech Connect (OSTI)

    Giefers, Hubertus; Pravica, Michael; Yang, Wenge; Liermann, Peter

    2008-11-03

    We present high-pressure and high temperature studies of the synchrotron radiation-induced decomposition of powder secondary high explosives pentaerythritol tetranitrate (PETN) and 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) using white beam synchrotron radiation at the 16 BM-B and 16 BM-D sectors of the HP-CAT beamline at the Advanced Photon Source. The radiation-induced decomposition rate TATB showed dramatic slowing with pressure up to 26.6 GPa (the highest pressure studied), implying a positive activation volume of the activated complex. The decomposition rate of PETN varied little with pressure up to 15.7 GPa (the highest pressure studied). Diffraction line intensities were measured as a function of time using energy-dispersive methods. By measuring the decomposition rate as a function of pressure and temperature, kinetic and other constants associated with the decomposition reactions were extracted.

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

    SciTech Connect (OSTI)

    Hartman, E. Frederick; Zarick, Thomas Andrew; Sheridan, Timothy J.; Preston, E.

    2013-05-01

    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.

  18. Measurements of prompt radiation induced conductivity of Kapton.

    SciTech Connect (OSTI)

    Preston, Eric F.; Zarick, Thomas Andrew; Sheridan, Timothy J.; Hartman, E. Frederick; Stringer, Thomas Arthur

    2010-10-01

    We performed measurements of the prompt radiation induced conductivity in thin samples of Kapton (polyimide) at the Little Mountain Medusa LINAC facility in Ogden, UT. Three mil samples were irradiated with a 0.5 {mu}s pulse of 20 MeV electrons, yielding dose rates of 1E9 to 1E10 rad/s. We applied variable potentials up to 2 kV across the samples and measured the prompt conduction current. Analysis rendered prompt conductivity coefficients between 6E-17 and 2E-16 mhos/m per rad/s, depending on the dose rate and the pulse width.

  19. Nature of Radiation-Induced Defects in Quartz

    E-Print Network [OSTI]

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

    2015-04-10

    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. Measurements of prompt radiation induced conductivity of alumina and sapphire.

    SciTech Connect (OSTI)

    Hartman, E. Frederick; Zarick, Thomas Andrew; Sheridan, Timothy J.; Preston, Eric F.

    2011-04-01

    We performed measurements of the prompt radiation induced conductivity in thin samples of Alumina and Sapphire at the Little Mountain Medusa LINAC facility in Ogden, UT. Five mil thick samples were irradiated with pulses of 20 MeV electrons, yielding dose rates of 1E7 to 1E9 rad/s. We applied variable potentials up to 1 kV across the samples and measured the prompt conduction current. Analysis rendered prompt conductivity coefficients between 1E10 and 1E9 mho/m/(rad/s), depending on the dose rate and the pulse width for Alumina and 1E7 to 6E7 mho/m/(rad/s) for Sapphire.

  1. Simulating and Detecting Radiation-Induced Errors for Onboard Machine Learning

    E-Print Network [OSTI]

    Simulating and Detecting Radiation-Induced Errors for Onboard Machine Learning Robert Granat, Kiri-based fault tolerance (ABFT) methods into onboard data analysis algorithms to detect radiation-induced errors for detecting and recovering from such errors. A common hardware technique for achieving radiation protection

  2. Mechanisms of radiation-induced neoplastic cell transformation

    SciTech Connect (OSTI)

    Yang, T.C.H.; Tobias, C.A.

    1984-04-01

    Studies with cultured mammalian cells demonstrated clearly that radiation can transform cells directly and can enhance the cell transformation by oncogenic DNA viruses. In general, high-LET heavy-ion radiation can be more effective than X and gamma rays in inducing neoplastic cell transformation. Various experimental results indicate that radiation-induced DNA damage, most likely double-strand breaks, is important for both the initiation of cell transformation and for the enhancement of viral transformation. Some of the transformation and enhancement lesions can be repaired properly in the cell, and the amount of irrepairable lesions produced by a given dose depends on the quality of radiation. An inhibition of repair processes with chemical agents can increase the transformation frequency of cells exposed to radiation and/or oncogenic viruses, suggesting that repair mechanisms may play an important role in the radiation transformation. The progression of radiation-transformed cells appears to be a long and complicated process that can be modulated by some nonmutagenic chemical agents, e.g., DMSO. Normal cells can inhibit the expression of transforming properties of tumorigenic cells through an as yet unknown mechanism. The progression and expression of transformation may involve some epigenetic changes in the irradiated cells. 38 references, 15 figures, 1 table.

  3. Radiation-Induced Notch Signaling in Breast Cancer Stem Cells

    SciTech Connect (OSTI)

    Lagadec, Chann; Vlashi, Erina; Alhiyari, Yazeed; Phillips, Tiffany M.; Bochkur Dratver, Milana; Pajonk, Frank

    2013-11-01

    Purpose: To explore patterns of Notch receptor and ligand expression in response to radiation that could be crucial in defining optimal dosing schemes for ?-secretase inhibitors if combined with radiation. Methods and Materials: Using MCF-7 and T47D breast cancer cell lines, we used real-time reverse transcription–polymerase chain reaction to study the Notch pathway in response to radiation. Results: We show that Notch receptor and ligand expression during the first 48 hours after irradiation followed a complex radiation dose–dependent pattern and was most pronounced in mammospheres, enriched for breast cancer stem cells. Additionally, radiation activated the Notch pathway. Treatment with a ?-secretase inhibitor prevented radiation-induced Notch family gene expression and led to a significant reduction in the size of the breast cancer stem cell pool. Conclusions: Our results indicate that, if combined with radiation, ?-secretase inhibitors may prevent up-regulation of Notch receptor and ligand family members and thus reduce the number of surviving breast cancer stem cells.

  4. 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)

    2012-09-01

    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.

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

    E-Print Network [OSTI]

    Niu, Yunyun

    Radiation-induced DNA damage is a precursor to mutagenesis and cytotoxicity. During radiotherapy, exposure of healthy tissues can lead to severe side effects. We explored the potential of mitochondrial SOD (MnSOD) gene ...

  6. Pressure-sensitive blackbody point radiation induced by infrared diode laser irradiation

    E-Print Network [OSTI]

    Cao, Wenwu

    Pressure-sensitive blackbody point radiation induced by infrared diode laser irradiation Feng Qin,1, by irradiation of well-matched infrared (IR) lasers upon the Yb3þ ions, ultrabroadband luminescence can

  7. The Contribution of Tissue Level Organization to Genomic Stability Following Low Dose/Low Dose Rate Gamma and Proton Irradiation

    SciTech Connect (OSTI)

    Cheryl G. Burrell, Ph.D.

    2012-05-14

    The formation of functional tissue units is necessary in maintaining homeostasis within living systems, with individual cells contributing to these functional units through their three-dimensional organization with integrin and adhesion proteins to form a complex extra-cellular matrix (ECM). This is of particular importance in those tissues susceptible to radiation-induced tumor formation, such as epithelial glands. The assembly of epithelial cells of the thyroid is critical to their normal receipt of, and response to, incoming signals. Traditional tissue culture and live animals present significant challenges to radiation exposure and continuous sampling, however, the production of bioreactor-engineered tissues aims to bridge this gap by improve capabilities in continuous sampling from the same functional tissue, thereby increasing the ability to extrapolate changes induced by radiation to animals and humans in vivo. Our study proposes that the level of tissue organization will affect the induction and persistence of low dose radiation-induced genomic instability. Rat thyroid cells, grown in vitro as 3D tissue analogs in bioreactors and as 2D flask grown cultures were exposed to acute low dose (1, 5, 10 and 200 cGy) gamma rays. To assess immediate (6 hours) and delayed (up to 30 days) responses post-irradiation, various biological endpoints were studied including cytogenetic analyses, apoptosis analysis and cell viability/cytotoxicity analyses. Data assessing caspase 3/7 activity levels show that, this activity varies with time post radiation and that, overall, 3D cultures display more genomic instability (as shown by the lower levels of apoptosis over time) when compared to the 2D cultures. Variation in cell viability levels were only observed at the intermediate and late time points post radiation. Extensive analysis of chromosomal aberrations will give further insight on the whether the level of tissue organization influences genomic instability patterns after low dose radiation exposure. Cells viability/cytotoxicity analysis data are currently being analyzed to determine how these endpoints are affected under our experimental conditions. The results from this study will be translatable to risk assessment for assigning limits to radiation workers, pre-dosing for more effective radiotherapy and the consequences of long duration space flight. The data from this study has been presented a various scientific meetings/workshops and a manuscript, containing the findings, is currently being prepared for publication. Due to unforeseen challenges in collecting the data and standardizing experimental procedures, the second and third aims have not been completed. However, attempts will be made, based on the availability of funds, to continue this project so that these aims can be satisfied.

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

    E-Print Network [OSTI]

    Yu, Peter K.N.

    brings potential hazards to normal tissues in radiotherapy, and imparts a higher risk from low-dose researches have been carried out on victims of atomic bomb explosions, occupational and accidental radiationMini-review Radiation-induced bystander effect: Early process and rapid assessment Hongzhi Wang

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

    E-Print Network [OSTI]

    Brenner, David Jonathan

    and carcinogenesis. At doses above 50 millisievert, the radiation- induced cancer risk can be estimated based, these irradiated cells. There is evidence that very low doses of -particles induced clastogenic responses by a particle (3, 5, 9). In CHO cells irradiated with low doses of particles where 1% of the nuclei were

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

    E-Print Network [OSTI]

    Brenner, David Jonathan

    Paper EXTRAPOLATING RADIATION-INDUCED CANCER RISKS FROM LOW DOSES TO VERY LOW DOSES David J are increased at low doses ( 10 mGy). Discussed here are the issues related to extrapolating radiation risks from low radiation doses to very low doses (

  11. Remote sensor response study in the regime of the microwave radiation-induced magnetoresistance oscillations

    SciTech Connect (OSTI)

    Ye, Tianyu; Mani, R. G. [Department of Physics and Astronomy, Georgia State University, Atlanta, Georgia 30303 (United States)] [Department of Physics and Astronomy, Georgia State University, Atlanta, Georgia 30303 (United States); Wegscheider, W. [Laboratorium für Festkörperphysik, ETH Zürich, 8093 Zürich (Switzerland)] [Laboratorium für Festkörperphysik, ETH Zürich, 8093 Zürich (Switzerland)

    2013-11-04

    A concurrent remote sensing and magneto-transport study of the microwave excited two dimensional electron system (2DES) at liquid helium temperatures has been carried out using a carbon detector to remotely sense the microwave activity of the 2D electron system in the GaAs/AlGaAs heterostructure during conventional magneto-transport measurements. Various correlations are observed and reported between the oscillatory magnetotransport and the remotely sensed reflection. In addition, the oscillatory remotely sensed signal is shown to exhibit a power law type variation in its amplitude, similar to the radiation-induced magnetoresistance oscillations.

  12. Stress-related phenomena in transient radiation-induced absorption in optical fibers

    SciTech Connect (OSTI)

    Looney, L.D.; Lyons, P.B.; Kelly, R.E.

    1988-01-01

    The optical properties of materials can be modified by exposure to radiation and research to investigate these radiation-induced phenomena has intensified over the last several decades. The advent of optical fiber technology and the many applications of optical fiber for information transmission have sharply increased the interest in these investigations. Optical fibers present a long optical transmission path and that path may traverse different adverse environments, including radiation areas. The long tranmission path provides increased potential for interactions between the optical information signal and the optical medium. 10 refs., 10 figs.

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

    SciTech Connect (OSTI)

    Azuddin, A. Yusof; Rahman, I. Abdul; Mohamed, F.; Siah, N. J.; Saadc, M.; Ismail, F.

    2014-09-03

    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.

  14. Sorafenib Enhances Radiation-Induced Apoptosis in Hepatocellular Carcinoma by Inhibiting STAT3

    SciTech Connect (OSTI)

    Huang, Chao-Yuan [Department of Oncology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan (China) [Department of Oncology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan (China); Department of Radiological Technology, Yuanpei University, Hsinchu, Taiwan (China); Lin, Chen-Si [School of Veterinary Medicine, National Taiwan University Hospital, Taipei, Taiwan (China)] [School of Veterinary Medicine, National Taiwan University Hospital, Taipei, Taiwan (China); Tai, Wei-Tien; Hsieh, Chi-Ying [Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan (China) [Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan (China); National Center of Excellence for Clinical Trial and Research, National Taiwan University Hospital, Taipei, Taiwan (China); Shiau, Chung-Wai [Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei, Taiwan (China)] [Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei, Taiwan (China); Cheng, Ann-Lii [Department of Oncology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan (China) [Department of Oncology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan (China); National Center of Excellence for Clinical Trial and Research, National Taiwan University Hospital, Taipei, Taiwan (China); Chen, Kuen-Feng, E-mail: kfchen1970@ntu.edu.tw [Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan (China) [Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan (China); National Center of Excellence for Clinical Trial and Research, National Taiwan University Hospital, Taipei, Taiwan (China)

    2013-07-01

    Purpose: Hepatocellular carcinoma (HCC) is one of the most common and lethal human malignancies. Lack of efficient therapy for advanced HCC is a pressing problem worldwide. This study aimed to determine the efficacy and mechanism of combined sorafenib and radiation therapy treatment for HCC. Methods and Materials: HCC cell lines (PLC5, Huh-7, Sk-Hep1, and Hep3B) were treated with sorafenib, radiation, or both, and apoptosis and signal transduction were analyzed. Results: All 4 HCC cell lines showed resistance to radiation-induced apoptosis; however, this resistance could be reversed in the presence of sorafenib. Inhibition of phospho-STAT3 was found in cells treated with sorafenib or sorafenib plus radiation and subsequently reduced the expression levels of STAT3-related proteins, Mcl-1, cyclin D1, and survivin. Silencing STAT3 by RNA interference overcame apoptotic resistance to radiation in HCC cells, and the ectopic expression of STAT3 in HCC cells abolished the radiosensitizing effect of sorafenib. Moreover, sorafenib plus radiation significantly suppressed PLC5 xenograft tumor growth. Conclusions: These results indicate that sorafenib sensitizes resistant HCC cells to radiation-induced apoptosis via downregulating phosphorylation of STAT3 in vitro and in vivo.

  15. Repair of radiation-induced heat-labile sites is independent of DNA-PKcs, XRCC1 or PARP

    SciTech Connect (OSTI)

    Stenerlöw, Bo; Karlsson, Karin H.; Radulescu, Irina; Rydberg, Bjorn; Stenerlow, Bo

    2008-04-29

    Ionizing radiation induces a variety of different DNA lesions: in addition to the most critical DNA damage, the DSB, numerous base alterations, SSBs and other modifications of the DNA double-helix are formed. When several non-DSB lesions are clustered within a short distance along DNA, or close to a DSB, they may interfere with the repair of DSBs and affect the measurement of DSB induction and repair. We have previously shown that a substantial fraction of DSBs measured by pulsed-field gel electrophoresis (PFGE) are in fact due to heat-labile sites (HLS) within clustered lesions, thus reflecting an artifact of preparation of genomic DNA at elevated temperature. To further characterize the influence of HLS on DSB induction and repair, four human cell lines (GM5758, GM7166, M059K, U-1810) with apparently normal DSB rejoining were tested for bi-phasic rejoining after gamma irradiation. When heat-released DSBs were excluded from the measurements the fraction of fast rejoining decreased to less than 50% of the total. However, neither the half-times of the fast (t{sub 1/2} = 7-8 min) or slow (t{sub 1/2} = 2.5 h) DSB rejoining were changed significantly. At t=0 the heat-released DSBs accounted for almost 40% of the DSBs, corresponding to 10 extra DSB/cell/Gy in the initial DSB yield. These heat-released DSBs were repaired within 60-90 min in all tested cells, including M059K cells treated with wortmannin or DNA-PKcs defect M059J cells. Furthermore, cells lacking XRCC1 or Poly(ADP-ribose) polymerase-1 (PARP-1) rejoined both total DSBs and heat-released DSBs similar to normal cells. In summary, the presence of heat-labile sites have a substantial impact on DSB induction yields and DSB rejoining rates measured by pulsed-field gel electrophoresis, and HLS repair is independent of DNA-PKcs, XRCC1 and PARP.

  16. Radiation-Induced Decomposition of PETN and TATB under Extreme Conditions

    SciTech Connect (OSTI)

    Giefers, Hubertus; Pravica, Michael

    2008-11-03

    We conducted a series of experiments investigating decomposition of secondary explosives PETN and TATB at varying static pressures and temperatures using synchrotron radiation. As seen in our earlier work, the decomposition rate of TATB at ambient temperature slows systematically with increasing pressure up to at least 26 GPa but varies little with pressure in PETN at ambient temperature up to 15.7 GPa, yielding important information pertaining to the activation complex volume in both cases. We also investigated the radiation-induced decomposition rate as a function of temperature at ambient pressure and 26 GPa for TATB up to 403 K, observing that the decomposition rate increases with increasing temperature as expected. The activation energy for the TATB reaction at ambient temperature was experimentally determined to be 16 {+-} 3 kJ/mol.

  17. Radiation induced leakage current and stress induced leakage current in ultra-thin gate oxides

    SciTech Connect (OSTI)

    Ceschia, M.; Paccagnella, A.; Cester, A.; Scarpa, A.; Ghidini, G.

    1998-12-01

    Low-field leakage current has been measured in thin oxides after exposure to ionizing radiation. This Radiation Induced Leakage Current (RILC) can be described as an inelastic tunneling process mediated by neutral traps in the oxide, with an energy loss of about 1 eV. The neutral trap distribution is influenced by the oxide field applied during irradiation, thus indicating that the precursors of the neutral defects are charged, likely being defects associated to trapped holes. The maximum leakage current is found under zero-field condition during irradiation, and it rapidly decreases as the field is enhanced, due to a displacement of the defect distribution across the oxide towards the cathodic interface. The RILC kinetics are linear with the cumulative dose, in contrast with the power law found on electrically stressed devices.

  18. Ionizing radiation induced leakage current on ultra-thin gate oxides

    SciTech Connect (OSTI)

    Scarpa, A.; Paccagnella, A.; Montera, F.; Ghibaudo, G.; Pananakakis, G.; Fuochi, P.G.

    1997-12-01

    MOS capacitors with a 4.4 nm thick gate oxide have been exposed to {gamma} radiation from a Co{sup 60} source. As a result, the authors have measured a stable leakage current at fields lower than those required for Fowler-Nordheim tunneling. This Radiation Induced Leakage Current (RILC) is similar to the usual Stress Induced Leakage Currents (SILC) observed after electrical stresses of MOS devices. They have verified that these two currents share the same dependence on the oxide field, and the RILC contribution can be normalized to an equivalent injected charge for Constant Current Stresses. They have also considered the dependence of the RILC from the cumulative radiation dose, and from the applied bias during irradiation, suggesting a correlation between RILC and the distribution of trapped holes and neutral levels in the oxide layer.

  19. Prompt radiation-induced conductivity in polyurethane foam and glass microballoons

    SciTech Connect (OSTI)

    Hartman, E. Frederick; Zarick, Thomas Andrew; Sheridan, Timothy J.; Preston, Eric F.

    2014-06-01

    We performed measurements and analyses of the prompt radiation-induced conductivity (RIC) in thin samples of polyurethane foam and glass microballoon foam at the Little Mountain Medusa LINAC facility in Ogden, UT. The RIC coefficient was non-linear with dose rate for polyurethane foam; however, typical values at 1E11 rad(si)/s dose rate was measured as 0.8E-11 mho/m/rad/s for 5 lb./cu ft. foam and 0.3E-11 mho/m/rad/s for 10 lb./cu ft. density polyurethane foam. For encapsulated glass microballoons (GMB) the RIC coefficient was approximately 1E-15 mho/m/rad/s and was not a strong function of dose rate.

  20. Endogenous retrovirus and radiation-induced leukemia in the RMF mouse

    SciTech Connect (OSTI)

    Tennant, R.W.; Boone, L.R.; Lalley, P.; Yang, W.K.

    1982-01-01

    The induction of myeloid leukemia in irradiated RFM/Un mice has been associated with retrovirus infection. However, two characteristics of this strain complicate efforts to define the role of the virus. This strain possesses only one inducible host range class of endogenous virus and a unique gene, in addition to the Fv-1/sup n/ locus, which specifically restricts exogenous infection by endogenous viruses. These characteristics possibly account for absence of recombinant viruses in this strain, even though virus is amply expressed during most of the animal's life span. We have examined further the distribution of retrovirus sequences and the chromosomal locus of the inducible virus in this strain. This report describes evidence for additional viral sequences in cells of a radiation-induced myeloid leukemia line and discusses the possible origin of these added copies.

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

    SciTech Connect (OSTI)

    Gary S. Was; Brian D. Wirth

    2011-05-29

    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.

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

    SciTech Connect (OSTI)

    Costes, Sylvain V; Chiolo, Irene; Pluth, Janice M.; Barcellos-Hoff, Mary Helen; Jakob, Burkhard

    2009-09-15

    DNA damage sensing proteins have been shown to localize to the sites of DSB within seconds to minutes following ionizing radiation (IR) exposure, resulting in the formation of microscopically visible nuclear domains referred to as radiation-induced foci (RIF). This review characterizes the spatio-temporal properties of RIF at physiological doses, minutes to hours following exposure to ionizing radiation, and it proposes a model describing RIF formation and resolution as a function of radiation quality and nuclear densities. Discussion is limited to RIF formed by three interrelated proteins ATM (Ataxia telangiectasia mutated), 53BP1 (p53 binding protein 1) and ?H2AX (phosphorylated variant histone H2AX). Early post-IR, we propose that RIF mark chromatin reorganization, leading to a local nuclear scaffold rigid enough to keep broken DNA from diffusing away, but open enough to allow the repair machinery. We review data indicating clear kinetic and physical differences between RIF emerging from dense and uncondensed regions of the nucleus. At later time post-IR, we propose that persistent RIF observed days following exposure to ionizing radiation are nuclear ?scars? marking permanent disruption of the chromatin architecture. When DNA damage is resolved, such chromatin modifications should not necessarily lead to growth arrest and it has been shown that persistent RIF can replicate during mitosis. Thus, heritable persistent RIF spanning over tens of Mbp may affect the transcriptome of a large progeny of cells. This opens the door for a non DNA mutation-based mechanism of radiation-induced phenotypes.

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

    SciTech Connect (OSTI)

    Lambert, Michele P.; Xiao Liqing; Nguyen, Yvonne; Kowalska, M. Anna; Poncz, Mortimer

    2011-08-01

    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.

  4. Mitigation and Treatment of Radiation-Induced Thoracic Injury With a Cyclooxygenase-2 Inhibitor, Celecoxib

    SciTech Connect (OSTI)

    Hunter, Nancy R.; Valdecanas, David [Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States)] [Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Liao Zhongxing [Division of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States)] [Division of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Milas, Luka [Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States)] [Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Thames, Howard D. [Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Texas (United States)] [Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Mason, Kathy A., E-mail: kmason@mdanderson.org [Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States)

    2013-02-01

    Purpose: To test whether a cyclooxygenase-2 inhibitor (celecoxib) could reduce mortality resulting from radiation-induced pneumonitis. Methods and Materials: Celecoxib was given to mice twice daily for 40 consecutive days starting on the day of local thoracic irradiation (LTI) or 40 or 80 days later. C3Hf/KamLaw mice were observed for morbidity, and time to death was determined. Results were analyzed using the Cox proportional hazards model. Results: Timing of celecoxib relative to LTI determined efficacy. A significant reduction in time to death was achieved only when celecoxib was started 80 days after LTI, corresponding to the time when pneumonitis is expressed. For these mice the reduction in mortality was quantified as a hazard ratio for mortality of treated vs untreated of 0.36 (95% confidence interval [CI] 0.24-0.53), thus significantly less than 1.0. Correspondingly, the median lethal dose for treated mice (12.9 Gy; 95% CI 12.55-13.25 Gy) was significantly (P=.026) higher than for untreated mice (12.4 Gy; 95% CI 12.2-12.65 Gy). Conclusions: Celecoxib significantly reduced lung toxicity when administered months after LTI when the deleterious effects of radiation were expressed. The schedule-dependent reduction in fatal pneumonitis suggests that celecoxib could be clinically useful by reintroduction of treatment months after completion of radiation therapy. These findings may be important for designing clinical trials using cyclooxygenase-2 inhibitors to treat radiation-induced lung toxicity as a complement to concurrent radiation therapy of lung cancers.

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

    E-Print Network [OSTI]

    Marchetti, Francesco

    2009-01-01

    Development and the DOE Low Dose Radiation Research Program.in vivo by low doses of gamma radiation. Rad Res 156, 324-7.

  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

    2009-01-01

    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. Analysis of Heterochromatin-Associated Genomic Instability

    E-Print Network [OSTI]

    Wang, Yehong

    2009-01-01

    of chromosome 1 in ovarian cancer patients. Cancer Detectdevelopment of breast and ovarian cancers, as well as otherJB (2003) Breast and ovarian cancer risks due to inherited

  8. Radiation-induced refraction artifacts in the optical CT readout of polymer gel dosimeters

    SciTech Connect (OSTI)

    Campbell, Warren G.; Jirasek, Andrew; Wells, Derek M.

    2014-11-01

    Purpose: The objective of this work is to demonstrate imaging artifacts that can occur during the optical computed tomography (CT) scanning of polymer gel dosimeters due to radiation-induced refractive index (RI) changes in polyacrylamide gels. Methods: A 1 L cylindrical polyacrylamide gel dosimeter was irradiated with 3 × 3 cm{sup 2} square beams of 6 MV photons. A prototype fan-beam optical CT scanner was used to image the dosimeter. Investigative optical CT scans were performed to examine two types of rayline bending: (i) bending within the plane of the fan-beam and (ii) bending out the plane of the fan-beam. To address structured errors, an iterative Savitzky–Golay (ISG) filtering routine was designed to filter 2D projections in sinogram space. For comparison, 2D projections were alternatively filtered using an adaptive-mean (AM) filter. Results: In-plane rayline bending was most notably observed in optical CT projections where rays of the fan-beam confronted a sustained dose gradient that was perpendicular to their trajectory but within the fan-beam plane. These errors caused distinct streaking artifacts in image reconstructions due to the refraction of higher intensity rays toward more opaque regions of the dosimeter. Out-of-plane rayline bending was observed in slices of the dosimeter that featured dose gradients perpendicular to the plane of the fan-beam. These errors caused widespread, severe overestimations of dose in image reconstructions due to the higher-than-actual opacity that is perceived by the scanner when light is bent off of the detector array. The ISG filtering routine outperformed AM filtering for both in-plane and out-of-plane rayline errors caused by radiation-induced RI changes. For in-plane rayline errors, streaks in an irradiated region (>7 Gy) were as high as 49% for unfiltered data, 14% for AM, and 6% for ISG. For out-of-plane rayline errors, overestimations of dose in a low-dose region (?50 cGy) were as high as 13 Gy for unfiltered data, 10 Gy for AM, and 3.1 Gy for ISG. The ISG routine also addressed unrelated artifacts that previously needed to be manually removed in sinogram space. However, the ISG routine blurred reconstructions, causing losses in spatial resolution of ?5 mm in the plane of the fan-beam and ?8 mm perpendicular to the fan-beam. Conclusions: This paper reveals a new category of imaging artifacts that can affect the optical CT readout of polyacrylamide gel dosimeters. Investigative scans show that radiation-induced RI changes can cause significant rayline errors when rays confront a prolonged dose gradient that runs perpendicular to their trajectory. In fan-beam optical CT, these errors manifested in two ways: (1) distinct streaking artifacts caused by in-plane rayline bending and (2) severe overestimations of opacity caused by rays bending out of the fan-beam plane and missing the detector array. Although the ISG filtering routine mitigated these errors better than an adaptive-mean filtering routine, it caused unacceptable losses in spatial resolution.

  9. Epidermal growth factor receptor expression in radiation-induced dog lung tumors by immunocytochemical localization

    SciTech Connect (OSTI)

    Leung, F.L.; Park, J.F.; Dagle, G.E.

    1993-06-01

    In studies to determine the role of growth factors in radiation-induced lung cancer, epidermal growth factor (EGFR) expression was examined by immunocytochemistry in 51 lung tumors from beagle dogs exposed to inhaled plutonium; 21 of 51 (41%) tumors were positive for EGFR. The traction of tumors positive for EGFR and the histological type of EGFR-positive tumors in the plutonium-exposed dogs were not different from spontaneous dog lung tumors, In which 36% were positive for EGFR. EGFR involvement in Pu-induced lung tumors appeared to be similar to that in spontaneous lung tumors. However, EGFR-positive staining was observed in only 1 of 16 tumors at the three lowest Pu exposure levels, compared to 20 of 35 tumors staining positive at the two highest Pu exposure levels. The results in dogs were in good agreement with the expression of EGFR reported in human non-small cell carcinoma of the lung, suggesting that Pu-induced lung tumors in the dog may be a suitable animal model to investigate the role of EGFR expression in lung carcinogenesis. In humans, EGFR expression in lung tumors has been primarily related to histological tumor types. In individual dogs with multiple primary lung tumors, the tumors were either all EGFR positive or EGFR negative, suggesting that EGFR expression may be related to the response of the individual dog as well as to the histological type of tumor.

  10. 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)

    2014-01-01

    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.

  11. Proteomic-based mechanistic investigation of low-dose radiation-induced cellular responses/effects

    SciTech Connect (OSTI)

    Chen, Xian

    2013-10-23

    The goal of our project is to apply our unique systems investigation strategy to reveal the molecular mechanisms underlying the radiation induction and transmission of oxidative damage, adaptive response, and bystander effect at low-doses. Beginning with simple in vitro systems such as fibroblast or epithelial pure culture, our amino acid-coded mass tagging (AACT) comparative proteomic platform will be used to measure quantitatively proteomic changes at high- or low-dose level with respect to their endogenous damage levels respectively, in which a broad range of unique regulated proteins sensitive to low-dose IR will be distinguished. To zoom in how these regulated proteins interact with other in the form of networks in induction/transmission pathways, these regulated proteins will be selected as baits for making a series of fibroblast cell lines that stably express each of them. Using our newly developed method of ?dual-tagging? quantitative proteomics that integrate the capabilities of natural complex expression/formation, simple epitope affinity isolation (not through tandem affinity purification or TAP), and ?in-spectra? AACT quantitative measurements using mass spectrometry (MS), we will be able to distinguish systematically interacting proteins with each bait in real time. Further, in addition to both proteome-wide (global differentially expressed proteins) and pathway-scale (bait-specific) profiling information, we will perform a computational network analysis to elucidate a global pathway/mechanisms underlying cellular responses to real-time low-dose IR. Similarly, we will extend our scheme to investigate systematically those induction/transmission pathways occurring in a fibroblast-epithelial interacting model in which the bystander cell (fibroblast) monitor the IR damage to the target cell (epithelial cell). The results will provide the proteome base (molecular mechanisms/pathways for signaling) for the low dose radiation-induced essential tissue environment interactions, including cell-cell, extracellular matrix and extracellular paracrine interactions.

  12. Radiatively Induced Type II seesaw and Vector-like 5/3 Charge Quarks

    E-Print Network [OSTI]

    R. Franceschini; R. N. Mohapatra

    2013-06-26

    Understanding small neutrino masses in type II seesaw models with TeV scale SM triplet Higgs bosons requires that its coupling with the standard model Higgs doublet H be dialed down to be order eV to KeV, which is a fine-tuning by a factor of $10^{-11}-10^{-8}$ with respect to the weak scale. We present a SUSY extension of the type II seesaw model where this dimensionful small coupling is radiatively induced, thus making its smallness natural. This model has an exotic vector-like quark doublet which contains a quark X with electric charge 5/3 and a top partner t'. We discuss in details the phenomenology of the model paying special attention to the consequences of the interactions of the the exotic heavy quarks and the scalars of the model. Implications for neutrinoless double beta decay and for the LHC experiments are discussed in detail. Remarkably, in this model both the seesaw triplet and the heavy quarks can manifest at colliders in a host of different signatures, including some that significantly differ from those of the minimal models. Depending on the choice of the hierarchy of couplings, the decay of the heavy quarks and of the seesaw triplet may be subject to bounds that can be tighter or looser than the bounds from standard LHC searches. Furthermore we point out a new short-distance contribution to neutrinoless double beta decay mediated by the simultaneous propagation of the type II triplet and exotic fermions. Remarkably this contribution to the neutrinoless double beta decay is parametrically quite independent from the scale of the generated neutrino mass.

  13. Formation mechanisms of precursors of radiation-induced color centers during fabrication of silica optical fiber preform

    SciTech Connect (OSTI)

    Tomashuk, A. L.; Zabezhailov, M. O.

    2011-04-15

    Samples in the form of transverse slices of rods and optical fiber preforms made from the high-hydroxyl KU-1 and low-hydroxyl KS-4V silica by the plasma outside deposition (POD) method are {gamma}-irradiated to a dose of {approx}1 MGy (SiO{sub 2}). Next, the radial dependences of the radiation-induced nonbridging oxygen hole center (NBOHC) and E'-center (three-coordinated silicon) in the samples are constructed by measuring the amplitudes of their 4.8 and 5.8 eV absorption bands, respectively. Based on the analysis of these radial dependences and considering the temperature and duration of the preirradiation heat treatment of the rods and preforms at the POD-installation, we determine the ratio of the oscillator strengths of the above bands and the microscopic thermoinduced processes occurring during preform fabrication and producing precursors of the radiation-induced NBOHC and E'-center. These processes are found to be associated with the escape of either H{sub 2} or H{sub 2}O from neighboring hydroxyl groups, and, therefore, can occur in high-hydroxyl silica only. It is concluded that enhancement of the radiation resistance of high-hydroxyl silica optical fibers requires decreasing the temperature and duration of the preform fabrication process, in particular, changing from the POD-technology to the low-temperature plasmachemical vapor deposition (PCVD) or surface PCVD (SPCVD)-technology.

  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.

    2012-03-03

    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. Analysis of single-event upset of magnetic tunnel junction used in spintronic circuits caused by radiation-induced current

    SciTech Connect (OSTI)

    Sakimura, N.; Nebashi, R.; Sugibayashi, T.; Natsui, M.; Hanyu, T.; Ohno, H.

    2014-05-07

    This paper describes the possibility of a switching upset of a magnetic tunnel junction (MTJ) caused by a terrestrial radiation-induced single-event-upset (SEU) current in spintronic integrated circuits. The current waveforms were simulated by using a 3-D device simulator in a basic circuit including MTJs designed using 90-nm CMOS parameters and design rules. The waveforms have a 400?-?A peak and a 200-ps elapsed time when neutron particles with a linear energy transfer value of 14?MeV cm{sup 2}/mg enter the silicon surface. The authors also found that the SEU current may cause soft errors with a probability of more than 10{sup ?12} per event, which was obtained by approximate solution of the ordinary differential equation of switching probability when the intrinsic critical current (I{sub C0}) became less than 30??A.

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

    SciTech Connect (OSTI)

    Mady, Franck Duchez, Jean-Bernard Mebrouk, Yasmine Benabdesselam, Mourad

    2014-10-21

    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.

  17. 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.; Boice, John D.; Stovall, Marilyn; Reiner, Anne S.; Bernstein, Leslie; John, Esther M.; Lynch, Charles F.; Mellemkjaer, Lene; Knight, Julia A.; Thomas, Duncan C.; Haile, Robert W.; Smith, Susan A.; Capanu, Marinela; Bernstein, Jonine L.; Shore, Roy E.; Radiation Effects Research Foundation, Hiroshima

    2012-11-15

    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.

  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. Molluscan Evolutionary Genomics

    E-Print Network [OSTI]

    Simison, W. Brian

    2010-01-01

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

  20. Genome Engineering

    SciTech Connect (OSTI)

    Voytas, Dan [University of Minnesota

    2014-03-20

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

  1. microRNA Alterations Driving Acute and Late Stages of Radiation-Induced Fibrosis in a Murine Skin Model

    SciTech Connect (OSTI)

    Simone, Brittany A.; Ly, David; Savage, Jason E.; Hewitt, Stephen M.; Dan, Tu D.; Ylaya, Kris; Shankavaram, Uma; Lim, Meng; Jin, Lianjin; Camphausen, Kevin; Mitchell, James B.; Simone, Nicole L.

    2014-09-01

    Purpose: Although ionizing radiation is critical in treating cancer, radiation-induced fibrosis (RIF) can have a devastating impact on patients' quality of life. The molecular changes leading to radiation-induced fibrosis must be elucidated so that novel treatments can be designed. Methods and Materials: To determine whether microRNAs (miRs) could be responsible for RIF, the fibrotic process was induced in the right hind legs of 9-week old CH3 mice by a single-fraction dose of irradiation to 35 Gy, and the left leg served as an unirradiated control. Fibrosis was quantified by measurements of leg length compared with control leg length. By 120 days after irradiation, the irradiated legs were 20% (P=.013) shorter on average than were the control legs. Results: Tissue analysis was done on muscle, skin, and subcutaneous tissue from irradiated and control legs. Fibrosis was noted on both gross and histologic examination by use of a pentachrome stain. Microarrays were performed at various times after irradiation, including 7 days, 14 days, 50 days, 90 days, and 120 days after irradiation. miR-15a, miR-21, miR-30a, and miR-34a were the miRs with the most significant alteration by array with miR-34a, proving most significant on confirmation by reverse transcriptase polymerase chain reaction, c-Met, a known effector of fibrosis and downstream molecule of miR-34a, was evaluated by use of 2 cell lines: HCT116 and 1522. The cell lines were exposed to various stressors to induce miR changes, specifically ionizing radiation. Additionally, in vitro transfections with pre-miRs and anti-miRs confirmed the relationship of miR-34a and c-Met. Conclusions: Our data demonstrate an inverse relationship with miR-34a and c-Met; the upregulation of miR-34a in RIF causes inhibition of c-Met production. miRs may play a role in RIF; in particular, miR-34a should be investigated as a potential target to prevent or treat this devastating side effect of irradiation.

  2. Ab Initio and Kinetic Rate Theory Modeling of 316SS with Oversized Solute Additions on Radiation-Induced Segregation

    SciTech Connect (OSTI)

    Hackett, Micah J.; Was, Gary S.

    2008-07-01

    Deleterious effects of radiation in nuclear reactor systems cause material degradation and the potential for component failure. Radiation damage is fundamentally due to freely migrating point defects produced in collision cascades. A reduction in the freely migrating point defect population should, then, reduce radiation damage and increase component lifetime. The addition of oversized solute atoms such as Zr or Hf to 316SS, a common structural material in reactors, is expected to reduce point defect population through a trapping mechanism that enhances recombination. The mechanism, however, requires a strong binding energy between the oversized solute atom and vacancies in order for the mechanism to significantly reduce the defect population. Experimental measurements of this binding energy are unavailable, but can be determined with atomistic calculations. Ab initio methods are used here to determine binding energies and atomic volumes of either Hf or Zr oversized solutes with vacancies in a face-centered cubic Fe matrix. The binding energies are then used to parameterize a kinetic rate-theory model, which is used here to calculate radiation-induced segregation (RIS). The calculated values of RIS are then compared to experimental measurements to benchmark the calculations and offer insight into the proposed point defect trapping mechanism. (author)

  3. Radiation-Induced Liver Fibrosis Is Mitigated by Gene Therapy Inhibiting Transforming Growth Factor-{beta} Signaling in the Rat

    SciTech Connect (OSTI)

    Du Shisuo; Qiang Ming [Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032 (China); Zeng Zhaochong, E-mail: zeng.zhaochong@zs-hospital.sh.c [Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032 (China); Zhou Jian [Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032 (China); Tan Yunshan [Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032 (China); Zhang Zhengyu [Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032 (China); Zeng Haiying [Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032 (China); Liu Zhongshan [Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032 (China)

    2010-12-01

    Purpose: We determined whether anti-transforming growth factor-{beta} (TGF-{beta}) intervention could halt the progression of established radiation-induced liver fibrosis (RILF). Methods and Materials: A replication-defective adenoviral vector expressing the extracellular portion of human T{beta}RII and the Fc portion of immunoglobulin G fusion protein (AdT{beta}RIIFc) was produced. The entire rat liver was exposed to 30 Gy irradiation to generate a RILF model (RILFM). Then, RILFM animals were treated with AdT{beta}RIIFc (1 x 10{sup 11} plaque-forming units [PFU] of T{beta}RII), control virus (1 x 10{sup 11} PFU of AdGFP), or saline. Delayed radiation liver injury was assessed by histology and immunohistochemistry. Chronic oxidative stress damage, hepatic stellate cell activation, and hepatocyte regeneration were also analyzed. Results: In rats infected with AdT{beta}RIIFc, fibrosis was significantly improved compared with rats treated with AdGFP or saline, as assessed by histology, hydroxyproline content, and serum level of hyaluronic acid. Compared with AdGFP rats, AdT{beta}RIIFc-treated rats exhibited decreased oxidative stress damage and hepatic stellate cell activation and preserved liver function. Conclusions: Our results demonstrate that TGF-{beta} plays a critical role in the progression of liver fibrosis and suggest that anti-TGF-{beta} intervention is feasible and ameliorates established liver fibrosis. In addition, chronic oxidative stress may be involved in the progression of RILF.

  4. Rotational Instabilities and Centrifugal Hangup

    E-Print Network [OSTI]

    Kimberly C. B. New; Joan M. Centrella

    2001-01-17

    One interesting class of gravitational radiation sources includes rapidly rotating astrophysical objects that encounter dynamical instabilities. We have carried out a set of simulations of rotationally induced instabilities in differentially rotating polytropes. An $n$=1.5 polytrope with the Maclaurin rotation law will encounter the $m$=2 bar instability at $T/|W| \\gtrsim 0.27$. Our results indicate that the remnant of this instability is a persistent bar-like structure that emits a long-lived gravitational radiation signal. Furthermore, dynamical instability is shown to occur in $n$=3.33 polytropes with the $j$-constant rotation law at $T/|W| \\gtrsim 0.14$. In this case, the dominant mode of instability is $m$=1. Such instability may allow a centrifugally-hung core to begin collapsing to neutron star densities on a dynamical timescale. If it occurs in a supermassive star, it may produce gravitational radiation detectable by LISA.

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

    SciTech Connect (OSTI)

    Balmain, Allan; Song, Ihn Young

    2013-05-15

    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.

  6. Effects of Adenovirus-Mediated Delivery of the Human Hepatocyte Growth Factor Gene in Experimental Radiation-Induced Heart Disease

    SciTech Connect (OSTI)

    Hu Shunying; Chen Yundai; Li Libing; Chen Jinlong; Wu Bin; Zhou, Xiao; Zhi Guang; Li Qingfang; Wang Rongliang; Duan Haifeng; Guo Zikuan; Yang Yuefeng; Xiao Fengjun; Wang Hua; Wang Lisheng

    2009-12-01

    Purpose: Irradiation to the heart may lead to late cardiovascular complications. The purpose of this study was to investigate whether adenovirus-mediated delivery of the human hepatocyte growth factor gene could reduce post-irradiation damage of the rat heart and improve heart function. Methods and Materials: Twenty rats received single-dose irradiation of 20 Gy gamma ray locally to the heart and were randomized into two groups. Two weeks after irradiation, these two groups of rats received Ad-HGF or mock adenovirus vector intramyocardial injection, respectively. Another 10 rats served as sham-irradiated controls. At post-irradiation Day 120, myocardial perfusion was tested by myocardial contrast echocardiography with contrast agent injected intravenously. At post-irradiation Day 180, cardiac function was assessed using the Langendorff technique with an isolated working heart model, after which heart samples were collected for histological evaluation. Results: Myocardial blood flow was significantly improved in HGF-treated animals as measured by myocardial contrast echocardiography at post-irradiation Day 120 . At post-irradiation Day 180, cardiac function was significantly improved in the HGF group compared with mock vector group, as measured by left ventricular peak systolic pressure (58.80 +- 9.01 vs. 41.94 +- 6.65 mm Hg, p < 0.05), the maximum dP/dt (5634 +- 1303 vs. 1667 +- 304 mm Hg/s, p < 0.01), and the minimum dP/dt (3477 +- 1084 vs. 1566 +- 499 mm Hg/s, p < 0.05). Picrosirius red staining analysis also revealed a significant reduction of fibrosis in the HGF group. Conclusion: Based on the study findings, hepatocyte growth factor gene transfer can attenuate radiation-induced cardiac injury and can preserve cardiac function.

  7. JGI Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2012-01-01

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

  8. JGI Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2011-01-01

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

  9. Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor

    2012-01-01

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

  10. Selecting Genomes for Reconstruction of Ancestral Genomes

    E-Print Network [OSTI]

    Zhang, Louxin

    Selecting Genomes for Reconstruction of Ancestral Genomes Guoliang Li1 , Jian Ma2 , and Louxin. It is often impossible to sequence all descendent genomes to reconstruct an ancestral genome. In addition, more genomes do not neces- sarily give a higher accuracy for the reconstruction of ancestral character

  11. Coiling Instabilities in Multilamellar Tubes

    E-Print Network [OSTI]

    C. D. Santangelo; P. Pincus

    2002-06-13

    Myelin figures are densely packed stacks of coaxial cylindrical bilayers that are unstable to the formation of coils or double helices. These myelin figures appear to have no intrinsic chirality. We show that such cylindrical membrane stacks can develop an instability when they acquire a spontaneous curvature or when the equilibrium distance between membranes is decreased. This instability breaks the chiral symmetry of the stack and may result in coiling. A unilamellar cylindrical vesicle, on the other hand, will develop an axisymmetric instability, possibly related to the pearling instability.

  12. 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)

    2012-11-01

    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.

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

    SciTech Connect (OSTI)

    Bakhshandeh, Mohsen; Hashemi, Bijan; Mahdavi, Seied Rabi Mehdi; Nikoofar, Alireza; Vasheghani, Maryam; Kazemnejad, Anoshirvan

    2013-02-01

    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.

  14. Instabilities of Advection-Dominated Accretion Flows

    E-Print Network [OSTI]

    Xingming Chen

    1996-01-22

    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.

  15. Equilibrium Electro-osmotic Instability

    E-Print Network [OSTI]

    Rubinstein, Isaak

    2014-01-01

    Since its prediction fifteen years ago, electro-osmotic instability has been attributed to non-equilibrium electro-osmosis related to the extended space charge which develops at the limiting current in the course of concentration polarization at a charge-selective interface. This attribution had a double basis. Firstly, it has been recognized that equilibrium electro-osmosis cannot yield instability for a perfectly charge-selective solid. Secondly, it has been shown that non-equilibrium electro-osmosis can. First theoretical studies in which electro-osmotic instability was predicted and analyzed employed the assumption of perfect charge-selectivity for the sake of simplicity and so did the subsequent numerical studies of various time-dependent and nonlinear features of electro-osmotic instability. In this letter, we show that relaxing the assumption of perfect charge-selectivity (tantamount to fixing the electrochemical potential in the solid) allows for equilibrium electro-osmotic instability. Moreover, we s...

  16. Solid-state polymerization of acrylamide and its derivatives complexed with some Lewis acids. II. Radiation-induced in-source polymerization

    SciTech Connect (OSTI)

    Zurakowska-Orszagh, J.; Mirowski, K.; Chajewski, A.

    1982-07-01

    Radiation-induced solid-state polymerizations of complexes of N-tert-butylacrylamide, N-tert-amylacrylamide, and N-tert-hexylacrylamide with zinc chloride and zinc bromide have been studied. An accelerating effect of temperature and an inhibiting effect of oxygen on the polymerization process were observed. The activation energies have been established. The influence of monomer structure as well as the halide used on the polymerization rate have been discussed and some regularities have been pointed out. The polymers obtained show good solubilities in common solvents, which proves that they are not crosslinked.

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

    SciTech Connect (OSTI)

    Dynan, William S.

    2013-05-31

    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.

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

    SciTech Connect (OSTI)

    Geard, Charles R.

    2014-12-12

    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.

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

    E-Print Network [OSTI]

    Kelsoe, J R

    2004-01-01

    300 Genomics and the Human Genome Project: implications forpast decade the Human Genome Project has made extraordinaryto each other. The Human Genome Project has approached human

  20. Coupling of Kelvin-Helmholtz instability and buoyancy instability in a thermally laminar plasma

    SciTech Connect (OSTI)

    Ren Haijun; Wu Zhengwei [CAS Key Laboratory of Basic Plasma Physics, University of Science and Technology of China, Hefei 230026 (China); Department of Physics and Materials Science, City University of Hong Kong, Tat Chee Avenue, Kowloon (Hong Kong); Cao Jintao; Dong Chao [CAS Key Laboratory of Basic Plasma Physics, University of Science and Technology of China, Hefei 230026 (China); Chu, Paul K. [Department of Physics and Materials Science, City University of Hong Kong, Tat Chee Avenue, Kowloon (Hong Kong)

    2011-02-15

    Thermal convective instability is investigated in a thermally stratified plasma in the presence of shear flow, which is known to give rise to the Kelvin-Helmholtz (KH) instability. We examine how the KH instability and magnetothermal instability (MTI) affect each other. Based on the sharp boundary model, the KH instability coupled with the MTI is studied. We present the growth rate and instability criteria. The shear flow is shown to significantly alter the critical condition for the occurrence of thermal convective instability.

  1. Preliminary Observations on Program Instability

    E-Print Network [OSTI]

    Rebentisch, Eric

    1996-10-10

    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 ...

  2. Equilibrium Electro-osmotic Instability

    E-Print Network [OSTI]

    Isaak Rubinstein; Boris Zaltzman

    2014-03-18

    Since its prediction fifteen years ago, electro-osmotic instability has been attributed to non-equilibrium electro-osmosis related to the extended space charge which develops at the limiting current in the course of concentration polarization at a charge-selective interface. This attribution had a double basis. Firstly, it has been recognized that equilibrium electro-osmosis cannot yield instability for a perfectly charge-selective solid. Secondly, it has been shown that non-equilibrium electro-osmosis can. First theoretical studies in which electro-osmotic instability was predicted and analyzed employed the assumption of perfect charge-selectivity for the sake of simplicity and so did the subsequent numerical studies of various time-dependent and nonlinear features of electro-osmotic instability. In this letter, we show that relaxing the assumption of perfect charge-selectivity (tantamount to fixing the electrochemical potential in the solid) allows for equilibrium electro-osmotic instability. Moreover, we suggest a simple experimental test for determining the true, either equilibrium or non-equilibrium, origin of electro-osmotic instability.

  3. The Human Genome From human genome to other

    E-Print Network [OSTI]

    Linial, Michal

    The Human Genome Project From human genome to other genomes and to gene function June 2000 From genome to health Structural Genomics initiative #12;What is the Human Genome Project? · U.S. govt that arise from genome research #12;The Human Genome Project Project began in 1990 as a $3 billion, 15-year

  4. 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...

  5. Sci—Fri AM: Mountain — 04: Label-free Raman spectroscopy of single tumour cells detects early radiation-induced glycogen synthesis associated with increased radiation resistance

    SciTech Connect (OSTI)

    Matthews, Q; Lum, JJ; Isabelle, M; Harder, S; Jirasek, A; Brolo, AG

    2014-08-15

    Purpose: To use label-free Raman spectroscopy (RS) for early treatment monitoring of tumour cell radioresistance. Methods: Three human tumour cell lines, two radioresistant (H460, SF{sub 2} = 0.57 and MCF7, SF{sub 2} = 0.70) and one radiosensitive (LNCaP, SF{sub 2} = 0.36), were irradiated with single fractions of 2, 4, 6, 8 or 10 Gy. In additional experiments, H460 and MCF7 cells were irradiated under co-treatment with the anti-diabetic drug metformin, a known radiosensitizing agent. Treated and control cultures were analyzed with RS daily for 3 days post-treatment. Single-cell Raman spectra were acquired from 20 live cells per sample, and experiments were repeated in triplicate. The combined data sets were analyzed with principal component analysis using standard algorithms. Cells from each culture were also subjected to standard assays for viability, proliferation, cell cycle, and radiation clonogenic survival. Results: The radioresistant cells (H460, MCF7) exhibited a RS molecular radiation response signature, detectable as early as 1 day post-treatment, of which radiation-induced glycogen synthesis is a significant contributor. The radiosensitive cells (LNCaP) exhibited negligible glycogen synthesis. Co-treatment with metformin in MCF7 cells blocked glycogen synthesis, reduced viability and proliferation, and increased radiosensitivity. Conversely, metformin co-treatment in H460 cells did not produce these same effects; importantly, both radiation-induced synthesis of glycogen and radiosensitivity were unaffected. Conclusions: Label-free RS can detect early glycogen synthesis post-irradiation, a previously undocumented metabolic mechanism associated with tumour cell radioresistance that can be targeted to increase radiosensitivity. RS monitoring of intratumoral glycogen may provide new opportunities for personalized combined modality radiotherapy treatments.

  6. Stellar explosions, instabilities, and turbulence

    SciTech Connect (OSTI)

    Drake, R. P.; Kuranz, C. C.; Miles, A. R.; Muthsam, H. J.; Plewa, T.

    2009-04-15

    It has become very clear that the evolution of structure during supernovae is centrally dependent on the pre-existing structure in the star. Modeling of the pre-existing structure has advanced significantly, leading to improved understanding and to a physically based assessment of the structure that will be present when a star explodes. It remains an open question whether low-mode asymmetries in the explosion process can produce the observed effects or whether the explosion mechanism somehow produces jets of material. In any event, the workhorse processes that produce structure in an exploding star are blast-wave driven instabilities. Laboratory experiments have explored these blast-wave-driven instabilities and specifically their dependence on initial conditions. Theoretical work has shown that the relative importance of Richtmyer-Meshkov and Rayleigh-Taylor instabilities varies with the initial conditions and does so in ways that can make sense of a range of astrophysical observations.

  7. Personal Genomics, Personalized Medicine,

    E-Print Network [OSTI]

    Napp, Nils

    /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 of a free living organism: Haemophilus Influenzae #12;Personal Genome Project HSLS, U.Pitt #12;Why get

  8. Observation of Parametric Instability in Advanced LIGO

    E-Print Network [OSTI]

    Gras, Slawek

    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 ...

  9. Vortex driven flame dynamics and combustion instability

    E-Print Network [OSTI]

    Altay, Hurrem Murat

    2005-01-01

    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 ...

  10. A General Approach to Optomechanical Parametric Instabilities

    E-Print Network [OSTI]

    M. Evans; L. Barsotti; P. Fritschel

    2009-10-14

    We present a simple feedback description of parametric instabilities which can be applied to a variety of optical systems. Parametric instabilities are of particular interest to the field of gravitational-wave interferometry where high mechanical quality factors and a large amount of stored optical power have the potential for instability. In our use of Advanced LIGO as an example application, we find that parametric instabilities, if left unaddressed, present a potential threat to the stability of high-power operation.

  11. 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

    2015-01-01

    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.

  12. The US Department of Energy Joint Genome Institute Microbial Genome Program

    E-Print Network [OSTI]

    Lapidus, Alla

    2005-01-01

    Department of Energy Joint Genome Institute Microbial GenomeDepartment of Energy Joint Genome Institute Microbial Genome

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

    E-Print Network [OSTI]

    Kelsoe, J R

    2004-01-01

    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:

  14. Combustion instability modeling and analysis

    SciTech Connect (OSTI)

    Santoro, R.J.; Yang, V.; Santavicca, D.A.; Sheppard, E.J.

    1995-12-31

    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.

  15. Comparative genomic workflow

    E-Print Network [OSTI]

    Rajapakse, Jagath

    his article describes a workflow for identifying conserved patterns in noncoding regions of vertebrate genomes, with an intention of investigating possible functions of the conserved regions. The annotations of genomes are ...

  16. The human genome project

    SciTech Connect (OSTI)

    Yager, T.D.; Zewert, T.E.; Hood, L.E. )

    1994-04-01

    The Human Genome Project (HGP) is a coordinated worldwide effort to precisely map the human genome and the genomes of selected model organisms. The first explicit proposal for this project dates from 1985 although its foundations (both conceptual and technological) can be traced back many years in genetics, molecular biology, and biotechnology. The HGP has matured rapidly and is producing results of great significance.

  17. Advances in Whole Genome

    E-Print Network [OSTI]

    Ciocan-Fontanine, Ionut

    Advances in Whole Genome Sequencing IMA Public Lecture: Tuesday, May 6, 2003, 7:30 p.m. Moos Tower sequenced genome, the virus Lambda at 50,000 nucleotides, was sequenced via the shotgun method by Sanger that this approach could not be applied to genomes over 100,000 nucleotides long, so a long period followed where

  18. Spinodal instability growth in new stochastic approaches

    E-Print Network [OSTI]

    P. Napolitani; M. Colonna; V. de la Mota

    2014-09-21

    Are spinodal instabilities the leading mechanism in the fragmentation of a fermionic system? Numerous experimental indications suggest such a scenario and stimulated much effort in giving a suitable description, without being finalised in a dedicated transport model. On the one hand, the bulk character of spinodal behaviour requires an accurate treatment of the one-body dynamics, in presence of mechanical instabilities. On the other hand, pure mean-field implementations do not apply to situations where instabilities, bifurcations and chaos are present. The evolution of instabilities should be treated in a large-amplitude framework requiring fluctuations of Langevin type. We present new stochastic approaches constructed by requiring a thorough description of the mean-field response in presence of instabilities. Their particular relevance is an improved description of the spinodal fragmentation mechanism at the threshold, where the instability growth is frustrated by the mean-field resilience.

  19. Centrifugally driven electrostatic instability in extragalactic jets

    E-Print Network [OSTI]

    Z. Osmanov

    2008-01-29

    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.

  20. Two-Beam Instability in Electron Cooling

    SciTech Connect (OSTI)

    Burov, Alexey V.; /Fermilab

    2006-04-01

    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.

  1. Sheet Beam Klystron Instability Analysis

    SciTech Connect (OSTI)

    Bane, K.L.F.; Jensen, A.; Li, Z.; Stupakov, G.; Adolphsen, C.; /SLAC

    2009-05-08

    Using the principle of energy balance we develop a 2D theory for calculating growth rates of instability in a two-cavity model of a sheet beam klystron. An important ingredient is a TE-like mode in the gap that also gives a longitudinal kick to the beam. When compared with a self-consistent particle-in-cell calculation, with sheet beam klystron-type parameters, agreement is quite good up to half the design current, 65 A; at full current, however, other, current-dependent effects come in and the results deviate significantly.

  2. 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; K. G. Jebsen Breast cancer centre, Institute for Clinical Medicine, University of Oslo, Oslo ; Landmark-Høyvik, Hege; K. G. Jebsen Breast cancer centre, Institute for Clinical Medicine, University of Oslo, Oslo ; Reinertsen, Kristin V.; Zhao, Xi; K. G. Jebsen Breast cancer centre, Institute for Clinical Medicine, University of Oslo, Oslo ; Grenaker-Alnæs, Grethe Irene; Nebdal, Daniel; Syvänen, Ann-Christine; Rødningen, Olaug; Alsner, Jan; Overgaard, Jens; Borresen-Dale, Anne-Lise; K. G. Jebsen Breast cancer centre, Institute for Clinical Medicine, University of Oslo, Oslo ; Fosså, Sophie D.; National Resource Centre for Late Effects after Cancer Treatment, OUS Radiumhospitalet, Oslo ; Kristensen, Vessela N.; K. G. Jebsen Breast cancer centre, Institute for Clinical Medicine, University of Oslo, Oslo; Department of Clinical Molecular Biology , Division of Medicine, Ahus University Hospital

    2013-07-15

    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.

  3. 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)

    2012-11-01

    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.

  4. Dynamic Genomes of Eukaryotes and the Maintenance of Genomic Integrity

    E-Print Network [OSTI]

    Katz, Laura

    Dynamic Genomes of Eukaryotes and the Maintenance of Genomic Integrity Eukaryotes specify a genome to be inherited stably, enabling dynamic rearrangements and amplifications of other genomic elements Laura Wegener Parfrey and Laura A. Katz M any biologists assume that eu- karyotic genomes are transmit- ted stably

  5. Ultraviolet radiation induced discharge laser

    DOE Patents [OSTI]

    Gilson, Verle A. (Livermore, CA); Schriever, Richard L. (Livermore, CA); Shearer, James W. (Livermore, CA)

    1978-01-01

    An ultraviolet radiation source associated with a suitable cathode-anode electrode structure, disposed in a gas-filled cavity of a high pressure pulsed laser, such as a transverse electric atmosphere (TEA) laser, to achieve free electron production in the gas by photoelectric interaction between ultraviolet radiation and the cathode prior to the gas-exciting cathode-to-anode electrical discharge, thereby providing volume ionization of the gas. The ultraviolet radiation is produced by a light source or by a spark discharge.

  6. Radiation-induced lung injury

    SciTech Connect (OSTI)

    Rosiello, R.A.; Merrill, W.W. )

    1990-03-01

    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.

    1996-12-31

    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. Bias Temperature Instability Analysis, Monitoring and Mitigation for

    E-Print Network [OSTI]

    Bias Temperature Instability Analysis, Monitoring and Mitigation for Nano-scaled Circuits Seyab #12;#12;Bias Temperature Instability Analysis, Monitoring and Mitigation for Nano-scaled Circuits Proefschrift: Semiconductor reliability, Failure mechanisms, Negative Bias Temperature Instability, Failure monitoring, Static

  9. 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

  10. 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

  11. Planning the Genome Institute's Future

    E-Print Network [OSTI]

    Botstein, David

    floors of a house, resting on a foundation of the Human Genome Project, with "Genomics to Society" on top planning that society will realize the scientific and public health benefits of the Human Genome Project. It has been a genome community tradi- tion since before there was a Human Genome Project, and NHGRI

  12. Parametric instabilities in the LCGT arm cavity

    E-Print Network [OSTI]

    K Yamamoto; T Uchiyama; S Miyoki; M Ohashi; K Kuroda; K Numata

    2008-05-15

    We evaluated the parametric instabilities of LCGT (Japanese interferometric gravitational wave detector project) arm cavity. The number of unstable modes of LCGT is 10-times smaller than that of Advanced LIGO (U.S.A.). Since the strength of the instabilities of LCGT depends on the mirror curvature more weakly than that of Advanced LIGO, the requirement of the mirror curvature accuracy is easier to be achieved. The difference in the parametric instabilities between LCGT and Advanced LIGO is because of the thermal noise reduction methods (LCGT, cooling sapphire mirrors; Advanced LIGO, fused silica mirrors with larger laser beams), which are the main strategies of the projects. Elastic Q reduction by the barrel surface (0.2 mm thickness Ta$_2$O$_5$) coating is effective to suppress instabilities in the LCGT arm cavity. Therefore, the cryogenic interferometer is a smart solution for the parametric instabilities in addition to thermal noise and thermal lensing.

  13. Instability of large solitary water waves

    E-Print Network [OSTI]

    Zhiwu Lin

    2008-03-03

    We consider the linearized instability of 2D irrotational solitary water waves. The maxima of energy and the travel speed of solitary waves are not obtained at the highest wave, which has a 120 degree angle at the crest. Under the assumption of non-existence of secondary bifurcation which is confirmed numerically, we prove linear instability of solitary waves which are higher than the wave of maximal energy and lower than the wave of maximal travel speed. It is also shown that there exist unstable solitary waves approaching the highest wave. The unstable waves are of large amplitude and therefore this type of instability can not be captured by the approximate models derived under small amplitude assumptions. For the proof, we introduce a family of nonlocal dispersion operators to relate the linear instability problem with the elliptic nature of solitary waves. A continuity argument with a moving kernel formula is used to study these dispersion operators to yield the instability criterion.

  14. Linear theory of microwave instability in electron storage rings...

    Office of Scientific and Technical Information (OSTI)

    Linear theory of microwave instability in electron storage rings Citation Details In-Document Search Title: Linear theory of microwave instability in electron storage rings...

  15. 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.

  16. Genomics and Systems Biology

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

    and structural genomics, and applications for such work cover diverse fields such as energy, agriculture, and environmental cleanup. Get Expertise Babetta Marrone Biofuels...

  17. Genomics Division Home

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

    to the most primitive soil microbe represent a watershed opportunity for biology. The Genomics Division is taking advantage of this wealth of new information. While it is well...

  18. Genome Science/Technologies

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

    primary focus is to develop technologies to obtain near complete genomes from single cells for the purposes of improved taxonomic identification and determining metabolic...

  19. 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

  20. Nicole Gurtler Genomics and Medicine

    E-Print Network [OSTI]

    Brutlag, Doug

    Gurtler 1 Nicole Gurtler Genomics and Medicine Final Paper Genomics and Multiple Sclerosis The recent breakthroughs in genomics have contributed greatly to the advancement of multiple sclerosis than previously maintenance-oriented treatments. What is Multiple Sclerosis? "Multiple sclerosis (MS

  1. Enhancer Identification through Comparative Genomics

    E-Print Network [OSTI]

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

    2006-01-01

    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

  2. The Future of Microbial Genomics

    SciTech Connect (OSTI)

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

    2010-06-02

    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

  3. Ginny Scholtes Genomics and Medicine

    E-Print Network [OSTI]

    Brutlag, Doug

    Ginny Scholtes Genomics and Medicine Professor Douglas Brutlag December 2, 2010 How Hard Could It Be? The Integration of Personal Genomics into Medical Practice Personal genomics carries incredible potential to revolutionize the way

  4. Evolutionary Genomics of Salmonella enterica Subspecies

    E-Print Network [OSTI]

    2013-01-01

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

  5. Evolutionary Genomics of Salmonella enterica Subspecies

    E-Print Network [OSTI]

    2013-01-01

    Evolutionary genomics of Salmonella enterica subspecies.Evolutionary Genomics of Salmonella enterica Subspecies

  6. SciTech Connect: genomics

    Office of Scientific and Technical Information (OSTI)

    genomics Find + Advanced Search Term Search Semantic Search Advanced Search All Fields: genomics Semantic Semantic Term Title: Full Text: Bibliographic Data: Creator Author:...

  7. Instabilities and Mixing in SN 1993J

    E-Print Network [OSTI]

    K. Iwamoto; T. R. Young; N. Nakasato; T. Shigeyama; K. Nomoto; I. Hachisu; H. Saio

    1997-01-15

    Rayleigh-Taylor (R-T) instabilities in the explosion of SN 1993J are investigated by means of two-dimensional hydrodynamical simulations. It is found that the extent of mixing is sensitive to the progenitor's core mass and the envelope mass. Because the helium core mass (3 - 4 \\ms) is smaller than that of SN 1987A, R-T instabilities at the He/C+O interfaces develop to induce a large scale mixing in the helium core, while the instability is relatively weak at the H/He interface due to the small envelope mass. The predicted abundance distribution, in particular the amount of the \

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

    E-Print Network [OSTI]

    2013-01-01

    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

  9. Vortices in rotating systems: Centrifugal, elliptic and hyperbolic type instabilities

    E-Print Network [OSTI]

    Lauga, Eric

    Vortices in rotating systems: Centrifugal, elliptic and hyperbolic type instabilities D. Sipp, E and centrifugal instabilities. A complete picture of the short-wave stability properties of the flow is given that anticyclones undergo centrifugal instability if the Rossby number verifies Ro 1, elliptic instability for all

  10. 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 the expression of genes. In this introductory manuscript, I discuss select algae and how genomics is impacting our understanding of these organisms. Four algae for which near-full genome information has become

  11. 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

  12. 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

  13. 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

  14. Unraveling the 3D genome: genomics tools for multiscale exploration

    E-Print Network [OSTI]

    Straight, Aaron

    Unraveling the 3D genome: genomics tools for multiscale exploration Viviana I. Risca and William J genome and the roles it may play in regulating transcription. Here we review core methods and new tools-scale chromosomal domains, and discuss the emerging pic- ture of the 3D genome that these tools have revealed. Blind

  15. Fuzzy Genome Sequence Assembly for Single and Environmental Genomes

    E-Print Network [OSTI]

    Nicolescu, Monica

    and to the first genome sequence as- sembly, Bacteriophage X174 [38]. In 1990 the Human Genome Project in 2003, two years before its projected date. #12;2 Sara Nasser, et al In 1993 The Institute for Genome advancements in technology that lead the to complete sequencing of the Human Genome and the H. influenzae

  16. COMPUTATIONAL GENOMICS: MAPPING, COMPARISON, AND ANNOTATION OF GENOMES

    E-Print Network [OSTI]

    address key issues in the different stages of genome research: planning of a genome sequencing project areas: (1) In relation to the early stages of a genome project, we address physical mapping, and we structure and sequence analysis of orthologous human and mouse genomic regions, and develop ROSETTA

  17. 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.

  18. Instabilities in particle-laden flows

    E-Print Network [OSTI]

    Dupuy, Benjamin, 1981-

    2004-01-01

    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 ...

  19. Magnetorotational instability in protoplanetary discs

    E-Print Network [OSTI]

    Raquel Salmeron; Mark Wardle

    2004-08-24

    We investigate the linear growth and vertical structure of the magnetorotational instability (MRI) in weakly ionised, stratified accretion discs. The magnetic field is initially vertical and dust grains are assumed to have settled towards the midplane, so charges are carried by electrons and ions only. Solutions are obtained at representative radial locations from the central protostar for different choices of the initial magnetic field strength, sources of ionisation, and disc surface density. The MRI is active over a wide range of magnetic field strengths and fluid conditions in low conductivity discs. For the minimum-mass solar nebula model, incorporating cosmic ray ionisation, perturbations grow at 1 AU for B < 8 G. For a significant subset of these strengths (0.2 - 5 G), the growth rate is of order the ideal MHD rate (0.75 Omega). Similarly, when cosmic rays are assumed to be excluded from the disc by the winds emitted by the magnetically active protostar, unstable modes grow at this radius for B less than about 2 G. This study shows that, despite the low magnetic coupling, the magnetic field is dynamically important for a large range of fluid conditions and field strengths in protostellar discs. Hall diffusion largely determines the structure and growth rate of these perturbations for all studied radii. At radii of order 1 AU, in particular, it is crucial to incorporate the full conductivity tensor in studies of the dynamics of astrophysical discs. (Abridged)

  20. Magnetorotational instability in protoplanetary discs

    E-Print Network [OSTI]

    Salmeron, Roberto Aureliano; Salmeron, Raquel; Wardle, Mark

    2004-01-01

    We investigate the linear growth and vertical structure of the magnetorotational instability (MRI) in weakly ionised, stratified accretion discs. The magnetic field is initially vertical and dust grains are assumed to have settled towards the midplane, so charges are carried by electrons and ions only. Solutions are obtained at representative radial locations from the central protostar for different choices of the initial magnetic field strength, sources of ionisation, and disc surface density. The MRI is active over a wide range of magnetic field strengths and fluid conditions in low conductivity discs. For the minimum-mass solar nebula model, incorporating cosmic ray ionisation, perturbations grow at 1 AU for B < 8 G. For a significant subset of these strengths (0.2 - 5 G), the growth rate is of order the ideal MHD rate (0.75 Omega). Similarly, when cosmic rays are assumed to be excluded from the disc by the winds emitted by the magnetically active protostar, unstable modes grow at this radius for B less...

  1. SUPERSONIC SHEAR INSTABILITIES IN ASTROPHYSICAL BOUNDARY LAYERS

    SciTech Connect (OSTI)

    Belyaev, Mikhail A.; Rafikov, Roman R., E-mail: rrr@astro.princeton.edu [Department of Astrophysical Sciences, Princeton University, Ivy Lane, Princeton, NJ 08540 (United States)

    2012-06-20

    Disk accretion onto weakly magnetized astrophysical objects often proceeds via a boundary layer (BL) that forms near the object's surface, in which the rotation speed of the accreted gas changes rapidly. Here, we study the initial stages of formation for such a BL around a white dwarf or a young star by examining the hydrodynamical shear instabilities that may initiate mixing and momentum transport between the two fluids of different densities moving supersonically with respect to each other. We find that an initially laminar BL is unstable to two different kinds of instabilities. One is an instability of a supersonic vortex sheet (implying a discontinuous initial profile of the angular speed of the gas) in the presence of gravity, which we find to have a growth rate of order (but less than) the orbital frequency. The other is a sonic instability of a finite width, supersonic shear layer, which is similar to the Papaloizou-Pringle instability. It has a growth rate proportional to the shear inside the transition layer, which is of order the orbital frequency times the ratio of stellar radius to the BL thickness. For a BL that is thin compared to the radius of the star, the shear rate is much larger than the orbital frequency. Thus, we conclude that sonic instabilities play a dominant role in the initial stages of nonmagnetic BL formation and give rise to very fast mixing between disk gas and stellar fluid in the supersonic regime.

  2. 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

  3. Human Genome Program

    SciTech Connect (OSTI)

    Not Available

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

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

    E-Print Network [OSTI]

    Posada-Buitrago, Martha Lucia

    2005-01-01

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

  5. Hidden Breakpoints in Genome Alignments

    E-Print Network [OSTI]

    Spang, Rainer

    in Genome Alignments #12;11 Simulated evolution Hidden Breakpoints in Genome Alignments 400 alignments in Genome Alignments #12;13 Simulated evolution Hidden Breakpoints in Genome Alignments 400 alignments genome Sum-of-Pairs: d(A,B) + d(A,C) + d(B,C) argmin {d(A,M) + d(B,M) + d(C,M)} M A C #12;16 Hidden

  6. 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

  7. Genomic library construction

    DOE Patents [OSTI]

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

    2011-07-26

    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.

  8. Genomic definition of species

    SciTech Connect (OSTI)

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01

    The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.

  9. 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 Genome Engineering with TAL Effector Nucleases Print Tuesday, 24 April 2012 09:48 Genome engineering (GE), an emerging discipline in...

  10. Fueling the Future with Fungal Genomics

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2011-01-01

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

  11. VISTA - computational tools for comparative genomics

    E-Print Network [OSTI]

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

    2004-01-01

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

  12. Bioinformatics and Genomics Degree Requirements Booklet

    E-Print Network [OSTI]

    dePamphilis, Claude

    Bioinformatics and Genomics Degree Requirements Booklet Fall 2011 #12;- -2 Contents Course Bioinformatics and Genomics Curriculum ------------------------------------------------------ 8 General--------------------------------------------------------------------- 14 #12;- -3 Bioinformatics and Genomics Option (BG

  13. 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

  14. DOE Joint Genome Institute 2008 Progress Report

    E-Print Network [OSTI]

    Gilbert, David

    2009-01-01

    completion of the Human Genome Project, sequencing and itsimagined when the Human Genome Project first began. Accord-genes. Instead, the Human Genome Project found that hu- mans

  15. The Genome Portal of the Department of Energy Joint Genome Institute

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2014-01-01

    The Genome Portal of the Department of Energy Joint Genome 10.1093/nar/gkr947 The Genome Portal of the Department ofthe web. The JGI Genome Portal (http://genome.jgi.doe.gov)

  16. Strings, vortex rings, and modes of instability

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

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

    2015-03-01

    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

  17. Bernstein instability driven by thermal ring distribution

    SciTech Connect (OSTI)

    Yoon, Peter H.; Hadi, Fazal; Qamar, Anisa

    2014-07-15

    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.

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

    E-Print Network [OSTI]

    Wurtele, Eve Syrkin

    Biology, Iowa State University, Ames IA 50011, USA 2Bioinformatics and Computational Biology Program, Iowa Encyclopedia of Genes and Genomes [9] (KEGG) (http://www.genome.ad.jp/ kegg) provide molecular networks based

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

    E-Print Network [OSTI]

    Batzoglou, Serafim

    2000-01-01

    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 ...

  20. Metal pad instabilities in liquid metal batteries

    E-Print Network [OSTI]

    Zikanov, Oleg

    2015-01-01

    A mechanical analogy is used to analyze the interaction between the magnetic field, electric current and deformation of interfaces in liquid metal batteries. It is found that, during charging or discharging, a sufficiently large battery is prone to instabilities of two types. One is similar to the metal pad instability known for aluminum reduction cells. Another type is new. It is related to the destabilizing effect of the Lorentz force formed by the azimuthal magnetic field induced by the base current and the current perturbations caused by the local variations of the thickness of the electrolyte layer.

  1. Understanding magnetic instability in gapless superconductors

    E-Print Network [OSTI]

    Mei Huang

    2005-09-18

    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.

  2. 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.

  3. 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

  4. 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

  5. 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

    2007-01-01

    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...

  6. Viscoelastic effects on electromechanical instabilities in dielectric elastomers

    E-Print Network [OSTI]

    Park, Harold S.

    Viscoelastic effects on electromechanical instabilities in dielectric elastomers Harold S. Park on the electromechanical behavior of dielectric elastomers. A dynamic, finite deformation finite element formulation, we evaluate the effects of the shear and bulk relaxation times on the electromechanical instability

  7. 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

  8. Mammalian comparative genomics and epigenomics

    E-Print Network [OSTI]

    Mikkelsen, Tarjei Sigurd, 1978-

    2009-01-01

    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 ...

  9. Next-generation nematode genomes 

    E-Print Network [OSTI]

    Kumar, Sujai

    2013-06-29

    The first metazoan to be sequenced was a nematode (Caenorhabditis elegans), and understanding the genome of this model organism has led to many insights about all animals. Although eleven nematode genomes have been ...

  10. 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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation Current HABFESOpportunities NuclearlongGeneral Tables The GeneralGenomeGenomics

  11. A Linear Theory of Microwave Instability in Electron Storage...

    Office of Scientific and Technical Information (OSTI)

    United States Language: English Subject: 43 PARTICLE ACCELERATORS; DISTRIBUTION; ELECTRONS; INSTABILITY; LAGUERRE POLYNOMIALS; STABILITY; STORAGE RINGS; SYNCHROTRON RADIATION;...

  12. Chemical and mechanical instability in warm and dense nuclear matter

    E-Print Network [OSTI]

    Lavagno, A; 10.1103/PhysRevC.86.024917

    2012-01-01

    We investigate the possible thermodynamic instability in a warm and dense nuclear medium (Tliquid-gas phase transition, we show that the nucleon-Delta matter phase transition is characterized by both mechanical instability (fluctuations on the baryon density) and by chemical-diffusive instability (fluctuations on the charge concentration) in asymmetric nuclear matter. We then perform an investigation and a comparative study on the different nature of such instabilities and phase transitions.

  13. 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

  14. Wetting and lubricating film instabilities in microchannels

    E-Print Network [OSTI]

    Cubaud, Thomas

    Wetting and lubricating film instabilities in microchannels Thomas Cubaud Department of Mechanical, and silicone oils . Dynamic wetting transitions: a pearl flow thick lubricating film , b spider flow thin lubricating film , c ghost flow metastable dewetting patches . Droplet-decorated streams: d droplets

  15. Morphological instability in freezing colloidal suspensions

    E-Print Network [OSTI]

    Wettlaufer, John S.

    Morphological instability in freezing colloidal suspensions BY STEPHEN S. L. PEPPIN 1,2, *, M. GRAE of colloidal systems is that they do not freeze uniformly. Instead the ice segregates, aligning the expelled particles into different configurations depending on the freezing conditions (figure 1). One of the major

  16. Termination of the magnetorotational instability via parasitic instabilities in core-collapse supernovae

    E-Print Network [OSTI]

    Rembiasz, Tomasz; Cerdá-Durán, Pablo; Müller, Ewald; Aloy, Miguel-Ángel

    2015-01-01

    The magnetorotational instability (MRI) can be a powerful mechanism amplifying the magnetic field in core collapse supernovae. However, whether initially weak magnetic fields can be amplified by this instability to dynamically relevant strengths is still a matter of active scientific debate. One of the main uncertainties concerns the process that terminates the growth of the instability. Parasitic instabilities of both Kelvin-Helmholtz (KH) and tearing-mode type have been suggested to play a crucial role in this process, disrupting MRI channel flows and quenching magnetic field amplification. We performed two-dimensional and three-dimensional sheering-disc simulations of a differentially rotating proto-neutron star layer in non-ideal MHD with unprecedented high numerical resolution. Our simulations show that KH parasitic modes dominate tearing modes in the regime of large hydrodynamic and magnetic Reynolds numbers, as encountered in proto-neutron stars. They also determine the maximum magnetic field stress ac...

  17. Comparative Genomics of Mycobacterium Tuberculosis

    E-Print Network [OSTI]

    Brutlag, Doug

    Comparative Genomics of Mycobacterium Tuberculosis #12;My Questions · What is TB ­ What in the literature. · Emphasize that genomics techniques are not limited to hereditary diseases. #12;Methods · Deciphering the biology of Mycobacterium Tuberculosis from the complete genome sequence, Stuart Cole et al

  18. 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

  19. Radiating Instability of a Meridional Boundary Current HRISTINA G. HRISTOVA

    E-Print Network [OSTI]

    energy away from the source of instability. It can be contrasted with a trapped instability ocean basins. Un- stable boundary currents can be an important source of eddy kinetic energy. Radiating instabilities propagate energy away from the locally unstable region by coupling to the free

  20. Electromechanical instability in semicrystalline polymers Xuanhe Zhao and Zhigang Suoa

    E-Print Network [OSTI]

    Suo, Zhigang

    Electromechanical instability in semicrystalline polymers Xuanhe Zhao and Zhigang Suoa School homogeneous, but it then localizes. The electromechanical instability sets in when the force and the voltage. The electromechanical instability typically sets in at a large deformation. At such a large deformation, the change

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

    SciTech Connect (OSTI)

    Chuang Ren

    2013-02-13

    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.

  2. 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

  3. Genome Medicine 2009, 11

    E-Print Network [OSTI]

    Dehene, Frank

    Genome Medicine 2009, 11::88 Correspondence BBrriiddggiinngg tthhee ggaapp bbeettwweeeenn Care Medicine and CRISMA laboratory, University of Pittsburgh School of Medicine, Scaife 602, 3550 Biotechnology Center, University of Torino, Via Nizza 52, I, 10126 Torino, Italy; 10Institutionen för Medicin

  4. 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

    2008-01-01

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

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

    E-Print Network [OSTI]

    2014-01-01

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

  6. Computational methods and analyses in comparative genomics and epigenomics

    E-Print Network [OSTI]

    Peng, Qian

    2012-01-01

    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–

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

    E-Print Network [OSTI]

    Mukhopadhyay, Aindrila

    2010-01-01

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

  8. Microwave Instability Simulations for NSLS-II

    SciTech Connect (OSTI)

    Blednykh,A.; Krinsky, S.; Nash, B.; Yu, L.

    2009-05-04

    Potential-well distortion and the microwave instability in the NSLS-II storage ring are investigated. The longitudinal wakepotential is calculated as a sum of the contributions due to vacuum chamber components distributed around the ring. An approximation to the wakepotential for a 0.05-mm charge distribution length, much shorter than the 4.5-mm length of the unperturbed circulating bunch, is used as a pseudo-Green's function for beam dynamics simulations. Comparison of particle tracking simulations using the TRANFT code with the Haissinski solution shows good agreement below the instability threshold current. Above threshold two regimes are observed: (1) energy spread and bunch length are time-dependent (saw tooth behavior); (2) both are time-independent.

  9. Nonideal magnetohydrodynamic instabilities and toroidal magnetic confinement

    SciTech Connect (OSTI)

    Furth, H.P.

    1985-05-01

    The marked divergence of experimentally observed plasma instability phenomena from the predictions of ideal magnetohydrodynamics led in the early 1960s to the formulations of finite-resistivity stability theory. Beginning in the 1970s, advanced plasma diagnostics have served to establish a detailed correspondence between the predictions of the finite-resistivity theory and experimental plasma behavior - particularly in the case of the resistive kink mode and the tokamak plasma. Nonlinear resistive-kink phenomena have been found to govern the transport of magnetic flux and plasma energy in the reversed-field pinch. The other predicted finite-resistivity instability modes have been more difficult to identify directly and their implications for toroidal magnetic confinement are still unresolved.

  10. Beam instability studies for the SSC

    SciTech Connect (OSTI)

    Chou, W.

    1994-09-01

    Beam instability studies of the Superconducting Super Collider (SSC) during the period 1989--1993 are briefly reviewed in this paper. Various topics are covered: single bunch and multi-bunch, single beam and beam-beam, parasitic heating and active feedback, etc. Although the SSC will not be built, many of the results obtained from these studies remain as useful references to the accelerator community.

  11. Coherent instabilities of a relativistic bunched beam

    SciTech Connect (OSTI)

    Chao, A.W.

    1982-06-01

    A charge-particle beam contained in an accelerator vacuum chamber interacts electromagnetically with its environment to create a wake field. This field than acts back on the beam, perturbing the particle motion. If the beam intensity is high enough, this beam-environment interaction may lead to an instability and to subsequent beam loss. The beam and its environment form a dynamical system, and it is this system that will be studied. 84 references.

  12. PEP-X IMPEDANCE AND INSTABILITY CALCULATIONS

    SciTech Connect (OSTI)

    Bane, K.L.F.; Lee, L.-Q.; Ng, C.; Stupakov, G.; au Wang, L.; Xiao, L.; /SLAC

    2010-08-25

    PEP-X, a next generation, ring-based light source is designed to run with beams of high current and low emittance. Important parameters are: energy 4.5 GeV, circumference 2.2 km, beam current 1.5 A, and horizontal and vertical emittances, 185 pm by 8 pm. In such a machine it is important that impedance driven instabilities not degrade the beam quality. In this report they study the strength of the impedance and its effects in PEP-X. For the present, lacking a detailed knowledge of the vacuum chamber shape, they create a straw man design comprising important vacuum chamber objects to be found in the ring, for which they then compute the wake functions. From the wake functions they generate an impedance budget and a pseudo-Green function wake representing the entire ring, which they, in turn, use for performing microwave instability calculations. In this report they, in addition, consider in PEP-X the transverse mode-coupling, multi-bunch transverse, and beam-ion instabilities.

  13. 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

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

    E-Print Network [OSTI]

    2007-01-01

    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

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

    E-Print Network [OSTI]

    Chen, Huaming

    2000-01-01

    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...

  16. 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

  17. Genome: Unlocking Life's Code for Teachers of

    E-Print Network [OSTI]

    Miller, Scott

    GENOME CODE LIFE'S UNLOCKING Genome: Unlocking Life's Code Educator's Guide for Teachers of Grades Glossary 30 Other Resources 32 What the Exhibit Offers Genomics--the study of the entire genome. It is important that students understand what genomics is and what it teaches us about ourselves and the rest

  18. 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

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

    E-Print Network [OSTI]

    Gent, Universiteit

    of NGS is the re-sequencing of genomes, such as the 1000 human genomes project (http://www .1000genomes.org/) or the 1001 Arabidopsis genome project (http://www.1001genomes.org/). Genome (re)sequencing is importantGenomeView: a next-generation genome browser Thomas Abeel1,2,3, *, Thomas Van Parys1,2 , Yvan Saeys

  20. Editorial: The Human Genome Project

    E-Print Network [OSTI]

    Crawford, Michael H.; Baer, A.S.; Hall, R.; Omenn, G.S.; Thomson, G.J.; Wilson, A.C.

    1990-08-01

    iv / Editorial: The Human Genome Project Dear readers, The last few decades have seen a number of exciting developments in genetics. First, Watson and Crick broke the genetic code; since then, tech-nologic and methodologic breakthroughs have... permitted the study and direct manipulation of our DNA. Now there is an international ground swell to map and sequence the human genome. The Bush administration had originally requested $128 million in last year's budget for the Human Genome Project. However...

  1. 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.

    2014-12-31

    and detection of molecules involved in the response to exogenous DNA damaging agents DNA damage response (DDR) defects can be revealed by treating mice that show normal spontaneous micronucleus frequencies with genotoxic agents. Upon treatment, micronuclei... or for the identification of deficiencies that are only apparent, or amplified, in response to DDR challenge because they are only necessary for the response to exogenous DNA damaging 640 agents rather than endogenous DNA damaging agents. This procedure will enable...

  2. Genomic Sciences | Clean Energy | ORNL

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

    to clean energy and environmental applications. Multidisciplinary genomic science research and communication resources at ORNL include the following: Plant Systems Biology...

  3. Prospective Study Validating Inter- and Intraobserver Variability of Tissue Compliance Meter in Breast Tissue of Healthy Volunteers: Potential Implications for Patients With Radiation-Induced Fibrosis of the Breast

    SciTech Connect (OSTI)

    Wernicke, A. Gabriella, E-mail: gaw9008@med.cornell.ed [Stich Radiation Oncology, Weill Cornell Medical College of Cornell University, New York, NY (United States); Parashar, Bhupesh; Kulidzhanov, Fridon; Riley, Lillian [Stich Radiation Oncology, Weill Cornell Medical College of Cornell University, New York, NY (United States); Christos, Paul J. [Division of Biostatistics and Epidemiology, Department of Public Health, Weill Cornell Medical College of Cornell University, New York, NY (United States); Fischer, Andrew [Physical Medicine and Rehabilitation, Mount Sinai School of Medicine, New York, NY (United States); Nori, Dattatreyudu; Chao, K.S. Clifford [Stich Radiation Oncology, Weill Cornell Medical College of Cornell University, New York, NY (United States)

    2011-05-01

    Purpose: Accurate detection of radiation-induced fibrosis (RIF) is crucial in management of breast cancer survivors. Tissue compliance meter (TCM) has been validated in musculature. We validate TCM in healthy breast tissue with respect to interobserver and intraobserver variability before applying it in RIF. Methods and Materials: Three medical professionals obtained three consecutive TCM measurements in each of the four quadrants of the right and left breasts of 40 women with no breast disease or surgical intervention. The intraclass correlation coefficient (ICC) assessed interobserver variability. The paired t test and Pearson correlation coefficient (r) were used to assess intraobserver variability within each rater. Results: The median age was 45 years (range, 24-68 years). The median bra size was 35C (range, 32A-40DD). Of the participants, 27 were white (67%), 4 black (10%), 5 Asian (13%), and 4 Hispanic (10%). ICCs indicated excellent interrater reliability (low interobserver variability) among the three raters, by breast and quadrant (all ICC {>=}0.99). The paired t test and Pearson correlation coefficient both indicated low intraobserver variability within each rater (right vs. left breast), stratified by quadrant (all r{>=} 0.94, p < 0.0001). Conclusions: The interobserver and intraobserver variability is small using TCM in healthy mammary tissue. We are now embarking on a prospective study using TCM in women with breast cancer at risk of developing RIF that may guide early detection, timely therapeutic intervention, and assessment of success of therapy for RIF.

  4. Tissue sampling and standards for vertebrate genomics

    E-Print Network [OSTI]

    2012-01-01

    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

  5. Evolutionary Genomics of Salmonella enterica Subspecies

    E-Print Network [OSTI]

    2013-01-01

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

  6. Trichoderma: the genomics of opportunistic success

    E-Print Network [OSTI]

    Druzhinina, Irina S.

    2011-01-01

    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,

  7. Linear plasmoid instability of thin current sheets with shear flow

    SciTech Connect (OSTI)

    Ni Lei; Germaschewski, Kai; Huang Yimin; Sullivan, Brian P.; Yang Hongang; Bhattacharjee, Amitava

    2010-05-15

    This paper presents linear analytical and numerical studies of plasmoid instabilities in the presence of shear flow in high-Lundquist-number plasmas. Analysis demonstrates that the stability problem becomes essentially two dimensional as the stabilizing effects of shear flow become more prominent. Scaling results are presented for the two-dimensional instabilities. An approximate criterion is given for the critical aspect ratio of thin current sheets at which the plasmoid instability is triggered.

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

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

    at instabilities called islands and generates electrical current that eliminates the islands. The process links software-controlled mirrors to detection equipment, creating a...

  9. Flow instabilities of magnetic flux tubes II. Longitudinal flow

    E-Print Network [OSTI]

    V. Holzwarth; D. Schmitt; M. Schuessler

    2007-04-27

    Flow-induced instabilities are relevant for the storage and dynamics of magnetic fields in stellar convection zones and possibly also in other astrophysical contexts. We continue the study started in the first paper of this series by considering the stability properties of longitudinal flows along magnetic flux tubes. A linear stability analysis was carried out to determine criteria for the onset of instability in the framework of the approximation of thin magnetic flux tubes. In the non-dissipative case, we find Kelvin-Helmholtz instability for flow velocities exceeding a critical speed that depends on the Alfv{\\'e}n speed and on the ratio of the internal and external densities. Inclusion of a friction term proportional to the relative transverse velocity leads to a friction-driven instability connected with backward (or negative energy) waves. We discuss the physical nature of this instability. In the case of a stratified external medium, the Kelvin-Helmholtz instability and the friction-driven instability can set in for flow speeds significantly lower than the Alfv{\\'e}n speed. Dissipative effects can excite flow-driven instability below the thresholds for the Kelvin-Helmholtz and the undulatory (Parker-type) instabilities. This may be important for magnetic flux storage in stellar convection zones and for the stability of astrophysical jets.

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

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

    Qin, Hong; Davidson, Ronald C.

    2014-06-01

    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.

  11. Testing Disk Instability Models for Giant Planet Formation

    E-Print Network [OSTI]

    Alan P. Boss

    2007-04-09

    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.

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

    SciTech Connect (OSTI)

    Qin, Hong [Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08543 (United States); Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Davidson, Ronald C. [Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08543 (United States)

    2014-06-15

    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.

  13. Pair instability supernovae of very massive population III stars...

    Office of Scientific and Technical Information (OSTI)

    In red supergiant progenitors, the amplitudes of these instabilities are sufficient to mix the supernova ejecta. less Authors: Chen, Ke-Jung ; Woosley, Stan 1 ; Heger,...

  14. Teasing Out the Nature of Structural Instabilities in Ceramic...

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

    Instabilities in Ceramic Compounds MARCH 12, 2013 Bookmark and Share The simple perovskite structure of EuTiO3 illustrated above shows the essential competing structural...

  15. Density-shear instability in electron magneto-hydrodynamics

    SciTech Connect (OSTI)

    Wood, T. S. Hollerbach, R.; Lyutikov, M.

    2014-05-15

    We discuss a novel instability in inertia-less electron magneto-hydrodynamics (EMHD), which arises from a combination of electron velocity shear and electron density gradients. The unstable modes have a lengthscale longer than the transverse density scale, and a growth-rate of the order of the inverse Hall timescale. We suggest that this density-shear instability may be of importance in magnetic reconnection regions on scales smaller than the ion skin depth, and in neutron star crusts. We demonstrate that the so-called Hall drift instability, previously argued to be relevant in neutron star crusts, is a resistive tearing instability rather than an instability of the Hall term itself. We argue that the density-shear instability is of greater significance in neutron stars than the tearing instability, because it generally has a faster growth-rate and is less sensitive to geometry and boundary conditions. We prove that, for uniform electron density, EMHD is “at least as stable” as regular, incompressible MHD, in the sense that any field configuration that is stable in MHD is also stable in EMHD. We present a connection between the density-shear instability in EMHD and the magneto-buoyancy instability in anelastic MHD.

  16. Human Genome: DOE Origins

    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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would likeUniverse (JournalvivoHigh energyHighlandWorkshop-SummerHow is theHughHumanHuman Genome

  17. 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.

  18. Plasma planar filament instability and Alfven waves

    E-Print Network [OSTI]

    Garcia de Andrade

    2007-03-05

    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)\

  19. Instabilities in the Nuclear Energy Density Functional

    E-Print Network [OSTI]

    M. Kortelainen; T. Lesinski

    2010-02-05

    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.

  20. 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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass mapSpeedingProgramExemptionsProtein Dynamics Hit the Big ScreenProtein Instability and

  1. 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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass mapSpeedingProgramExemptionsProtein Dynamics Hit the Big ScreenProtein Instability

  2. Comparative Genome Structure, Secondary Metabolite, and Effector...

    Office of Scientific and Technical Information (OSTI)

    Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens Citation Details In-Document Search Title: Comparative Genome Structure,...

  3. Implications of structural genomics target selection strategies...

    Office of Scientific and Technical Information (OSTI)

    Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches Citation Details In-Document Search Title: Implications of structural...

  4. Corey Clemons Genomics and Medicine

    E-Print Network [OSTI]

    Brutlag, Doug

    the Human Genome Project was completed. The goal of the HGP was to sequence the entire human genome in order to the private sector.i One unintended consequence of the HGP is that it actually challenged previously held with previously misunderstood conditions and ailments. Some practical uses of the HGP are the development

  5. 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)

    2010-09-12

    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.

  6. Electrohydrodynamic instabilities in thin liquid trilayer films

    SciTech Connect (OSTI)

    Roberts, Scott A.; Kumar, Satish

    2010-01-01

    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 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.

  7. Electrohydrodynamic instabilities in thin liquid trilayer films

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

    Roberts, Scott A.; Kumar, Satish

    2010-12-09

    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 may be of interest for the creation of complex topographical patterns on polymer coatings and in microelectronics.« less

  8. 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

  9. The effect of lubrication film thickness on thermoelastic instability under fluid lubricating condition

    E-Print Network [OSTI]

    Yi, Yun-Bo

    The effect of lubrication film thickness on thermoelastic instability under fluid lubricating online 14 March 2013 Keywords: Thermoelastic instability Wet clutches Fluid lubrication Critical speed by a thin layer of lubricating fluid is developed to investigate thermoelastic instability with fluid

  10. Gene Action and Cellular Function in Parasitic Protozoa Genomics and post-genomics in parasitology: genome babble or

    E-Print Network [OSTI]

    Schnaufer, Achim

    Gene Action and Cellular Function in Parasitic Protozoa Genomics and post-genomics in parasitology: genome babble or a real opportunity? K. Gull1 School of Biological Sciences, University of Manchester, 2.205 Stopford Building, Oxford Road, Manchester M13 9PT, U.K. Abstract The genome projects represent one

  11. Electron-hose instability in an annular plasma sheath

    E-Print Network [OSTI]

    ;4 return currents requires kpb1low current.16 Throughout this work ion-motion5 and beam-head beam scalings are quite severe at low energy, single-bunch instability growth can in fact be reduced-stream instability7 ,8 arising from the presence of a low energy electron population in the beamline. Sources

  12. Viscosity driven instability in rotating relativistic stars Motoyuki Saijo*

    E-Print Network [OSTI]

    Gourgoulhon, Eric

    are secularly unstable to bar-mode formation when #12; * #12;sec ' 0:14. This instability can grow of the system. By contrast, a dynamical insta- bility to bar-mode formation sets in when #12; * #12;dyn ' 0. INTRODUCTION Stars in nature are usually rotating and subject to non- axisymmetric rotational instabilities

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

    E-Print Network [OSTI]

    Nicoud, Franck

    to compute azimuthal combustion instabilities is presented. It requires a thermoacoustic model using a n is investigated. Introduction Thermoacoustic instabilities result from the coupling between unstationary low CPU time cost. A thermoacoustic model is used to solve the wave equation in reactive media

  14. Self-Gravity Driven Instabilities in the ISM

    E-Print Network [OSTI]

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

    2006-03-29

    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.

  15. An Instability Leading to Failure of Polyethylene in Uniaxial Creep

    E-Print Network [OSTI]

    An Instability Leading to Failure of Polyethylene in Uniaxial Creep L. J. ZAPAS and J. M. CRISSMAN model, a point of instability is pre- dicted for the uniaxial creep of high density polyethylene. From dead load experiments it has been found that the instabil- ity occurs for linear -polyethylene

  16. Flow Forcing Techniques for Numerical Simulation of Combustion Instabilities

    E-Print Network [OSTI]

    Nicoud, Franck

    Flow Forcing Techniques for Numerical Simulation of Combustion Instabilities A. KAUFMANN* and F of combustion instabilities in gas turbine combustors require the knowledge of flame transfer functions. Those flame) and for one case where a CFD code is necessary (a laminar Bunsen-type flame). © 2002

  17. Adhesion-Induced Instability Patterns in Thin Confined Elastic Film

    E-Print Network [OSTI]

    Chaudhury, Manoj K.

    the instability while not determining its wavelength. The instability also throws light on cavitation phenomena in confined adhesive layers. Introduction Hydrodynamic-force-driven nonequilibrium systems give rise to many Deborah numbers (De , 1), the hydrodynamic forces dominate pattern formation, whereas at high Deborah

  18. Pair instability supernovae of very massive population III stars

    SciTech Connect (OSTI)

    Chen, Ke-Jung; Woosley, Stan [Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA 95064 (United States); Heger, Alexander [Monash Centre for Astrophysics, Monash University, Victoria 3800 (Australia); Almgren, Ann [Center for Computational Sciences and Engineering, Lawrence Berkeley National Lab, Berkeley, CA 94720 (United States); Whalen, Daniel J., E-mail: kchen@ucolick.org [T-2, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)

    2014-09-01

    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 M {sub ?} 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 contraction, to capture any dynamical instabilities that may be seeded by core contraction 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 arise at the upper and lower boundaries of the oxygen shell ?20-100 s after core bounce. Instabilities driven by burning freeze out after the SN shock exits the helium core. As the shock later propagates through the hydrogen envelope, a strong reverse shock forms that drives the growth of Rayleigh-Taylor instabilities. In red supergiant progenitors, the amplitudes of these instabilities are sufficient to mix the supernova ejecta.

  19. Electromechanical instability on dielectric polymer surface: Modeling and experiment

    E-Print Network [OSTI]

    Park, Harold S.

    Electromechanical instability on dielectric polymer surface: Modeling and experiment Harold S. Park this by modifying the Q1P0 formulation of Simo et al. [1], and adapting it to the electromechanical coupling on the critical electric fields that are necessary to induce electromechanical instabilities such as creasing

  20. Selective pressures for and against genetic instability in cancer

    E-Print Network [OSTI]

    Wan, Frederic Yui-Ming

    Selective pressures for and against genetic instability in cancer: a time-dependent problem Natalia instability in cancer is a two-edge sword. It can both increase the rate of cancer progression (by increasing the probability of cancerous mutations) and decrease the rate of cancer growth (by imposing a large death toll

  1. 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

  2. Observation of Beam ION Instability in Spear3

    SciTech Connect (OSTI)

    Teytelman, D.; /Dimtel, Redwood City; Cai, Y.; Corbett, W.J.; Raubenheimer, T.O.; Safranek, J.A.; Schmerge, J.F.; Sebek, J.J.; Wang, L.; /SLAC

    2011-12-14

    Weak vertical coupled bunch instability with oscillation amplitude at {mu}m level has been observed in SPEAR3. The instability becomes stronger when there is a vacuum pressure rise by partially turning off vacuum pumps and it becomes weaker when the vertical beam emittance is increased by turning off the skew quadrupole magnets. These confirmed that the instability was driven by ions in the vacuum. The threshold of the beam ion instability when running with a single bunch train is just under 200 mA. This paper presents the comprehensive observations of the beam ion instability in SPEAR3. The effects of vacuum pressure, beam current, beam filling pattern, chromaticity, beam emittance and bunch-by-bunch feedback are investigated in great detail. In an electron accelerator, ions generated from the residual gas molecules can be trapped by the beam. Then these trapped ions interact resonantly with the beam and cause beam instability and emittance blow-up. Most existing light sources use a long single bunch train filling pattern, followed by a long gap to avoid multi-turn ion trapping. However, such a gap does not preclude ions from accumulating during one passage of the single bunch train beam, and those ions can still cause a Fast Ion Instability (FII) as predicted by Raubenheimer and Zimmermann. FII has been observed in ALS, and PLS by artificially increasing the vacuum pressure by injecting helium gas into the vacuum chamber or by turning off the ion pumps in order to observe the beam ion instability. In some existing rings, for instance B factory, the beam ion instability was observed at the beginning of the machine operation after a long period of shutdown and then it automatically disappeared when the vacuum was better. However, when the beam emittance becomes smaller, the FII can occur at nominal conditions as observed in PLS, SOLEIL and SSRF. This paper reports the observations of beam ion instabilities in SPEAR3 under different condition during a period of one year, which includes single bunch train instability (FII) and multi-bunch train instability. Note that the instability may be not the same even with the same beam due to the change of the vacuum with time. SPEAR3 has a circumference of 234 m with a harmonic number of 372. SPEAR3 runs with six bunch train filling pattern in order to suppress the possible beam ion instability. Table 1 lists the main parameters of SPEAR3. The vacuum of SPEAR3 ranges from 0.1 to 0.5 nTorr, which varies from section to section.

  3. Pair Instability Supernovae of Very Massive Population III Stars

    E-Print Network [OSTI]

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

    2014-01-01

    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...

  4. Probing instabilities in arc plasma devices using binary gas mixtures

    SciTech Connect (OSTI)

    Ghorui, S.; Vysohlid, M.; Heberlein, J. V. R.; Pfender, E.

    2007-07-15

    This paper presents an experimental approach to identify the sources of instabilities in arc plasma devices. The phenomena of demixing in arcs have been utilized to explore the characteristics of different instabilities. Problems in explaining the observed behavior with our current understanding of the phenomena are discussed. Hydrogen is used as a secondary gas with argon as the primary plasma gas for this study. Results indicate that the observed behavior such as steady, takeover, and restrike modes of instabilities in arcs may essentially originate from the thin boundary layer over the anode wall primarily at the location of the anodic arc root. The bulk core flow apparently does not play any significant role in such instabilities. Arc currents rather than flow rates control the behavior of the instabilities in frequency space. Bifurcation of the system behavior and evidence for the existence of quadratic zones in flow space of binary gas mixtures separating steady and unsteady behavior are discussed.

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

    SciTech Connect (OSTI)

    Niknam, A. R.; Rastbood, E.; Bafandeh, F.; Khorashadizadeh, S. M.

    2014-04-15

    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.

  6. Genome patent fight erupts

    SciTech Connect (OSTI)

    Roberts, L.

    1991-10-11

    At a Congressional briefing while describing a new project to sequence partially every gene active in the human brain, it was made known that the National Institutes of Health was planning to file patent applications on 1,000 of these sequences a month. The scheme has engendered a firestorm of criticism from genome scientists and project officials alike. The critics argue that these sequences probably can't be patented in the first place - and even if they can, they shouldn't be. The plan would undercut patent protection for those who labor long and hard at the real task of elucidating the function of the proteins encoded by the genes, thereby driving industry away from developing inventions based on that work.

  7. 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

  8. Genome Biology 2004, 5:R56 commentreviewsreportsdepositedresearchrefereedresearchinteractionsinformation

    E-Print Network [OSTI]

    . Although various genomic datasets are rele-vant to this issue, each dataset provides relatively weak

  9. A Million Cancer Genome Warehouse David Haussler

    E-Print Network [OSTI]

    McAuliffe, Jon

    Warehouse Regional Warehouses Design and Cost to Build and Operate a Million Cancer Genome Warehouse CAPEX

  10. Doug Brutlag 2015 Genomics, Bioinformatics & Medicine

    E-Print Network [OSTI]

    Brutlag, Doug

    in -Amylase Gene Tandem Repeat Arrays Sharp, Cheng & Eichler, Annu. Rev. Genomics Hum. Genet. 2006. 7

  11. 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

  12. SHORT REVIEW Ecological genomics: understanding gene and

    E-Print Network [OSTI]

    Herman, Mike

    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

  13. Yangzhong Tang Functional Genomics Platform@ Whitehead Institute

    E-Print Network [OSTI]

    Sabatini, David M.

    Yangzhong Tang Functional Genomics Platform@ Whitehead Institute June 1st, 2015 Entering the CRISPR-Cas9 Era #12;Outline · The Human Genome o Basics and timeline o Exponential increase in genomic data o How to use the big data for biological discoveries · Functional Genomics · CRISPR-Cas systems o

  14. 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

    2011-01-01

    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.

  15. 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

  16. Shotgun coverage of human genome computing

    E-Print Network [OSTI]

    Eddy, Sean

    take about 1.5 million pages. The Human Genome Project would not be possible if our revolution were-author collection of chapters on the various uses of computing in the Human Genome Project. Peculiarly absent fromShotgun coverage of human genome computing Human Genome Computing, Second Edition edited by Martin

  17. Doug Brutlag 2015 Sequencing the Human Genome

    E-Print Network [OSTI]

    Brutlag, Doug

    Project: Should we do it? · Service, R. F. (2001). The human genome: Objection #1: big biology is bad://www.elec-intro.com/m13-cloning #12;© Doug Brutlag 2015 Public Human Genome Project Strategy Published in Nature 15 The Human Genome Project: How should we do it? · Weber, J. L., & Myers, E. W. (1997). Human whole-genome

  18. 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

  19. Pseudo Boolean Programming for Partially Ordered Genomes

    E-Print Network [OSTI]

    Fertin, Guillaume

    Pseudo Boolean Programming for Partially Ordered Genomes Sébastien Angibaud1 , Guillaume Fertin1.Angibaud,Guillaume.Fertin}@univ-nantes.fr, thevenin@lri.fr, vialette@univ-mlv.fr Abstract. Comparing genomes of different species is a crucial problem in comparative genomics. Different measures have been proposed to com- pare two genomes: number of common

  20. 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

  1. 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

  2. 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

  3. 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

  4. Genomics and vertebrate adaptive radiation: a celebration of the first cichlid genome

    E-Print Network [OSTI]

    Renn, Susan C.P.

    Genomics and vertebrate adaptive radiation: a celebration of the first cichlid genome C. Darrin ``Genomics and Vertebrate Adaptive Radiation: A Celebration of the First Cichlid Genome'' was held the central topic was the genomics of adaptive radiation in cichlid fishes, the symposium integrated speakers

  5. 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

  6. 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

  7. Human genome. 1993 Program report

    SciTech Connect (OSTI)

    Not Available

    1994-03-01

    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.

  8. Immortalization of normal human mammary epithelial cells in two steps by direct targeting of senescence barriers does not require gross genomic alterations

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

    Garbe, James C.; Vrba, Lukas; Sputova, Klara; Fuchs, Laura; Novak, Petr; Brothman, Arthur R.; Jackson, Mark; Chin, Koei; LaBarge, Mark A.; Watts, George; et al

    2014-10-29

    Telomerase reactivation and immortalization are critical for human carcinoma progression. However, little is known about the mechanisms controlling this crucial step, due in part to the paucity of experimentally tractable model systems that can examine human epithelial cell immortalization as it might occur in vivo. We achieved efficient non-clonal immortalization of normal human mammary epithelial cells (HMEC) by directly targeting the 2 main senescence barriers encountered by cultured HMEC. The stress-associated stasis barrier was bypassed using shRNA to p16INK4; replicative senescence due to critically shortened telomeres was bypassed in post-stasis HMEC by c-MYC transduction. Thus, 2 pathologically relevant oncogenic agentsmore »are sufficient to immortally transform normal HMEC. The resultant non-clonal immortalized lines exhibited normal karyotypes. Most human carcinomas contain genomically unstable cells, with widespread instability first observed in vivo in pre-malignant stages; in vitro, instability is seen as finite cells with critically shortened telomeres approach replicative senescence. Our results support our hypotheses that: (1) telomere-dysfunction induced genomic instability in pre-malignant finite cells may generate the errors required for telomerase reactivation and immortalization, as well as many additional “passenger” errors carried forward into resulting carcinomas; (2) genomic instability during cancer progression is needed to generate errors that overcome tumor suppressive barriers, but not required per se; bypassing the senescence barriers by direct targeting eliminated a need for genomic errors to generate immortalization. Achieving efficient HMEC immortalization, in the absence of “passenger” genomic errors, should facilitate examination of telomerase regulation during human carcinoma progression, and exploration of agents that could prevent immortalization.« less

  9. Immortalization of normal human mammary epithelial cells in two steps by direct targeting of senescence barriers does not require gross genomic alterations

    SciTech Connect (OSTI)

    Garbe, James C.; Vrba, Lukas; Sputova, Klara; Fuchs, Laura; Novak, Petr; Brothman, Arthur R.; Jackson, Mark; Chin, Koei; LaBarge, Mark A.; Watts, George; Futscher, Bernard W.; Stampfer, Martha R.

    2014-10-29

    Telomerase reactivation and immortalization are critical for human carcinoma progression. However, little is known about the mechanisms controlling this crucial step, due in part to the paucity of experimentally tractable model systems that can examine human epithelial cell immortalization as it might occur in vivo. We achieved efficient non-clonal immortalization of normal human mammary epithelial cells (HMEC) by directly targeting the 2 main senescence barriers encountered by cultured HMEC. The stress-associated stasis barrier was bypassed using shRNA to p16INK4; replicative senescence due to critically shortened telomeres was bypassed in post-stasis HMEC by c-MYC transduction. Thus, 2 pathologically relevant oncogenic agents are sufficient to immortally transform normal HMEC. The resultant non-clonal immortalized lines exhibited normal karyotypes. Most human carcinomas contain genomically unstable cells, with widespread instability first observed in vivo in pre-malignant stages; in vitro, instability is seen as finite cells with critically shortened telomeres approach replicative senescence. Our results support our hypotheses that: (1) telomere-dysfunction induced genomic instability in pre-malignant finite cells may generate the errors required for telomerase reactivation and immortalization, as well as many additional “passenger” errors carried forward into resulting carcinomas; (2) genomic instability during cancer progression is needed to generate errors that overcome tumor suppressive barriers, but not required per se; bypassing the senescence barriers by direct targeting eliminated a need for genomic errors to generate immortalization. Achieving efficient HMEC immortalization, in the absence of “passenger” genomic errors, should facilitate examination of telomerase regulation during human carcinoma progression, and exploration of agents that could prevent immortalization.

  10. Electron-ion hybrid instability experiment upgrades to the Auburn Linear Experiment for Instability Studies

    SciTech Connect (OSTI)

    DuBois, A. M.; Arnold, I.; Thomas, E. Jr.; Tejero, E.; Amatucci, W. E.

    2013-04-15

    The Auburn Linear EXperiment for Instability Studies (ALEXIS) is a laboratory plasma physics experiment used to study spatially inhomogeneous flows in a magnetized cylindrical plasma column that are driven by crossed electric (E) and magnetic (B) fields. ALEXIS was recently upgraded to include a small, secondary plasma source for a new dual source, interpenetrating plasma experiment. Using two plasma sources allows for highly localized electric fields to be made at the boundary of the two plasmas, inducing strong E Multiplication-Sign B velocity shear in the plasma, which can give rise to a regime of instabilities that have not previously been studied in ALEXIS. The dual plasma configuration makes it possible to have independent control over the velocity shear and the density gradient. This paper discusses the recent addition of the secondary plasma source to ALEXIS, as well as the plasma diagnostics used to measure electric fields and electron densities.

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

    SciTech Connect (OSTI)

    Kuo, Alan; Grigoriev, Igor

    2009-04-17

    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.

  12. Indeterminacy and instability in Petschek reconnection

    SciTech Connect (OSTI)

    Forbes, Terry G.; Priest, Eric R.; Seaton, Daniel B.; Litvinenko, Yuri E.

    2013-05-15

    We explain two puzzling aspects of Petschek's model for fast reconnection. One is its failure to occur in plasma simulations with uniform resistivity. The other is its inability to provide anything more than an upper limit for the reconnection rate. We have found that previously published analytical solutions based on Petschek's model are structurally unstable if the electrical resistivity is uniform. The structural instability is associated with the presence of an essential singularity at the X-line that is unphysical. By requiring that such a singularity does not exist, we obtain a formula that predicts a specific rate of reconnection. For uniform resistivity, reconnection can only occur at the slow, Sweet-Parker rate. For nonuniform resistivity, reconnection can occur at a much faster rate provided that the resistivity profile is not too flat near the X-line. If this condition is satisfied, then the scale length of the nonuniformity determines the reconnection rate.

  13. Time-Resonant Tokamak Plasma Edge Instabilities?

    E-Print Network [OSTI]

    Webster, A J; Calderon, F A; Chapman, S C; Delabie, E; Dodt, D; Felton, R; Todd, T N; Maviglia, F; Morris, J; Riccardo, V; Alper, B; Brezinsek, S; Coad, P; Likonen, J; Rubel, M; Contributors, JET EFDA

    2013-01-01

    For a two week period during the Joint European Torus (JET) 2012 experimental campaign, the same high confinement plasma was repeated 151 times. The dataset was analysed to produce a probability density function (pdf) for the waiting times between edge-localised plasma instabilities ("ELMS"). The result was entirely unexpected. Instead of a smooth single peaked pdf, a succession of 4-5 sharp maxima and minima uniformly separated by 7-8 millisecond intervals was found. Here we explore the causes of this newly observed phenomenon, and conclude that it is either due to a self-organised plasma phenomenon or an interaction between the plasma and a real-time control system. If the maxima are a result of "resonant" frequencies at which ELMs can be triggered more easily, then future ELM control techniques can, and probably will, use them. Either way, these results demand a deeper understanding of the ELMing process.

  14. Mitigation of radiation induced surface contamination

    DOE Patents [OSTI]

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

    2003-01-01

    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.

  15. Simulation of radiation-induced defects

    E-Print Network [OSTI]

    Peltola, Timo

    2015-01-01

    Mainly due to their outstanding performance the position sensitive silicon detectors are widely used in the tracking systems of High Energy Physics experiments such as the ALICE, ATLAS, CMS and LHCb at LHC, the world's largest particle physics accelerator at CERN, Geneva. The foreseen upgrade of the LHC to its high luminosity (HL) phase (HL-LHC scheduled for 2023), will enable the use of maximal physics potential of the facility. After 10 years of operation the expected fluence will expose the tracking systems at HL-LHC to a radiation environment that is beyond the capacity of the present system design. Thus, for the required upgrade of the all-silicon central trackers extensive measurements and simulation studies for silicon sensors of different designs and materials with sufficient radiation tolerance have been initiated within the RD50 Collaboration. Supplementing measurements, simulations are in vital role for e.g. device structure optimization or predicting the electric fields and trapping in the silicon...

  16. Simulation of radiation-induced defects

    E-Print Network [OSTI]

    Timo Peltola

    2015-09-29

    Mainly due to their outstanding performance the position sensitive silicon detectors are widely used in the tracking systems of High Energy Physics experiments such as the ALICE, ATLAS, CMS and LHCb at LHC, the world's largest particle physics accelerator at CERN, Geneva. The foreseen upgrade of the LHC to its high luminosity (HL) phase (HL-LHC scheduled for 2023), will enable the use of maximal physics potential of the facility. After 10 years of operation the expected fluence will expose the tracking systems at HL-LHC to a radiation environment that is beyond the capacity of the present system design. Thus, for the required upgrade of the all-silicon central trackers extensive measurements and simulation studies for silicon sensors of different designs and materials with sufficient radiation tolerance have been initiated within the RD50 Collaboration. Supplementing measurements, simulations are in vital role for e.g. device structure optimization or predicting the electric fields and trapping in the silicon sensors. The main objective of the device simulations in the RD50 Collaboration is to develop an approach to model and predict the performance of the irradiated silicon detectors using professional software. The first successfully developed quantitative models for radiation damage, based on two effective midgap levels, are able to reproduce the experimentally observed detector characteristics like leakage current, full depletion voltage and charge collection efficiency (CCE). Recent implementations of additional traps at the SiO$_2$/Si interface or close to it have expanded the scope of the experimentally agreeing simulations to such surface properties as the interstrip resistance and capacitance, and the position dependency of CCE for strip sensors irradiated up to $\\sim$$1.5\\times10^{15}$ n$_{\\textrm{eq}}\\textrm{cm}^{-2}$.

  17. Mechanisms of radiation-induced gene responses

    SciTech Connect (OSTI)

    Woloschak, G.E.; Paunesku, T.

    1996-10-01

    In the process of identifying genes differentially expressed in cells exposed ultraviolet radiation, we have identified a transcript having a 26-bp region that is highly conserved in a variety of species including Bacillus circulans, yeast, pumpkin, Drosophila, mouse, and man. When the 5` region (flanking region or UTR) of a gene, the sequence is predominantly in +/+ orientation with respect to the coding DNA strand; while in the coding region and the 3` region (UTR), the sequence is most frequently in the +/-orientation with respect to the coding DNA strand. In two genes, the element is split into two parts; however, in most cases, it is found only once but with a minimum of 11 consecutive nucleotides precisely depicting the original sequence. The element is found in a large number of different genes with diverse functions (from human ras p21 to B. circulans chitonase). Gel shift assays demonstrated the presence of a protein in HeLa cell extracts that binds to the sense and antisense single-stranded consensus oligomers, as well as to the double- stranded oligonucleotide. When double-stranded oligomer was used, the size shift demonstrated as additional protein-oligomer complex larger than the one bound to either sense or antisense single-stranded consensus oligomers alone. It is speculated either that this element binds to protein(s) important in maintaining DNA is a single-stranded orientation for transcription or, alternatively that this element is important in the transcription-coupled DNA repair process.

  18. Radiation Induced Nanocrystal Formation in Metallic Glasses 

    E-Print Network [OSTI]

    Carter, Jesse

    2010-01-14

    diameter up to approximately 100 nm in Cu irradiated Zr55Cu30Al10Ni5. Studies of di raction patterns of irradiated specimens showed nucleation of Cu10Zr7 phases in both specimens, as well as evidence of CuZr2 in Cu50Zr45Ti5 and both CuZr2 and NiZr2 in Zr55...

  19. Synthetic Genomics: Options for Governance

    E-Print Network [OSTI]

    Garfinkel, Michele

    2007-10-17

    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 ...

  20. Complete chloroplast genome of Trachelium caeruleum: extensiverearrangements are associated with repeats and tRNAs

    SciTech Connect (OSTI)

    Haberle, Rosemarie C.; Fourcade, Matthew L.; Boore, Jeffrey L.; Jansen, Robert K.

    2006-01-09

    Chloroplast genome structure, gene order and content arehighly conserved in land plants. We sequenced the complete chloroplastgenome sequence of Trachelium caeruleum (Campanulaceae) a member of anangiosperm family known for highly rearranged chloroplast genomes. Thetotal genome size is 162,321 bp with an IR of 27,273 bp, LSC of 100,113bp and SSC of 7,661 bp. The genome encodes 115 unique genes, with 19duplicated in the IR, a tRNA (trnI-CAU) duplicated once in the LSC and aprotein coding gene (psbJ) duplicated twice, for a total of 137 genes.Four genes (ycf15, rpl23, infA and accD) are truncated and likelynonfunctional; three others (clpP, ycf1 and ycf2) are so highly divergedthat they may now be pseudogenes. The most conspicuous feature of theTrachelium genome is the presence of eighteen internally unrearrangedblocks of genes that have been inverted or relocated within the genome,relative to the typical gene order of most angiosperm chloroplastgenomes. Recombination between repeats or tRNAs has been suggested as twomeans of chloroplast genome rearrangements. We compared the relativenumber of repeats in Trachelium to eight other angiosperm chloroplastgenomes, and evaluated the location of repeats and tRNAs in relation torearrangements. Trachelium has the highest number and largest repeats,which are concentrated near inversion endpoints or other rearrangements.tRNAs occur at many but not all inversion endpoints. There is likely nosingle mechanism responsible for the remarkable number of alterations inthis genome, but both repeats and tRNAs are clearly associated with theserearrangements. Land plant chloroplast genomes are highly conserved instructure, gene order and content. The chloroplast genomes of ferns, thegymnosperm Ginkgo, and most angiosperms are nearly collinear, reflectingthe gene order in lineages that diverged from lycopsids and the ancestralchloroplast gene order over 350 million years ago (Raubeson and Jansen,1992). Although earlier mapping studies identified a number of taxa inwhich several rearrangements have occurred (reviewed in Raubeson andJansen, 2005), an extraordinary number of chloroplast genome alterationsare concentrated in several families in the angiosperm order Asterales(sensu APGII, Bremer et al., 2003). Gene mapping studies ofrepresentatives of the Campanulaceae (Cosner, 1993; Cosner et al.,1997,2004) and Lobeliaceae (Knox et al., 1993; Knox and Palmer, 1999)identified large inversions, contraction and expansion of the invertedrepeat regions, and several insertions and deletions in the cpDNAs ofthese closely related taxa. Detailed restriction site and gene mapping ofthe chloroplast genome of Trachelium caeruleum (Campanulaceae) identifiedseven to ten large inversions, families of repeats associated withrearrangements, possible transpositions, and even the disruption ofoperons (Cosner et al., 1997). Seventeen other members of theCampanulaceae were mapped and exhibit many additional rearrangements(Cosner et al., 2004). What happened in this lineage that made itsusceptible to so many chloroplast genome rearrangements? How do normallyvery conserved chloroplast genomes change? The cause of rearrangements inthis group is unclear based on the limited resolution available withmapping techniques. Several mechanisms have been proposed to explain howrearrangements occur: recombination between repeats, transposition, ortemporary instability due to loss of the inverted repeat (Raubeson andJansen, 2005). Sequencing whole chloroplast genomes within theCampanulaceae offers a unique opportunity to examine both the extent andmechanisms of rearrangements within a phylogenetic framework.We reporthere the first complete chloroplast genome sequence of a member of theCampanulaceae, Trachelium caeruleum. This work will serve as a benchmarkfor subsequent, comparative sequencing and analysis of other members ofthis family and close relatives, with the goal of further understandingchloroplast genome evolution. We confirmed features previously identifiedthrough mapping, and discovered many additional structural changes,i

  1. 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

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

    E-Print Network [OSTI]

    Chandonia, John-Marc; Brenner, Steven E.

    2004-01-01

    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):

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

    E-Print Network [OSTI]

    2011-01-01

    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://

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

    E-Print Network [OSTI]

    Eisen, Jonathan A; MacCallum, Catriona J

    2009-01-01

    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,

  5. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    E-Print Network [OSTI]

    Ditty, Jayna L.

    2012-01-01

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

  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

    2010-01-01

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

  7. MicrobesOnline: an integrated portal for comparative functional genomics

    E-Print Network [OSTI]

    Joachimiak, Marcin P.

    2014-01-01

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

  8. Validation in Genomics: CpG Island Methylation Revisited

    E-Print Network [OSTI]

    Segal, Mark R

    2006-01-01

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

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

    E-Print Network [OSTI]

    Rodriguez-Salus, Melinda Sue

    2012-01-01

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

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

    E-Print Network [OSTI]

    Arkin, Adam P.

    2014-01-01

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

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

    E-Print Network [OSTI]

    Arkin, Adam P.

    2014-01-01

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

  12. The Human Genome Project and its Social Implications

    E-Print Network [OSTI]

    Meyer, Paul B

    1990-01-01

    The Human Genome Project and its Social Implications By Paulit is about the Human Genome Project. In a sense this isheredity. The Human Genome Project is concerned essentially

  13. Genome-scale reconstruction and analysis of eukaryotic metabolic networks

    E-Print Network [OSTI]

    Hurlen, Natalie Christine

    2006-01-01

    803. Leja, D. , Human Genome Project Timeline, 38-72.jpg,p. Illustration of Human Genome Project Timeline. Varki,Human Genome Project. ..

  14. Feedback techniques and SPS Ecloud instabilities - design estimates

    SciTech Connect (OSTI)

    Fox,J.D.; Mastorides, T.; Ndabashimiye, G.; Rivetta, C.; Van Winkle, D.; Byrd, J.; Vay, J-L.; Hofle, W.; Rumolo, G.; de Maria, R.

    2009-05-04

    The SPS at high intensities exhibits transverse single-bunch instabilities with signatures consistent with an Ecloud driven instability. While the SPS has a coupled-bunch transverse feedback system, control of Ecloud driven motion requires a much wider control bandwidth capable of sensing and controlling motion within each bunched beam. This paper draws beam dynamics data from the measurements and simulations of this SPS instability, and estimates system requirements for a feedback system with 2-4 GS/sec. sampling rates to damp Ecloud-driven transverse motion in the SPS at intensities desired for high-current LHC operation.

  15. Castaing Instability and Precessing Domains in Confined Alkali Gases

    E-Print Network [OSTI]

    A. Kuklov; A. E. Meyerovich

    2002-02-05

    We explore analogy between two-component quantum alkali gases and spin-polarized helium systems. Recent experiments in trapped gases are put into the frame of the existing theory for Castaing instability in transverse channel and formation of homogeneous precessing domains in spin-polarized systems. Analogous effects have already been observed in spin-polarized $% ^{3}He$ and $^{3}He- ^{4}He$ mixtures systems. The threshold effect of the confining potential on the instability is analyzed. New experimental possibilities for observation of transverse instability in a trap are discussed.

  16. Instability Model of the Universe with De Sitter Beginning

    E-Print Network [OSTI]

    Yurii Ignat'ev

    2015-08-21

    The physical instability of the Universe model with de Sitter beginning is proved in this article. 1. It is shown that even a small addition of ultrarelativistic matter turns the de Sitter Universe into the Universe with finite past. 2. Constant solution of equation of model with constant scalar field is shown to be instable. 3. It is also shown that lateral gravitational perturbations of such model make it instable near of cosmological singularity. The conclusion is made that de Sitter stage of the Universe evolution most likely should be preceded by the ultrarelativistic stage.

  17. 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

    2014-01-01

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

  18. The mouse genome informatics and the mouse genome database

    SciTech Connect (OSTI)

    Maltais, L.J.; Blackburn, R.E.; Bradt, D.W.

    1994-09-01

    The Mouse Genome Database (MGD) is a centralized, comprehensive database of the mouse genome that includes genetic mapping data, comparative mapping data, gene descriptions, mutant phenotype descriptions, strains and allelic polymorphism data, inbred strain characteristics, physical mapping data, and molecular probes and clones data. Data in MGD are obtained from the published literature and by electronic transfer from laboratories working on large backcross panels of mice. MGD provides tools that enable the user to search the database, retrieve data, generate reports, analyze data, annotate records, and build genetic maps. The Encyclopedia of the Mouse Genome provides a graphic user interface to mouse genome data. It consists of software tools including: LinkMap, a graphic display of genetic linkage maps with the ability to magnify regions of high locus density: CytoMap, a graphic display of cytogenetic maps showing banded chromosomes with cytogenetic locations of genes and chromosomal aberrations; CATS, a catalog searching tool for text retrieval of mouse locus descriptions. These software tools provide access to the following data sets: Chromosome Committee Reports, MIT Genome Center data, GBASE reports, Mouse Locus Catalog (MLC), and Mouse Cytogenetic Mapping Data. The MGD is available to the scientific community through the World Wide Web (WWW) and Gopher. In addition GBASE can be accessed via the Internet.

  19. 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.; Coplowitz, Shana; Greenwood, Eleni; Barney, Christian L.; Christos, Paul J.; Parashar, Bhupesh; Nori, Dattatreyudu; Chao, K. S. Clifford; Wernicke, A. Gabriella

    2013-12-01

    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.

  20. 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)

  1. Frequency-Sweeping Alfvén Instabilities Driven by Super-Alfvénic Beams in the Spherical Tokamak START

    E-Print Network [OSTI]

    Frequency-Sweeping Alfvén Instabilities Driven by Super-Alfvénic Beams in the Spherical Tokamak START

  2. 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

  3. Control of Magnetohydrodynamic Instabilities by Phase Space Engineering of Energetic Ions in Tokamak Plasmas

    E-Print Network [OSTI]

    Control of Magnetohydrodynamic Instabilities by Phase Space Engineering of Energetic Ions in Tokamak Plasmas

  4. Activation of conductive pathways via deformation-induced instabilities

    E-Print Network [OSTI]

    Ni, Xinchen

    2014-01-01

    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 ...

  5. PPPL successfully tests system for mitigating instabilities called...

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

    the size of instabilities known as "edge localized modes (ELMs)" on the DIII-D tokamak that General Atomics operates for the U.S. Department of Energy in San Diego. Such...

  6. The role of phase instabilities in the early material response...

    Office of Scientific and Technical Information (OSTI)

    The role of phase instabilities in the early material response during laser-induced breakdown in bulk fused silica Citation Details In-Document Search Title: The role of phase...

  7. A viscous instability in axially symmetric laminar shear flows

    E-Print Network [OSTI]

    Shakura, Nikolai

    2015-01-01

    A viscous instability in shearing laminar axisymmetric hydrodynamic flows around a gravitating center is described. In the linearized hydrodynamic equations written in the Boussinesq approximation with microscopic molecular transport coefficients, the instability arises when the viscous dissipation is taken into account in the energy equation. Using the local WKB approximation, we derive a third-order algebraic dispersion equation with two modes representing the modified Rayleigh modes R+ and R-, and the third X-mode. We show that in thin accretion flows the viscosity destabilizes one of the Rayleigh modes in a wide range of wavenumbers, while the X-mode always remains stable. In Keplerian flows, the instability increment is found to be a few Keplerian rotational periods at wavelengths with $kr\\sim 10-50$. This instability may cause turbulence in astrophysical accretion discs even in the absence of magnetic field.

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

    E-Print Network [OSTI]

    Altay, Hurrem Murat

    2009-01-01

    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 ...

  9. Investigation of thermal filamentation instability over Gakona, Alaska

    E-Print Network [OSTI]

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

    2007-01-01

    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 ...

  10. Two-dimensional simulations of pulsational pair-instability supernovae...

    Office of Scientific and Technical Information (OSTI)

    thermonuclear outbursts due to a recurring pair-instability. In some of these events, solar masses of material are ejected in repeated outbursts of several 10sup 50 erg...

  11. Kink instability suppression with stochastic cooling pickup and kicker

    SciTech Connect (OSTI)

    Hao Y.; Blaskiewicz, M.; Litvinenko, V.N.; Ptitsyn, V.

    2012-05-20

    The kink instability is one of the major beam dynamics issues of the linac-ring based electron ion collider. This head-tail type instability arises from the oscillation of the electron beam inside the opposing ion beam. It must be suppressed to achieve the desired luminosity. There are various ways to suppress the instability, such as tuning the chromaticity in the ion ring or by a dedicated feedback system of the electron beam position at IP, etc. However, each method has its own limitation. In this paper, we will discuss an alternative opportunity of suppressing the kink instability of the proposed eRHIC at BNL using the existing pickup-kicker system of the stochastic cooling system in RHIC.

  12. Ageostrophic Instabilities of Interior Horizontal and Vertical Shear Flows

    E-Print Network [OSTI]

    Wang, Peng

    2012-01-01

    Y. H. , and W. R. Peltier (2001b), Baroclinic instability inMoore, G. W. K. , and W. R. Peltier (1987), Cyclogenesis inG. W. K. , and W. R. Peltier (1990), Nonseparable Baroclinic

  13. Simulation of E-Cloud Driven Instability And Its Attenuation...

    Office of Scientific and Technical Information (OSTI)

    Simulation of E-Cloud Driven Instability And Its Attenuation Using a Feedback System in the CERN SPS Citation Details In-Document Search Title: Simulation of E-Cloud Driven...

  14. OBJECTIVE EVALUATION OF FUNCTIONAL ANKLE INSTABILITY AND BALANCE EXERCISE TREATMENT

    E-Print Network [OSTI]

    Jain, Tarang Kumar

    2014-08-31

    OBJECTIVE EVALUATION OF FUNCTIONAL ANKLE INSTABILITY AND BALANCE EXERCISE TREATMENT By Copyright 2014 Tarang Kumar Jain D.P.T., University of Kansas Medical Center, 2012 B.P.T., MGM Medical College, DAVV University, Indore, INDIA, 2003...

  15. Material instability in complex fluids -from conjecture to reality

    E-Print Network [OSTI]

    Goddard, Joe

    ) · Polymers, 21 (4 before 1996) · Colloids, 4 · Suspensions (noncolloidal), 1 (unpublished) · Foams. · Analysis suggests that theoretical model "self destructs". #12;Linear stability analysis* *Ann. Rev. Fluid, 2006. Migrational Instabilities in Suspensions ??* · (a)Two-phase structure arising from (b) particle

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

    E-Print Network [OSTI]

    Al-Baz, Khalid A

    2001-01-01

    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 ...

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

    E-Print Network [OSTI]

    Mir, MD. Mofazzal Hossain

    2001-01-01

    An investigation of the effect of shrink fits on threshold speeds of rotordynamic instability has been performed. It is known that running rotors at supercritical speed can result in some rotordynamic problems (asynchronous ...

  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)

    2014-05-15

    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. Acceleration Mechanics in Relativistic Shocks by the Weibel Instability

    E-Print Network [OSTI]

    K. -I. Nishikawa; P. E. Hardee; C. B. Hededal; G. J. Fishman

    2006-01-11

    Plasma instabilities (e.g., Buneman, Weibel and other two-stream instabilities) created in collisionless shocks may be responsible for particle (electron, positron, and ion) acceleration. Using a 3-D relativistic electromagnetic particle (REMP) code, we have investigated long-term particle acceleration associated with relativistic electron-ion or electron-positron jet fronts propagating into an unmagnetized ambient electron-ion or electron-positron plasma. These simulations have been performed with a longer simulation system than our previous simulations in order to investigate the nonlinear stage of the Weibel instability and its particle acceleration mechanism. The current channels generated by the Weibel instability are surrounded by toroidal magnetic fields and radial electric fields. This radial electric field is quasi stationary and accelerates particles which are then deflected by the magnetic field.

  20. Instabilities in relativistic two-component (super)fluids

    E-Print Network [OSTI]

    Haber, Alexander; Stetina, Stephan

    2015-01-01

    We study two-fluid systems with nonzero fluid velocities and compute their sound modes, which indicate various instabilities. For the case of two zero-temperature superfluids we employ a microscopic field-theoretical model of two coupled bosonic fields, including an entrainment coupling and a non-entrainment coupling. We analyse the onset of the various instabilities systematically and point out that the dynamical two-stream instability can only occur beyond Landau's critical velocity, i.e., in an already energetically unstable regime. A qualitative difference is found for the case of two normal fluids, where certain transverse modes suffer a two-stream instability in an energetically stable regime if there is entrainment between the fluids. Since we work in a fully relativistic setup, our results are very general and of potential relevance for (super)fluids in neutron stars and, in the non-relativistic limit of our results, in the laboratory.

  1. Microturbulence in DIII-D tokamak pedestal. I. Electrostatic instabilities

    SciTech Connect (OSTI)

    Fulton, D. P.; Holod, I.; Lin, Z.; Xiao, Y.

    2014-04-15

    Gyrokinetic simulations of electrostatic driftwave instabilities in a tokamak edge have been carried out to study the turbulent transport in the pedestal of an H-mode plasma. The simulations use annulus geometry and focus on two radial regions of a DIII-D experiment: the pedestal top with a mild pressure gradient and the middle of the pedestal with a steep pressure gradient. A reactive trapped electron instability with a typical ballooning mode structure is excited by trapped electrons in the pedestal top. In the middle of the pedestal, the electrostatic instability exhibits an unusual mode structure, which peaks at the poloidal angle ?=±?/2. The simulations find that this unusual mode structure is due to the steep pressure gradients in the pedestal but not due to the particular DIII-D magnetic geometry. Realistic DIII-D geometry appears to have a stabilizing effect on the instability when compared to a simple circular tokamak geometry.

  2. A quantitative analysis of baroclinic instability in extratropical cyclogenesis 

    E-Print Network [OSTI]

    Gold, David Arthur

    1996-01-01

    Piecewise tendency diagnosis (PTD) is employed to quantify the contribution made by the baroclinic instability (BI) mechanism, as described by Hoskins et al. (1985), to extratropical cyclogenesis occuring near the United ...

  3. Growth of filaments and saturation of the filamentation instability

    SciTech Connect (OSTI)

    Gedalin, M.; Medvedev, M.; Spitkovsky, A.; Krasnoselskikh, V.; Vaivads, A.; Perri, S.

    2010-03-15

    The filamentation instability of counterstreaming beams is a nonresonant hydrodynamic-type instability whose growth rate is a smooth function of the wavelength (scale). As a result, perturbations with all unstable wavelengths develop, and the growth saturates due to the saturation of available current. For a given scale, the magnetic field at saturation is proportional to the scale. As a result, the instability develops in a nearly linear regime, where the unstable modes stop growing as soon as the saturation of the corresponding wavelength is reached. At each moment there exists a dominant scale of the magnetic field which is the scale that reached saturation at this particular time. The smaller scales do not disappear and can be easily distinguished in the current structure. The overall growth of the instability stops when the loss of the streaming ion energy because of deceleration is comparable to the initial ion energy.

  4. The (In)Stability of Planetary Systems

    E-Print Network [OSTI]

    Rory Barnes; Thomas Quinn

    2004-01-09

    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.

  5. MHD Ballooning Instability in the Plasma Sheet

    SciTech Connect (OSTI)

    C.Z. Cheng; S. Zaharia

    2003-10-20

    Based on the ideal-MHD model the stability of ballooning modes is investigated by employing realistic 3D magnetospheric equilibria, in particular for the substorm growth phase. Previous MHD ballooning stability calculations making use of approximations on the plasma compressibility can give rise to erroneous conclusions. Our results show that without making approximations on the plasma compressibility the MHD ballooning modes are unstable for the entire plasma sheet where beta (sub)eq is greater than or equal to 1, and the most unstable modes are located in the strong cross-tail current sheet region in the near-Earth plasma sheet, which maps to the initial brightening location of the breakup arc in the ionosphere. However, the MHD beq threshold is too low in comparison with observations by AMPTE/CCE at X = -(8 - 9)R(sub)E, which show that a low-frequency instability is excited only when beq increases over 50. The difficulty is mitigated by considering the kinetic effects of ion gyrorad ii and trapped electron dynamics, which can greatly increase the stabilizing effects of field line tension and thus enhance the beta(sub)eq threshold [Cheng and Lui, 1998]. The consequence is to reduce the equatorial region of the unstable ballooning modes to the strong cross-tail current sheet region where the free energy associated with the plasma pressure gradient and magnetic field curvature is maximum.

  6. Strange Attractors Characterizing the Osmotic Instability

    E-Print Network [OSTI]

    Tzenov, Stephan I

    2014-01-01

    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 Loren...

  7. Strange Attractors Characterizing the Osmotic Instability

    E-Print Network [OSTI]

    Stephan I. Tzenov

    2014-06-04

    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.

  8. Nebular spectra of pair-instability supernovae

    E-Print Network [OSTI]

    Jerkstrand, A; Heger, A

    2015-01-01

    If very massive stars (M >~ 100 Msun) can form and avoid too strong mass loss during their evolution, they are predicted to explode as pair-instability supernovae (PISNe). One critical test for candidate events is whether their nucleosynthesis yields and internal ejecta structure, being revealed through nebular-phase spectra at t >~ 1 yr, match those of model predictions. Here we compute theoretical spectra based on model PISN ejecta at 1-3 years post-explosion to allow quantitative comparison with observations. The high column densities of PISNe lead to complete gamma-ray trapping for t >~ 2 years which, combined with fulfilled conditions of steady state, leads to bolometric supernova luminosities matching the 56Co decay. Most of the gamma-rays are absorbed by the deep-lying iron and silicon/sulphur layers. The ionization balance shows a predominantly neutral gas state, which leads to emission lines of Fe I, Si I, and S I. For low-mass PISNe the metal core expands slowly enough to produce a forest of distinc...

  9. Suppression of Rayleigh Taylor instability in strongly coupled plasmas

    SciTech Connect (OSTI)

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

    2014-06-15

    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.

  10. Influence of flavor oscillations on neutrino beam instabilities

    SciTech Connect (OSTI)

    Mendonça, J. T.; Haas, F.; Bret, A.

    2014-09-15

    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.

  11. Weibel instability in the field of a short laser pulse

    SciTech Connect (OSTI)

    Grishkov, V. E.; Uryupin, S. A. [Russian Academy of Sciences, Lebedev Physical Institute (Russian Federation)] [Russian Academy of Sciences, Lebedev Physical Institute (Russian Federation)

    2013-03-15

    The growth rate of Weibel instability in a plasma interacting with a high-frequency pulse with a duration less or comparable with the electron mean free time is determined. The growth rate is shown to decrease with decreasing pulse duration. It is found that instability can develop after the short pulse is switched off and the generated magnetic field no longer affects electron motion in the high-frequency field.

  12. INSTABILITY OF MAGNETIZED IONIZATION FRONTS SURROUNDING H II REGIONS

    SciTech Connect (OSTI)

    Kim, Jeong-Gyu; Kim, Woong-Tae, E-mail: jgkim@astro.snu.ac.kr, E-mail: wkim@astro.snu.ac.kr [Center for the Exploration of the Origin of the Universe (CEOU), Astronomy Program, Department of Physics and Astronomy, Seoul National University, Seoul 151-742 (Korea, Republic of)

    2014-12-20

    An ionization front (IF) surrounding an H II region is a sharp interface where a cold neutral gas makes the transition to a warm ionized phase by absorbing UV photons from central stars. We investigate the instability of a plane-parallel D-type IF threaded by parallel magnetic fields, by neglecting the effects of recombination within the ionized gas. We find that weak D-type IFs always have the post-IF magnetosonic Mach number M{sub M2}?1. For such fronts, magnetic fields increase the maximum propagation speed of the IFs, while reducing the expansion factor ? by a factor of 1 + 1/(2?{sub 1}) compared to the unmagnetized case, with ?{sub 1} denoting the plasma beta in the pre-IF region. IFs become unstable to distortional perturbations owing to gas expansion across the fronts, exactly analogous to the Darrieus-Landau instability of ablation fronts in terrestrial flames. The growth rate of the IF instability is proportional linearly to the perturbation wavenumber, as well as the upstream flow speed, and approximately to ?{sup 1/2}. The IF instability is stabilized by gas compressibility and becomes completely quenched when the front is D-critical. The instability is also stabilized by magnetic pressure when the perturbations propagate in the direction perpendicular to the fields. When the perturbations propagate in the direction parallel to the fields, on the other hand, it is magnetic tension that reduces the growth rate, completely suppressing the instability when M{sub M2}{sup 2}<2/(2?{sub 1}?1). When the front experiences an acceleration, the IF instability cooperates with the Rayleigh-Taylor instability to make the front more unstable.

  13. Finite-size instabilities in nuclear energy density functionals

    SciTech Connect (OSTI)

    Hellemans, V.; Heenen, P.-H.; Bender, M.

    2012-10-20

    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.

  14. Decay instability of a whistler in a plasma

    SciTech Connect (OSTI)

    Tewari, D.P.; Sharma, R.R.

    1981-08-01

    The parametric instabilities of a high power whistler in a high-density plasma possess large growth rates when the scattered sideband is an electrostatic lower hybrid mode. The efficient channels of decay include oscillating two stream instability, nonlinear Landau damping, and resonant decay involving ion acoustic and ion cyclotron modes. The processes of nonlinear scattering i.e., the ones possessing whistler sidebands are relatively less significant.

  15. Expanding genomics of mycorrhizal symbiosis

    SciTech Connect (OSTI)

    Kuo, Alan; Kohler, Annegret; Martin, Francis M.; Grigoriev, Igor V.

    2014-11-04

    The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant nutrition, soil health, and carbon cycling. The symbiosis evolved repeatedly and independently as multiple morphotypes [e.g., arbuscular mycorrhizae (AM), ectomycorrhizal (ECM)] in multiple fungal clades (e.g., phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and cultivability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first three mycorrhizal fungal genomes, representing two morphotypes and three phyla. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolve through loss of plant cell wall-degrading enzymes (PCWDEs) and expansion of lineage-specific gene families such as short secreted protein (SSP) effectors. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of families as in Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other two fungi, symbiosis can involve similar solutions as symbiosis-induced SSPs and loss of PCWDEs. The three genomes provide a solid base for addressing fundamental questions about the nature and role of a vital mutualism.

  16. Pair-instability supernovae in the local universe

    SciTech Connect (OSTI)

    Whalen, Daniel J. [Zentrum für Astronomie, Institut für Theoretische Astrophysik, Universität Heidelberg, Albert-Ueberle-Str. 2, D-69120 Heidelberg (Germany); Smidt, Joseph [CCS-2, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Heger, Alexander [Monash Centre for Astrophysics, Monash University, Victoria 3800 (Australia); Hirschi, Raphael [Astrophysics Group, EPSAM, University of Keele, Lennard-Jones Labs, Keele ST5 5BG (United Kingdom); Yusof, Norhasliza [Department of Physics, University of Malaysia, 50603 Kuala Lampur (Malaysia); Even, Wesley; Fryer, Chris L. [T-2, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Stiavelli, Massimo [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Chen, Ke-Jung [Department of Astronomy and Astrophysics, UCSC, Santa Cruz, CA 95064 (United States); Joggerst, Candace C. [XTD-3, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)

    2014-12-10

    The discovery of 150-300 M {sub ?} stars in the Local Group and pair-instability supernova candidates at low redshifts has excited interest in this exotic explosion mechanism. Realistic light curves for pair-instability supernovae at near-solar metallicities are key to identifying and properly interpreting these events as more are found. We have modeled pair-instability supernovae of 150-500 M {sub ?} Z ? 0.1-0.4 Z {sub ?} stars. These stars lose up to 80% of their mass to strong line-driven winds and explode as bare He cores. We find that their light curves and spectra are quite different from those of Population III pair-instability explosions, which therefore cannot be used as templates for low-redshift events. Although non-zero metallicity pair-instability supernovae are generally dimmer than their Population III counterparts, in some cases they will be bright enough to be detected at the earliest epochs at which they can occur, the formation of the first galaxies at z ? 10-15. Others can masquerade as dim, short duration supernovae that are only visible in the local universe and that under the right conditions could be hidden in a wide variety of supernova classes. We also report for the first time that some pair-instability explosions can create black holes with masses of ?100 M {sub ?}.

  17. ; 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

  18. Enhancer Identification through Comparative Genomics

    SciTech Connect (OSTI)

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

    2006-10-01

    With the availability of genomic sequence from numerousvertebrates, a paradigm shift has occurred in the identification ofdistant-acting gene regulatory elements. In contrast to traditionalgene-centric studies in which investigators randomly scanned genomicfragments that flank genes of interest in functional assays, the modernapproach begins electronically with publicly available comparativesequence datasets that provide investigators with prioritized lists ofputative functional sequences based on their evolutionary conservation.However, although a large number of tools and resources are nowavailable, application of comparative genomic approaches remains far fromtrivial. In particular, it requires users to dynamically consider thespecies and methods for comparison depending on the specific biologicalquestion under investigation. While there is currently no single generalrule to this end, it is clear that when applied appropriately,comparative genomic approaches exponentially increase our power ingenerating biological hypotheses for subsequent experimentaltesting.

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

    E-Print Network [OSTI]

    Penn, Kevin; Jensen, Paul R

    2012-01-01

    in microbial nutrient utilization and energy transduction.Energy Joint Genome Institute website (http://genome. ornl.gov/microbial/

  20. The Genome of the Epsilonproteobacterial Chemolithoautotroph Sulfurimonas dentrificans

    E-Print Network [OSTI]

    Sievert, Stefan M.; USF Genomics Class

    2008-01-01

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

  1. Human Genome Education Program

    SciTech Connect (OSTI)

    Richard Myers; Lane Conn

    2000-05-01

    The funds from the DOE Human Genome Program, for the project period 2/1/96 through 1/31/98, have provided major support for the curriculum development and field testing efforts for two high school level instructional units: Unit 1, ''Exploring Genetic Conditions: Genes, Culture and Choices''; and Unit 2, ''DNA Snapshots: Peaking at Your DNA''. In the original proposal, they requested DOE support for the partial salary and benefits of a Field Test Coordinator position to: (1) complete the field testing and revision of two high school curriculum units, and (2) initiate the education of teachers using these units. During the project period of this two-year DOE grant, a part-time Field-Test Coordinator was hired (Ms. Geraldine Horsma) and significant progress has been made in both of the original proposal objectives. Field testing for Unit 1 has occurred in over 12 schools (local and non-local sites with diverse student populations). Field testing for Unit 2 has occurred in over 15 schools (local and non-local sites) and will continue in 12-15 schools during the 96-97 school year. For both curricula, field-test sites and site teachers were selected for their interest in genetics education and in hands-on science education. Many of the site teachers had no previous experience with HGEP or the unit under development. Both of these first-year biology curriculum units, which contain genetics, biotechnology, societal, ethical and cultural issues related to HGP, are being implemented in many local and non-local schools (SF Bay Area, Southern California, Nebraska, Hawaii, and Texas) and in programs for teachers. These units will reach over 10,000 students in the SF Bay Area and continues to receive support from local corporate and private philanthropic organizations. Although HGEP unit development is nearing completion for both units, data is still being gathered and analyzed on unit effectiveness and student learning. The final field testing result from this analysis will contribute to the final revisions of each unit during the second-year of this grant.

  2. Joint Genome Institute's Automation Approach and History

    SciTech Connect (OSTI)

    Roberts, Simon

    2006-07-05

    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.

  3. The Materials Genome Initiative September 25, 2013

    E-Print Network [OSTI]

    Nair, Sankar

    The Materials Genome Initiative September 25, 2013 Dr. Cyrus Wadia Assistant Director, Clean Energy're launching what we call the Materials Genome Initiative. The invention of silicon circuits and lithium ion

  4. 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...

  5. INVESTIGATION Genomic Background and Generation Time

    E-Print Network [OSTI]

    Lynch, Michael

    INVESTIGATION Genomic Background and Generation Time Influence Deleterious Mutation Rates variation is generated and how selection shapes mutation rates over evolutionary time requires knowledge, genomic background and generation time, on deleterious mutation in Daphnia pulicaria, a cyclically

  6. Strategies and tools for whole genome alignments

    SciTech Connect (OSTI)

    Couronne, Olivier; Poliakov, Alexander; Bray, Nicolas; Ishkhanov,Tigran; Ryaboy, Dmitriy; Rubin, Edward; Pachter, Lior; Dubchak, Inna

    2002-11-25

    The availability of the assembled mouse genome makespossible, for the first time, an alignment and comparison of two largevertebrate genomes. We have investigated different strategies ofalignment for the subsequent analysis of conservation of genomes that areeffective for different quality assemblies. These strategies were appliedto the comparison of the working draft of the human genome with the MouseGenome Sequencing Consortium assembly, as well as other intermediatemouse assemblies. Our methods are fast and the resulting alignmentsexhibit a high degree of sensitivity, covering more than 90 percent ofknown coding exons in the human genome. We have obtained such coveragewhile preserving specificity. With a view towards the end user, we havedeveloped a suite of tools and websites for automatically aligning, andsubsequently browsing and working with whole genome comparisons. Wedescribe the use of these tools to identify conserved non-coding regionsbetween the human and mouse genomes, some of which have not beenidentified by other methods.

  7. Unlocking the Secrets of the Genome

    E-Print Network [OSTI]

    Celniker, Susan E.

    The primary objective of the Human Genome Project was to produce high-quality sequences not just for the human genome but also for those of the chief model organisms: Escherichia coli, yeast (Saccharomyces cerevisiae), ...

  8. 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

  9. 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

  10. 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

  11. Correction for measurement error from genotyping-by-sequencing in genomic variance and genomic prediction models

    E-Print Network [OSTI]

    Schierup, Mikkel Heide

    Correction for measurement error from genotyping-by-sequencing in genomic variance and genomic for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University Denmark DLF-Trfolium, Store Heddinge, Denmark CENTER FOR QUANTITATIVE GENETICS AND GENOMICS F2 F2 Simulate sequencing Genotype

  12. The importance of reptilian genomics The study of reptilian genomes is essential if we are to

    E-Print Network [OSTI]

    Georgia, University of

    The importance of reptilian genomics The study of reptilian genomes is essential if we are to understand the patterns of genomic evolution across amniotes (mammals, birds and non-avian reptiles). Non of genome sequencing efforts [2,3]. The green anole (Anolis caroli nensis) is the only non-avian reptilian

  13. A Possible Genome To Architecture Project (GenToA) [The Meta-Genome Project?

    E-Print Network [OSTI]

    Sloman, Aaron

    concern about the Human Genome project, comparing it with buying a book written in a language nobodyA Possible Genome To Architecture Project (GenToA) [The Meta-Genome Project?] Installed: 2 Aug 2010 can a genome specify an information-processing architecture that grows itself guided by interaction

  14. 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

  15. Genomic potential for polysaccharide deconstruction in bacteria

    E-Print Network [OSTI]

    Berlemont, R; Martiny, AC; Martiny, AC

    2015-01-01

    improved data processing and web-based tools. Nucleic Acidsthe SEED genome databases via Web services API: tools for

  16. Joint Genome Institute's Automation Approach and History

    E-Print Network [OSTI]

    Roberts, Simon

    2006-01-01

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

  17. GDB - Human Genome Database final report

    SciTech Connect (OSTI)

    Talbot, C. Conover, Jr.

    2002-01-08

    This is the DOE final report for the GDB, Human Genome Database, project at the Johns Hopkins University.

  18. Materials Genome Initiative for Global Competitiveness

    E-Print Network [OSTI]

    Chandy, John A.

    Materials Genome Initiative for Global Competitiveness June 2011 #12;2 Materials Genome Initiative information visit www.ostp.gov. #12;3Materials Genome Initiative for Global Competitiveness EXECUTIVE OFFICE, the development of advanced materials will fuel many of the emerging industries that will address challenges

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. Introduction to Theme "Genomics in Ecology,

    E-Print Network [OSTI]

    Shaffer, H. Bradley

    Introduction to Theme "Genomics in Ecology, Evolution, and Systematics" H. Bradley Shaffer1, Los Angeles, California 90095; email: brad.shaffer@ucla.edu 2 Center for Genomics and Systems Biology.1146/annurev-ecolsys-081913-123118 Copyright c 2013 by Annual Reviews. All rights reserved Keywords genome

  8. Genome Biology 2005, 6:312 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch

    E-Print Network [OSTI]

    Kellis, Manolis

    Genome Biology 2005, 6-mail: bbernst@fas.harvard.edu. Manolis Kellis. E-mail: manoli@mit.edu Published: 1 March 2005 Genome Biology- tium, which aims to identify a comprehensive `Encyclopedia of DNA elements' in the human genome [http

  9. Methodological Review Data integration and genomic medicine

    E-Print Network [OSTI]

    Petropoulos, Michalis

    Methodological Review Data integration and genomic medicine Brenton Louie a,*, Peter Mork b 2006 Abstract Genomic medicine aims to revolutionize health care by applying our growing understanding the opportunities of genomic medicine as well as identify the informatics challenges in this domain. We also review

  10. DATA QUALITY IN GENOME DATABASES (Research Paper)

    E-Print Network [OSTI]

    Freytag, Johann-Christoph

    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

  11. Genomic Comparisons of Humans and Chimpanzees

    E-Print Network [OSTI]

    Genomic Comparisons of Humans and Chimpanzees Ajit Varki1 and David L. Nelson2 1 Glycobiology, anthropogeny, genetics, evolution, hominid Abstract The genome consists of the entire DNA present of the chimpanzee genome is now available, providing opportunities to better understand genetic contributions

  12. Genome Biology 2006, 7:320 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch

    E-Print Network [OSTI]

    Feschotte, Cedric

    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

  13. 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

  14. Filamentation instability of nonextensive current-driven plasma in the ion acoustic frequency range

    SciTech Connect (OSTI)

    Khorashadizadeh, S. M. Rastbood, E.; Niknam, A. R.

    2014-12-15

    The filamentation and ion acoustic instabilities of nonextensive current-driven plasma in the ion acoustic frequency range have been studied using the Lorentz transformation formulas. Based on the kinetic theory, the possibility of filamentation instability and its growth rate as well as the ion acoustic instability have been investigated. The results of the research show that the possibility and growth rate of these instabilities are significantly dependent on the electron nonextensive parameter and drift velocity. Besides, the increase of electrons nonextensive parameter and drift velocity lead to the increase of the growth rates of both instabilities. In addition, the wavelength region in which the filamentation instability occurs is more stretched in the presence of higher values of drift velocity and nonextensive parameter. Finally, the results of filamentation and ion acoustic instabilities have been compared and the conditions for filamentation instability to be dominant mode of instability have been presented.

  15. 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

  16. LOCAL RADIATION MAGNETOHYDRODYNAMIC INSTABILITIES IN MAGNETICALLY STRATIFIED MEDIA

    SciTech Connect (OSTI)

    Tao, Ted; Blaes, Omer

    2011-11-20

    We study local radiation magnetohydrodynamic instabilities in static, optically thick, vertically stratified media with constant flux mean opacity. We include the effects of vertical gradients in a horizontal background magnetic field. Assuming rapid radiative diffusion, we use the zero gas pressure limit as an entry point for investigating the coupling between the photon bubble instability and the Parker instability. Apart from factors that depend on wavenumber orientation, the Parker instability exists for wavelengths longer than a characteristic wavelength {lambda}{sub tran}, while photon bubbles exist for wavelengths shorter than {lambda}{sub tran}. The growth rate in the Parker regime is independent of the orientation of the horizontal component of the wavenumber when radiative diffusion is rapid, but the range of Parker-like wavenumbers is extended if there exists strong horizontal shear between field lines (i.e., horizontal wavenumber perpendicular to the magnetic field). Finite gas pressure introduces an additional short-wavelength limit to the Parker-like behavior, and also limits the growth rate of the photon bubble instability to a constant value at short wavelengths. We also consider the effects of differential rotation with accretion disk applications in mind. Our results may explain why photon bubbles have not yet been observed in recent stratified shearing box accretion disk simulations. Photon bubbles may physically exist in simulations with high radiation to gas pressure ratios, but higher spatial resolution will be needed to resolve the asymptotically growing unstable wavelengths.

  17. 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.

    2011-02-04

    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.

  18. Genome informatics: Requirements and challenges

    SciTech Connect (OSTI)

    Robbins, R.J.

    1993-12-31

    Informatics of some kind will play a role in every aspect of the Human Genome Project (HGP); data acquisition, data analysis, data exchange, data publication, and data visualization. What are the real requirements and challenges? The primary requirement is clear thinking and the main challenge is design. If good design is lacking, the price will be failure of genome informatics and ultimately failure of the genome project itself. Scientists need good designs to deliver the tools necessary for acquiring and analyzing DNA sequences. As these tools become more efficient, they will need new tools for comparative genomic analyses. To make the tools work, the scientists will need to address and solve nomenclature issues that are essential, if also tedious. They must devise systems that will scale gracefully with the increasing flow of data. The scientists must be able to move data easily from one system to another, with no loss of content. As scientists, they will have failed in their responsibility to share results, should repeating experiments ever become preferable to searching the literature. Their databases must become a new kind of scientific literature and the scientists must develop ways to make electronic data publishing as routine as traditional journal publishing. Ultimately, they must build systems so advanced that they are virtually invisible. In summary, the HGP can be considered the most ambitious, most audacious information-management project ever undertaken. In the HGP, computers will not merely serve as tools for cataloging existing knowledge. Rather, they will serve as instruments, helping to create new knowledge by changing the way the scientists see the biological world. Computers will allow them to see genomes, just as radio telescopes let them see quasars and electron microscopes let them see viruses.

  19. Insights from Human/Mouse genome comparisons

    SciTech Connect (OSTI)

    Pennacchio, Len A.

    2003-03-30

    Large-scale public genomic sequencing efforts have provided a wealth of vertebrate sequence data poised to provide insights into mammalian biology. These include deep genomic sequence coverage of human, mouse, rat, zebrafish, and two pufferfish (Fugu rubripes and Tetraodon nigroviridis) (Aparicio et al. 2002; Lander et al. 2001; Venter et al. 2001; Waterston et al. 2002). In addition, a high-priority has been placed on determining the genomic sequence of chimpanzee, dog, cow, frog, and chicken (Boguski 2002). While only recently available, whole genome sequence data have provided the unique opportunity to globally compare complete genome contents. Furthermore, the shared evolutionary ancestry of vertebrate species has allowed the development of comparative genomic approaches to identify ancient conserved sequences with functionality. Accordingly, this review focuses on the initial comparison of available mammalian genomes and describes various insights derived from such analysis.

  20. Generalized Lyapunov exponent as a unified characterization of dynamical instabilities

    E-Print Network [OSTI]

    Takuma Akimoto; Masaki Nakagawa; Soya Shinkai; Yoji Aizawa

    2014-12-22

    The Lyapunov exponent characterizes an exponential growth rate of the difference of nearby orbits. A positive Lyapunov exponent is a manifestation of chaos. Here, we propose the Lyapunov pair, which is based on the generalized Lyapunov exponent, as a unified characterization of non-exponential and exponential dynamical instabilities in one-dimensional maps. Chaos is classified into three different types, i.e., super-exponential, exponential, and sub-exponential dynamical instabilities. Using one-dimensional maps, we demonstrate super-exponential and sub-exponential chaos and quantify the dynamical instabilities by the Lyapunov pair. In sub-exponential chaos, we show super-weak chaos, which means that the growth of the difference of nearby orbits is slower than a stretched exponential growth. The scaling of the growth is analytically studied by a recently developed theory of a continuous accumulation process, which is related to infinite ergodic theory.

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

    SciTech Connect (OSTI)

    Venturini, M.; Migliorati, M.; Ronsivalle, C.; Vaccarezza, C.

    2009-05-01

    Velocity (or rf) compression has been suggested as a technique for bunch compression complementary to the more established technique involving magnetic chicanes and represents an important research item being investigated at the SPARC test facility. One of the aspects of this technique still not sufficiently understood is its possible impact on the microbunching instability. The purpose of this report is to present the analytical framework for investigating this instability in rf compressors. We use methods similar to those successfully applied to magnetic compressors and derive some integral equations yielding the gain for the instability in linear approximation. The focus here is on the derivation of the relevant equations. Although examples of solutions to these equations are provided we defer a more comprehensive discussion of their implication to a future report. The present study is part of a larger effort for a more comprehensive investigation that eventually will include macroparticle simulations and experiments.

  2. Transient growth of droplet instabilities in a stream

    SciTech Connect (OSTI)

    Jalaal, M., E-mail: mazi@mech.ubc.ca, E-mail: m-jalaal@yahoo.com [Department of Mechanical Engineering, The University of British Columbia, Vancouver, British Columbia V6T 1Z4 (Canada); Mehravaran, K. [School of Engineering, The University of British Columbia, Kelowna, British Columbia V1V 1V7 (Canada)] [School of Engineering, The University of British Columbia, Kelowna, British Columbia V1V 1V7 (Canada)

    2014-01-15

    Droplet deformation is the first stage of all aerodynamically induced-breakups, considerably affecting the characteristics of the atomization. In the present study, using an adaptive volume of fluid method, two and three-dimensional direct numerical simulations have been performed to understand droplet deformation. A high Reynolds number and a range of relatively high Weber numbers are chosen, addressing the shear breakup of droplets in a stream. The study is focused on the initiation and growth of instabilities over the droplet. The role of Kelvin-Helmholtz and Rayleigh-Taylor instabilities in wave formation and azimuthal transverse modulation are shown and the obtained results for the most amplified wave-numbers are compared with instability theories for zero and non-zero vorticity layers. The present results for the most amplified wave-numbers and deformation topologies are in good agreement with the previous experimental results.

  3. Collisionless shock experiments with lasers and observation of Weibel instabilities

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

    Park, H. -S.; Huntington, C. M.; Fiuza, F.; Drake, R. P.; Froula, D. H.; Gregori, G.; Koenig, M.; Kugland, N. L.; Kuranz, C. C.; Lamb, D. Q.; et al

    2015-05-13

    Astrophysical collisionless shocks are common in the universe, occurring in supernova remnants, gamma ray bursts, and protostellar jets. They appear in colliding plasma flows when the mean free path for ion-ion collisions is much larger than the system size. It is believed that such shocks could be mediated via the electromagnetic Weibel instability in astrophysical environments without preexisting magnetic fields. Here, we present laboratory experiments using high-power lasers and investigate the dynamics of high-Mach-number collisionless shock formation in two interpenetrating plasma streams. Our recent proton-probe experiments on Omega show the characteristic filamentary structures of the Weibel instability that are electromagneticmore »in nature with an inferred magnetization level as high as ~1% These results imply that electromagnetic instabilities are significant in the interaction of astrophysical conditions.« less

  4. Sub-ms dynamics of the instability onset of electrospinning

    E-Print Network [OSTI]

    Martina Montinaro; Vito Fasano; Maria Moffa; Andrea Camposeo; Luana Persano; Marco Lauricella; Sauro Succi; Dario Pisignano

    2015-05-01

    Electrospun polymer jets are imaged for the first time at an ultra-high rate of 10,000 frames per second, investigating the process dynamics, and the instability propagation velocity and displacement in space. The polymer concentration, applied voltage bias and needle-collector distance are systematically varied, and their influence on the instability propagation velocity and on the jet angular fluctuations analyzed. This allows us to unveil the instability formation and cycling behavior, and its exponential growth at the onset, exhibiting radial growth rates of the order of 10^3 s^-1. Allowing the conformation and evolution of polymeric solutions to be studied in depth, high-speed imaging at sub-ms scale shows a significant potential for improving the fundamental knowledge of electrified jets, leading to obtain finely controllable bending and solution stretching in electrospinning, and consequently better designed nanofibers morphologies and structures.

  5. Bulk elastic fingering instability in Hele-Shaw cells

    E-Print Network [OSTI]

    Baudouin Saintyves; Olivier Dauchot; Elisabeth Bouchaud

    2013-08-17

    We demonstrate experimentally the existence of a purely elastic fingering instability which arises when air penetrates into an elastomer confined in a Hele-Shaw cell. Fingers appear sequentially and propagate within the bulk of the material as soon as a critical strain, independent of the elastic modulus, is exceeded. Their width depends non-linearly on the distance between the confining glass plates. A key element in the driving force of the instability is the adhesion of layers of gels to the plates, which results in a considerable expense of elastic energy during the growth of the air bubble.

  6. Gauge theories on hyperbolic spaces and dual wormhole instabilities

    SciTech Connect (OSTI)

    Buchel, Alex

    2004-09-15

    We study supergravity duals of strongly coupled four-dimensional gauge theories formulated on compact quotients of hyperbolic spaces. The resulting background geometries are represented by Euclidean wormholes, which complicate establishing the precise gauge theory/string theory correspondence dictionary. These backgrounds suffer from the nonperturbative instabilities arising from the D3D3-bar pair-production in the background four-form potential. We discuss conditions for suppressing this Schwingerlike instability. We find that Euclidean wormholes arising in this construction develop a naked singularity before they can be stabilized.

  7. Instability and Evolution of Nonlinearly Interacting Water Waves

    E-Print Network [OSTI]

    P. K. Shukla; I. Kourakis; B. Eliasson; M. Marklund; L. Stenflo

    2006-08-07

    We consider the modulational instability of nonlinearly interacting two-dimensional waves in deep water, which are described by a pair of two-dimensional coupled nonlinear Schroedinger equations. We derive a nonlinear dispersion relation. The latter is numerically analyzed to obtain the regions and the associated growth rates of the modulational instability. Furthermore, we follow the long term evolution of the latter by means of computer simulations of the governing nonlinear equations and demonstrate the formation of localized coherent wave envelopes. Our results should be useful for understanding the formation and nonlinear propagation characteristics of large amplitude freak waves in deep water.

  8. Universality of the Plastic Instability in Strained Amorphous Solids

    E-Print Network [OSTI]

    Ratul Dasgupta; Smarajit Karmakar; Itamar Procaccia

    2011-11-03

    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.

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

    SciTech Connect (OSTI)

    Rat, V.; Coudert, J. F.

    2010-03-08

    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.

  10. Shear Flow instability in a strongly coupled dusty plasma

    E-Print Network [OSTI]

    Banerjee, D; Chakrabarti, N

    2013-01-01

    Linear stability analysis of strongly coupled incompressible dusty plasma in presence of shear flow has been carried out using Generalized Hydrodynamical(GH) model. With the proper Galilean invariant GH model, a nonlocal eigenvalue analysis has been done using different velocity profiles. It is shown that the effect of elasticity enhances the growth rate of shear flow driven Kelvin- Helmholtz (KH) instability. The interplay between viscosity and elasticity not only enhances the growth rate but the spatial domain of the instability is also widened. The growth rate in various parameter space and the corresponding eigen functions are presented.

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

    SciTech Connect (OSTI)

    M. Ishii; X. Sunn; S. Kuran

    2004-09-27

    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. Genome Improvement at JGI-HAGSC

    SciTech Connect (OSTI)

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

    2012-03-03

    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. 10. international mouse genome conference

    SciTech Connect (OSTI)

    Meisler, M.H.

    1996-12-31

    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.

  14. Role of phase instabilities in the early response of bulk fused...

    Office of Scientific and Technical Information (OSTI)

    Role of phase instabilities in the early response of bulk fused silica during laser-induced breakdown Citation Details In-Document Search Title: Role of phase instabilities in the...

  15. A STUDY OF MICROWAVE INSTABILITIES BY MEANS OF A SQUARE-WELL POTENTIAL

    E-Print Network [OSTI]

    Kim, K.-J.

    2010-01-01

    a more realistic theory of microwave·~nstabi1ities.16-27, 1979 A STUDY OF MICROWAVE INSTABILITIES BY MEANS OF ABerkeley A Study of Microwave Instabilities by means of a

  16. Geophys. Astrophys. Fluid Dynamics, 2002, Vol. 96, No. 1, pp. 3148 EXPERIMENTS ON INSTABILITY OF COLUMNAR

    E-Print Network [OSTI]

    Afanassiev, Iakov

    ) instability due to the background rotation (see e.g., Smyth and Peltier, 1994; Carnevale et al., 1997; Afanasyev and Peltier, 1998; Potylitsin and Peltier, 1998, 1999, 2002) or elliptical instability due

  17. Diagnostics of subsynchronous vibrations in rotating machinery - methodologies to identify potential instability 

    E-Print Network [OSTI]

    Kar, Rahul

    2005-11-01

    Rotordynamic instability can be disastrous for the operation of high speed turbomachinery in the industry. Most ??instabilities?? are due to de-stabilizing cross coupled forces from variable fluid dynamic pressure around a rotor component, acting...

  18. 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

  19. 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

  20. Simulation of e-cloud driven instability and its attenuation using a simulated feedback system in the CERN SPS

    E-Print Network [OSTI]

    Vay, J.-L.

    2011-01-01

    system for the attenuation of e-cloud driven instability”, Proceed- ings Particle Acceleratorsystem for electron cloud-driven instabilities in the CERN SPS”, Proceedings Particle Accelerator

  1. 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)

    2011-11-15

    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.

  2. 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

    2014-03-20

    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.

  3. 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

  4. 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;T he promise of genomics to revolutionize. We imagine a future in which genomic data is a tool for fighting diseases--from childhood cancer Genome Project to today's effort to create international protocols for sharing and interpreting genomic

  5. Prediction of Membrane Proteins in Post-Genomic Era

    E-Print Network [OSTI]

    Kihara, Daisuke

    by the report that the human genome sequencing project has been completed [1,2]. Beyond the human genome, a surge of world-wide genome projects in the last decade have been producing complete genome sequences1 Prediction of Membrane Proteins in Post-Genomic Era Daisuke Kihara1* & Minoru Kanehisa2 1) Donald

  6. ACTIVE INSTABILITY CONTROL EFFECTIVENESS IN A LIQUID FUELED COMBUSTOR

    E-Print Network [OSTI]

    Lieuwen, Timothy C.

    in aircraft and land based gas turbines (Cohen and Banaszuk, 2003; Paschereit et al., 1998). Active control Laboratory or the DOE. Ã Address correspondence to tim.lieuwen@aerospace.gatech.edu Combust. Sci. and Tech effectiveness. Keywords: combustion control, combustion instability INTRODUCTION This note describes

  7. Theory of magnetohydrodynamic instabilities excited by energetic particles in tokamaks*

    E-Print Network [OSTI]

    Chen, Liu

    Theory of magnetohydrodynamic instabilities excited by energetic particles in tokamaks* Liu Chent by the energetic ions/ alpha particles in tokamaks are theoretically analyzed.Here, n is the toroidal modenumber the effectsof energeticions/alpha par- ticles on the magnetohydrodynamic (MHD) stability of tokamak plasmas

  8. Landfill Instability and Its Implications Operation, Construction, and Design

    E-Print Network [OSTI]

    on geotechnical and stability analyses for the design of landfills and remedial closures. It is the mostLandfill Instability and Its Implications for Operation, Construction, and Design By: W. Douglas landfill waste slide, a 300,000 cubic yard landfill failure involving a geosynthetic clay liner, and a 100

  9. Reynolds number effects on RayleighTaylor instability with possible

    E-Print Network [OSTI]

    Loss, Daniel

    ­Taylor instability, a process by which fluids seek to reduce their combined potential energy, plays a key role in all of kinetic energy to released potential energy is not constant, but exhibits a weak Reynolds number­Taylor-driven turbulence as the dominant acceleration mechanism for thermonuclear flames in type-Ia supernovae7

  10. Water bell and sheet instabilities Jeffrey M. Aristoff, Chad Lieberman,

    E-Print Network [OSTI]

    Bush, John W.M.

    Water bell and sheet instabilities Jeffrey M. Aristoff, Chad Lieberman, Erica Chan, and John W. M­3 In our study, glycerol-water solutions with vis- cosities of 1­60 cS were pumped at flow rates of 10 nozzle before collapsing. In Fig. 2, we see the oscillations of a closed water bell formed

  11. 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

  12. FARLEY-BUNEMAN INSTABILITY IN THE SOLAR CHROMOSPHERE

    SciTech Connect (OSTI)

    Gogoberidze, G.; Voitenko, Y.; Poedts, S.; Goossens, M.

    2009-11-20

    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.

  13. Effects of the Hot Electron Interchange Instability on

    E-Print Network [OSTI]

    ? · Engineering: ·Superconducting magnet surrounded by fusion plasma? #12;EEO_ICC06_INVTLK 5 The Levitated DipoleEffects of the Hot Electron Interchange Instability on Plasma Confined in a Dipolar Magnetic Field Eugenio Ortiz For the Levitated Dipole Experiment Team Innovative Confinement Concepts 2006 Austin, Texas

  14. Transverse instabilities of deep-water solitary waves

    E-Print Network [OSTI]

    Carter, John

    Transverse instabilities of deep-water solitary waves BY BERNARD DECONINCK 1, *, DMITRY E train in deep water is described by a one-dimensional soliton solution of a two- dimensional nonlinear­ capillary waves in deep water that may be two-dimensional, nearly monochro- matic, and are slowly modulated

  15. Electron temperature anisotropy instabilities represented by superposition of streams

    SciTech Connect (OSTI)

    Inglebert, A.; Ghizzo, A.; Reveille, T.; Bertrand, P. [IJL UMR 7198, Universite de Lorraine, BP 70239 F-54506 Vandoeuvre les Nancy (France); Califano, F. [Department of Physics, University of Pisa, Pisa (Italy)

    2012-12-15

    The generation of magnetic field, together with the electrostatic activity met in the saturation regime of the Weibel instability (WI), is investigated by means of an analytical multi-stream model in a Hamiltonian framework. Taking advantage from the invariance of the generalized canonical momentum, the model allows to reduce the full kinetic 1D2V Vlasov equation into several 1D1V equations while keeping its kinetic character. The multi-stream model provides a more complete and accurate picture of the Weibel instability, because it is possible to separate the specific contribution of each stream during the development of the Weibel instability. An interesting result for the multi-stream mode is a lower cost in the perpendicular treatment of the p{sub y} momentum component since no differential operator associated with some approximate numerical scheme has to be carried out on this variable. Indeed, a small number of streams or particle classes are sufficient to correctly describe the magnetic field generation and the mixed electrostatic- electromagnetic nature of the instability.

  16. Thermal Instability-Induced Interstellar Turbulence 1 Alexei Kritsuk

    E-Print Network [OSTI]

    Kritsuk, Alexei

    Thermal Instability-Induced Interstellar Turbulence 1 Alexei Kritsuk University of California, San Diego, USA Saint Petersburg State University, Russia In collaboration with Mike Norman, UCSD http://akpc.ucsd.edu/Thermal conditions: periodic box Parameters: box size L, 0, T0, heating rate , = 5 3 , metallicity Z = Z Thermal

  17. Experimental Verification of Morphological Instability in Freezing Aqueous Colloidal Suspensions

    E-Print Network [OSTI]

    Wettlaufer, John S.

    Experimental Verification of Morphological Instability in Freezing Aqueous Colloidal Suspensions S; published 9 June 2008) We describe an experimental test of a new theory of the unidirectional freezing of aqueous colloidal suspensions. At low freezing speeds a planar ice lens completely rejects the particles

  18. 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

  19. Electrical charging during the sharkskin instability of a metallocene melt

    E-Print Network [OSTI]

    S. Tonon; A. Lavernhe-Gerbier; F. Flores; A. Allal; C. Guerret-Piécourt

    2007-07-18

    Flow instabilities are widely studied because of their economical and theoretical interest, however few results have been published about the polymer electrification during the extrusion. Nevertheless the generation of the electrical charges is characteristic of the interaction between the polymer melt and the die walls. In our study, the capillary extrusion of a metallocene polyethylene (mPE) through a tungsten carbide die is characterized through accurate electrical measurements thanks a Faraday pail. No significant charges are observed since the extrudate surface remains smooth. However, as soon as the sharkskin distortion appears, measurable charges are collected (around 5 10-8 C/m2). Higher level of charges are measured during the spurt or the gross-melt fracture (g.m.f) defects. This work is focused on the electrical charging during the sharkskin instability. The variation of the electrical charges versus the apparent wall shear stress is investigated for different die geometries. This curve exhibits a linear increase, followed by a sudden growth just before the onset of the spurt instability. This abrupt charging corresponds also to the end of the sharkskin instability. It is also well-known that wall slip appears just at the same time, with smaller velocity values than during spurt flow. Our results indicate that electrification could be a signature of the wall slip. We show also that the electrification curves can be shifted according to the time-temperature superposition principle, leading to the conclusion that molecular features of the polymer are also involved in this process.

  20. The influence of internal friction on rotordynamic instability 

    E-Print Network [OSTI]

    Srinivasan, Anand

    2004-09-30

    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...

  1. Long-wave instabilities and saturation in thin film equations

    E-Print Network [OSTI]

    Pugh, Mary

    to shorter wavelengths which then dissipate the energy. The nonlinearity in the KS equation is advective.2) The equation arises as an interface model in bio-fluids [15], solar convec- tion [19], and binary alloys [48Long-wave instabilities and saturation in thin film equations A. L. Bertozzi Department

  2. Longwave instabilities and saturation in thin film equations

    E-Print Network [OSTI]

    Pugh, Mary

    then dissipate the energy. The nonlinearity in the KS equation is advective, and a#ects the dy­ namics di.2) The equation arises as an interface model in bio­fluids [15], solar convec­ tion [19], and binary alloys [48Long­wave instabilities and saturation in thin film equations A. L. Bertozzi Department

  3. LBL-35528/CBP-074 CHAPTER 12: BEAM INSTABILITIES

    E-Print Network [OSTI]

    Furman, Miguel

    of the particles in the accelerator in given external electric and magnetic fields. As the particles traverse and can influence the beam dynamics, and hence the machine performance, significantly. Some machines such as damping rings and e+-e­ colliders. At the core of any discussion on instabilities

  4. An Analysis of Time-instability in Web Search Results

    E-Print Network [OSTI]

    Murphy, Robert F.

    An Analysis of Time-instability in Web Search Results Jinyoung Kim1 and Vitor R. Carvalho2 1@cs.cmu.edu Abstract. Due to the dynamic nature of web and the complex architec- tures of modern commercial search collected from a commercial web search engine over several weeks. Our analysis shows that the results from

  5. Bulge growth through disk instabilities in high-redshift galaxies

    E-Print Network [OSTI]

    Bournaud, Frederic

    2015-01-01

    The role of disk instabilities, such as bars and spiral arms, and the associated resonances, in growing bulges in the inner regions of disk galaxies have long been studied in the low-redshift nearby Universe. There it has long been probed observationally, in particular through peanut-shaped bulges. This secular growth of bulges in modern disk galaxies is driven by weak, non-axisymmetric instabilities: it mostly produces pseudo-bulges at slow rates and with long star-formation timescales. Disk instabilities at high redshift (z>1) in moderate-mass to massive galaxies (10^10 to a few 10^11 Msun of stars) are very different from those found in modern spiral galaxies. High-redshift disks are globally unstable and fragment into giant clumps containing 10^8-10^9 Msun of gas and stars each, which results in highly irregular galaxy morphologies. The clumps and other features associated to the violent instability drive disk evolution and bulge growth through various mechanisms, on short timescales. The giant clumps can...

  6. Alfvénic instabilities driven by runaways in fusion plasmas

    SciTech Connect (OSTI)

    Fülöp, T.; Newton, S.

    2014-08-15

    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.

  7. Heavy-fermion instability in double-degenerate plasmas

    SciTech Connect (OSTI)

    Akbari-Moghanjoughi, M.

    2012-07-15

    In this work, we study the propagations of normal frequency modes for quantum hydrodynamic waves in the linear limit and introduce a new kind of instability in a double-degenerate plasma. Three different regimes, namely, low, intermediate, and high magnetic field strengths are considered which span the applicability of the work to a wide variety of environments. Distinct behavior is observed for different regimes, for instance, in the laboratory-scale field regime no frequency-mode instability occurs unlike those of intermediate and high magnetic-field strength regimes. It is also found that the instability of this kind is due to the heavy-fermions which appear below a critical effective-mass parameter ({mu}{sub cr}={radical}(3)) and that the responses of the two (lower and upper frequency) modes to fractional effective-mass change in different effective-mass parameter ranges (below and above the critical value) are quite opposite to each other. It is shown that the heavy-fermion instability due to extremely high magnetic field such as that encountered for a neutron-star crust can lead to confinement of stable propagations in both lower and upper frequency modes to the magnetic poles. Current study can have important implications for linear wave dynamics in both laboratory and astrophysical environments possessing high magnetic fields.

  8. Scholarly Paper Coupled Instability in the Equatorial Pacific Ocean

    E-Print Network [OSTI]

    Maryland at College Park, University of

    Scholarly Paper Coupled Instability in the Equatorial Pacific Ocean Hua Chen Advisor: Raghu's a cycle or an event depends on the mean state of equatorial Pacific Ocean, which is influenced by mean problem in the equatorial Pacific ocean. The control run with a coupling coefficient 0.4 and relatively

  9. Controlling Plasma Instabilities: A Multidisciplinary Approach Bedros Afeyan

    E-Print Network [OSTI]

    Levi, Anthony F. J.

    for optimal and adaptive control of instabilities. Biography Dr. Bedros Afeyan is a plasma physicist, worked at Chalk River Nuclear Labs in Ontario for two summers and received his Masters and PhD degrees and runs a small research company in Pleasanton, CA, Polymath Research Inc. where they work on federal

  10. Strategic Control of Transverse Jet Shear Layer Instabilities J. Davitian,

    E-Print Network [OSTI]

    M'Closkey, Robert T.

    engines, dilution jet injection in gas turbine combustors, thrust vectoring jets, and turbine blade filmStrategic Control of Transverse Jet Shear Layer Instabilities J. Davitian, C. Hendrickson, D jet in crossflow or transverse jet. Jet nozzles that are flush as well as elevated with respect

  11. A Mechanism for Extrusion Instabilities in Polymer Melts

    E-Print Network [OSTI]

    Georgiou, Georgios

    POLYMER ENGINEERINGAND SCIENCE, DECEMBER 1999, Vol. 39, No. 12 #12;A Mechanismfor ExtrusionA Mechanism for Extrusion Instabilities in Polymer Melts M.FWULLAS Faculty of Applied Physics Foundationfor Research and Technology-HeUas(Fo. R. T.H.) Znstitute of Electronic Structure and Laser,P.O. Box

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

    ScienceCinema (OSTI)

    Zimmer, Carl [New York Times

    2013-01-22

    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

  13. 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

    2012-03-20

    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

  14. Human-mouse comparative genomics: successes and failures to reveal functional regions of the human genome

    SciTech Connect (OSTI)

    Pennacchio, Len A.; Baroukh, Nadine; Rubin, Edward M.

    2003-05-15

    Deciphering the genetic code embedded within the human genome remains a significant challenge despite the human genome consortium's recent success at defining its linear sequence (Lander et al. 2001; Venter et al. 2001). While useful strategies exist to identify a large percentage of protein encoding regions, efforts to accurately define functional sequences in the remaining {approx}97 percent of the genome lag. Our primary interest has been to utilize the evolutionary relationship and the universal nature of genomic sequence information in vertebrates to reveal functional elements in the human genome. This has been achieved through the combined use of vertebrate comparative genomics to pinpoint highly conserved sequences as candidates for biological activity and transgenic mouse studies to address the functionality of defined human DNA fragments. Accordingly, we describe strategies and insights into functional sequences in the human genome through the use of comparative genomics coupled wit h functional studies in the mouse.

  15. Q-switching instability in a mode-locked semiconductor laser

    E-Print Network [OSTI]

    Vladimirov, Andrei G.

    Q-switching instability in a mode-locked semiconductor laser Dmitrii Rachinskii Department November 7, 2005 (Doc. ID 62428) We suggest semianalytic estimates for the Q-switching instability boundary situation for this class of lasers. The Q-switching instability boundary is obtained as a Neimark

  16. Shell-instability generated waves by low energy electrons on converging magnetic field lines

    E-Print Network [OSTI]

    California at Berkeley, University of

    Shell-instability generated waves by low energy electrons on converging magnetic field lines D that the shell-instability can generate electrostatic and electromagnetic wave modes: whistler waves, electron´cre´au (2006), Shell-instability generated waves by low energy electrons on converging magnetic field lines

  17. Lowsymmetric bubbles in RayleighTaylor instability S.I.Abarzhi

    E-Print Network [OSTI]

    New York at Stoney Brook, State University of

    The Rayleigh­Taylor instability (RTI) is the interface instability. RTI occurs if a heavy fluid layer of RTI applications [3]. Often in experiments on the Rayleigh­Taylor instability, the fluids mixing in RTI is poorly understood. Heuristic models of the turbulent mixing use self

  18. Rayleigh-Taylor instability with magnetic fluids: Experiment and theory G. Pacitto,1,2,

    E-Print Network [OSTI]

    Widom, Michael

    above a less dense fluid, a gravi- tational instability, called the Rayleigh-Taylor instability RTI 1 remains to be learned about it. The development of patterns resulting from the RTI can be divided melting of two miscible fluids by the RTI. This instability generates micron- sized drops

  19. Low-symmetric bubbles in Rayleigh-Taylor instability S.I.Abarzhi

    E-Print Network [OSTI]

    New York at Stoney Brook, State University of

    The Rayleigh-Taylor instability (RTI) is the interface instability. RTI occurs if a heavy fluid layer of RTI applications [3]. Often in experiments on the Rayleigh-Taylor instability, the fluids mixing in RTI is poorly understood. Heuristic models of the turbulent mixing use self

  20. 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

  1. Gap size effects on centrifugally and rotationally driven instabilities innocent MutabazP and Christiane Normand

    E-Print Network [OSTI]

    Wesfreid, José Eduardo

    Gap size effects on centrifugally and rotationally driven instabilities innocent Mutabaz 1991) The rotation effects on centrifugally driven instabilities in curved channel flow with a finite these instabilities are due to the curvature of streamlines in- ducing a centrifugal force which unbalances the radial

  2. Mixed Layer Instabilities and Restratification GIULIO BOCCALETTI, RAFFAELE FERRARI, AND BAYLOR FOX-KEMPER

    E-Print Network [OSTI]

    Cessi, Paola

    . These instabilities, which are referred to as mixed layer instabilities (MLIs), differ from instabilities in the ocean are on the order of a day. Linear stability analysis and fully nonlinear simulations are used to study MLIs and their impact on mixed layer restratification. The main result is that MLIs are a leading-order process

  3. Instabilities in Molecular Dynamics Integrators used in Hybrid Monte Carlo Simulations

    E-Print Network [OSTI]

    B. Joo; UKQCD Collaboration

    2001-10-11

    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.

  4. Strong instability of standing waves for nonlinear Klein-Gordon equation and

    E-Print Network [OSTI]

    Todorova, Grozdena

    Strong instability of standing waves for nonlinear Klein-Gordon equation and Klein Classification: Primary 35L70; Secondary 35B35, 35A15 Keywords: nonlinear Klein-Gordon equations, standing waves, instability, Klein-Gordon-Zakharov system Abstract The orbital instability of ground state standing waves eit

  5. Combustion instabilities in sudden expansion oxy-fuel flames

    SciTech Connect (OSTI)

    Ditaranto, Mario; Hals, Joergen

    2006-08-15

    An experimental study on combustion instability is presented with focus on oxy-fuel type combustion. Oxidants composed of CO{sub 2}/O{sub 2} and methane are the reactants flowing through a premixer-combustor system. The reaction starts downstream a symmetric sudden expansion and is at the origin of different instability patterns depending on oxygen concentration and Reynolds number. The analysis has been conducted through measurement of pressure, CH* chemiluminescence, and velocity. As far as stability is concerned, oxy-fuel combustion with oxygen concentration similar to that found in air combustion cannot be sustained, but requires at least 30% oxygen to perform in a comparable manner. Under these conditions and for the sudden expansion configuration used in this study, the instability is at low frequency and low amplitude, controlled by the flame length inside the combustion chamber. Above a threshold concentration in oxygen dependent on equivalence ratio, the flame becomes organized and concentrated in the near field. Strong thermoacoustic instability is then triggered at characteristic acoustic modes of the system. Different modes can be triggered depending on the ratio of flame speed to inlet velocity, but for all types of instability encountered, the heat release and pressure fluctuations are linked by a variation in mass-flow rate. An acoustic model of the system coupled with a time-lag-based flame model made it possible to elucidate the acoustic mode selection in the system as a function of laminar flame speed and Reynolds number. The overall work brings elements of reflection concerning the potential risk of strong pressure oscillations in future gas turbine combustors for oxy-fuel gas cycles. (author)

  6. The plasmoid instability during asymmetric inflow magnetic reconnection

    SciTech Connect (OSTI)

    Murphy, Nicholas A. [Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts 02138 (United States)] [Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts 02138 (United States); Young, Aleida K. [Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts 02138 (United States) [Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts 02138 (United States); Department of Atmospheric, Oceanic and Space Sciences, University of Michigan, Ann Arbor, Michigan 48109 (United States); Shen, Chengcai [Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts 02138 (United States) [Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts 02138 (United States); Yunnan Astronomical Observatory, Chinese Academy of Sciences, Kunming, Yunnan 650011 (China); Graduate School of the Chinese Academy of Sciences, Beijing 100049 (China); Lin, Jun [Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts 02138 (United States) [Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts 02138 (United States); Yunnan Astronomical Observatory, Chinese Academy of Sciences, Kunming, Yunnan 650011 (China); Ni, Lei [Yunnan Astronomical Observatory, Chinese Academy of Sciences, Kunming, Yunnan 650011 (China)] [Yunnan Astronomical Observatory, Chinese Academy of Sciences, Kunming, Yunnan 650011 (China)

    2013-06-15

    Theoretical studies of the plasmoid instability generally assume that the reconnecting magnetic fields are symmetric. We relax this assumption by performing two-dimensional resistive magnetohydrodynamic simulations of the plasmoid instability during asymmetric inflow magnetic reconnection. Magnetic asymmetry modifies the onset, scaling, and dynamics of this instability. Magnetic islands develop preferentially into the weak magnetic field upstream region. Outflow jets from individual X-points impact plasmoids obliquely rather than directly as in the symmetric case. Consequently, deposition of momentum by the outflow jets into the plasmoids is less efficient, the plasmoids develop net vorticity, and shear flow slows down secondary merging between islands. Secondary merging events have asymmetry along both the inflow and outflow directions. Downstream plasma is more turbulent in cases with magnetic asymmetry because islands are able to roll around each other after exiting the current sheet. As in the symmetric case, plasmoid formation facilitates faster reconnection for at least small and moderate magnetic asymmetries. However, when the upstream magnetic field strengths differ by a factor of 4, the reconnection rate plateaus at a lower value than expected from scaling the symmetric results. We perform a parameter study to investigate the onset of the plasmoid instability as a function of magnetic asymmetry and domain size. There exist domain sizes for which symmetric simulations are stable but asymmetric simulations are unstable, suggesting that moderate magnetic asymmetry is somewhat destabilizing. We discuss the implications for plasmoid and flux rope formation in solar eruptions, laboratory reconnection experiments, and space plasmas. The differences between symmetric and asymmetric simulations provide some hints regarding the nature of the three-dimensional plasmoid instability.

  7. Editorial: Human and Evolutionary Genomics Human Genomics has, from its outset, included a great deal of evolutionary analysis. The

    E-Print Network [OSTI]

    Pollock, David

    Editorial: Human and Evolutionary Genomics Human Genomics has, from its outset, included a great genomics. This inclusion is the result of an obvious trend in the field of genomics to incorporate more. The world now has over one hundred complete bacterial genomes, and with human, roundworm, multiple

  8. Unlocking the secrets of the genome Despite the successes of genomics, little is known about how genetic information produces complex

    E-Print Network [OSTI]

    Kellis, Manolis

    Unlocking the secrets of the genome Despite the successes of genomics, little is known about how genomes could change that. T he primary objective of the Human Genome Project was to produce high- quality sequences not just for the human genome but also for those of the chief model organisms:Escherichia coli

  9. Abstract--As the human genome project progresses and some microbial and eukaryotic genomes are recognized, a

    E-Print Network [OSTI]

    Zelikovsky, Alexander

    1 of 4 Abstract--As the human genome project progresses and some microbial and eukaryotic genomes. This technology promises to monitor the whole genome at once, so that researchers can study the whole genome virus as well as simulated data. Our experiments show that the genomic data follow the pattern predicted

  10. GenomePro -Processing Genomic Files Of All Sizes Technical Report FIU-SCIS-2015-01-20-1

    E-Print Network [OSTI]

    Robinson, Michael

    to further understand not only our humane genome but any life form genome. Keywords ­ Gigabytes, Terabytes, Genome, Sub-Sequence, I.INTRODUCTION The Genome Project, started in 1990 and completed in April 2003, sequenced the human genome producing files of about 3.2 Gigabytes. During the next 10 years a new sequencing

  11. 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.

    2009-06-18

    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.

  12. Diatom Genomics (2009 JGI User Meeting)

    ScienceCinema (OSTI)

    Ambrust, Ginger

    2011-04-25

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

  13. Metagenomics, metatranscriptomics and single cell genomics reveal...

    Office of Scientific and Technical Information (OSTI)

    and single cell genomics reveal functional response of active Oceanospirillales to Gulf oil spill Citation Details In-Document Search Title: Metagenomics, metatranscriptomics and...

  14. Nuclear and mitochondrial genome defects in autisms.

    E-Print Network [OSTI]

    Smith, M; Spence, MA; Flodman, P

    2009-01-01

    435– 439. Smith et al. : Nuclear and Mitochondrial Genomebe advantageous. Smith et al. : Nuclear and MitochondrialAND MEDICAL GENETICS 2009 Nuclear and Mitochondrial Genome

  15. DOE Joint Genome Institute 2008 Progress Report

    E-Print Network [OSTI]

    Gilbert, David

    2009-01-01

    proteins for biofuel production. Trends in Mi- crobiology,could help improve biofuel production. Diatom Genome Helpsa key target. Current biofuel production meth- ods, such as

  16. Statistical Challenges in Functional Genomics Paola Sebastiani and Marco Ramoni

    E-Print Network [OSTI]

    Spang, Rainer

    in Functional Genomics 1. The Human Genome Project The Human Genome Project (HGP) is a multi-year effort in 1990, the HGP is expected to render its final results in 2005, but the staggering technological

  17. ComBo : a visualization tool for comparative genomic data

    E-Print Network [OSTI]

    Yu, Tamara H. (Tamara Hui)

    2004-01-01

    Propelled by advances in sequencing technology, the advent of the genomic era brings the challenge of managing and interpreting massive amount of genomic data. A number of single-genome browsers have been developed for ...

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

    E-Print Network [OSTI]

    Payseur, Bret

    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

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

    E-Print Network [OSTI]

    Boore, Jeffrey L.

    2009-01-01

    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

  20. The common ground of genomics and systems biology

    E-Print Network [OSTI]

    Conesa, Ana; Mortazavi, Ali

    2014-01-01

    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.

  1. UV Decontamination of MDA Reagents for Single Cell Genomics

    E-Print Network [OSTI]

    Lee, Janey

    2011-01-01

    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

  2. Phytozome: A Comparative Platform for Green Plant Genomics

    E-Print Network [OSTI]

    Goodstein, David M.

    2012-01-01

    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-

  3. Structural Genomics of Minimal Organisms: Pipeline and Results

    E-Print Network [OSTI]

    Kim, Sung-Hou

    2008-01-01

    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

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

    E-Print Network [OSTI]

    Penn, Kevin; Jensen, Paul R

    2012-01-01

    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

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

    E-Print Network [OSTI]

    Boore, Jeffrey L.

    2009-01-01

    built for the Human Genome Project (Lander et al. , 2001;developed for the Human Genome Project can now best behuman genome, and nearly all of this is directed at projects

  6. The Impact of Structural Genomics: Expectations and Outcomes

    E-Print Network [OSTI]

    Chandonia, John-Marc; Brenner, Steven E.

    2005-01-01

    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

  7. Finding conserved patterns in biological sequences, networks and genomes 

    E-Print Network [OSTI]

    Yang, Qingwu

    2009-05-15

    approach for investigating clustering of related genes across multiple genomes for a given gene cluster. By analyzing gene clustering in 400 bacterial genomes, we show that our algorithm is efficient enough to study gene clusters across hundreds of genomes....

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

    SciTech Connect (OSTI)

    Chain, Patrick [DOE-JGI

    2009-05-27

    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"

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

    E-Print Network [OSTI]

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

    2005-01-01

    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

  10. 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.

    2014-01-01

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

  11. DOE JGI Whole Genome Shotgun Sequencing, part 2

    ScienceCinema (OSTI)

    Miranda Harmon-Smith

    2010-09-01

    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).

  12. DOE JGI Whole Genome Shotgun Sequencing, part 1

    ScienceCinema (OSTI)

    Miranda Harmon-Smith

    2010-09-01

    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).

  13. Illumina Production Sequencing at DOE Joint Genome Institute

    E-Print Network [OSTI]

    Tarver, Angela

    2014-01-01

    Production Sequencing at DOE Joint Genome Institute Angelathe US Department of Energy (DOE) Joint Genome Institute isthe Office of Science of the DOE under Contract Number DE-

  14. Target Selection and Deselection at the Berkeley StructuralGenomics...

    Office of Scientific and Technical Information (OSTI)

    and Deselection at the Berkeley StructuralGenomics Center At the Berkeley Structural Genomics Center (BSGC), our goalis to obtain a near-complete structural complement of proteins...

  15. Using Genomics to Dissect Seed Development (JGI Seventh Annual...

    Office of Scientific and Technical Information (OSTI)

    Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting) Citation Details In-Document Search Title: Using...

  16. DOE JGI Whole Genome Shotgun Sequencing, part 3

    ScienceCinema (OSTI)

    Miranda Harmon-Smith

    2010-09-01

    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).

  17. Fueling Future with Algal Genomics (Conference) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    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...

  18. 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

    2011-04-29

    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.

  19. Uses of antimicrobial genes from microbial genome

    DOE Patents [OSTI]

    Sorek, Rotem; Rubin, Edward M.

    2013-08-20

    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.

  20. Genome Biology 2004, 5:343 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch

    E-Print Network [OSTI]

    ://genomebiology.com/2004/5/9/343 © 2004 BioMed Central Ltd A report on the Keystone Symposium `Structural Genomics', held-dollar-plus folly? Two concurrent Keystone Symposia, `Structural Genomics' and `Frontiers in Structural Biology set up an auto- mated pipeline to annotate proteins of known structure but unknown function. The push

  1. INVITED: Comparative Microbial Genomics Giri Narasimhan

    E-Print Network [OSTI]

    Narasimhan, Giri

    with greater ease and greater confidence. Keywords-microbes; comparative genomics; I. INTRODUCTION Microbes, and functional capabilities, often in order to adapt to their harsh environments, compete with other microbes, or to reproduce. While there do exist microbes with enormous genomes, most microbes have smaller and simpler

  2. Fungal biology: compiling genomes and exploiting them

    SciTech Connect (OSTI)

    Labbe, Jessy L; Uehling, Jessie K; Payen, Thibaut; Plett, Jonathan

    2014-01-01

    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).

  3. Genome Biology 2004, 5:250 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch

    E-Print Network [OSTI]

    Gent, Universiteit

    :250 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch Minireview Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids Yves Van pufferfish Tetraodon nigroviridis. Ray-finned fish underwent a whole-genome duplication some 350 million have also yielded a surprising finding: ray-finned fish (Actinopterygii), such as pufferfish might have

  4. Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts

    E-Print Network [OSTI]

    2006-01-01

    and last nucleotide of the PMU on the AY-WB chromosome. ORFscontained truncated versions of PMU ORFs with similar geneIt is likely that these PMU-like clusters are in the process

  5. Functional Insights from Structural Genomics

    SciTech Connect (OSTI)

    Forouhar,F.; Kuzin, A.; Seetharaman, J.; Lee, I.; Zhou, W.; Abashidze, M.; Chen, Y.; Montelione, G.; Tong, L.; et al

    2007-01-01

    Structural genomics efforts have produced structural information, either directly or by modeling, for thousands of proteins over the past few years. While many of these proteins have known functions, a large percentage of them have not been characterized at the functional level. The structural information has provided valuable functional insights on some of these proteins, through careful structural analyses, serendipity, and structure-guided functional screening. Some of the success stories based on structures solved at the Northeast Structural Genomics Consortium (NESG) are reported here. These include a novel methyl salicylate esterase with important role in plant innate immunity, a novel RNA methyltransferase (H. influenzae yggJ (HI0303)), a novel spermidine/spermine N-acetyltransferase (B. subtilis PaiA), a novel methyltransferase or AdoMet binding protein (A. fulgidus AF{_}0241), an ATP:cob(I)alamin adenosyltransferase (B. subtilis YvqK), a novel carboxysome pore (E. coli EutN), a proline racemase homolog with a disrupted active site (B. melitensis BME11586), an FMN-dependent enzyme (S. pneumoniae SP{_}1951), and a 12-stranded {beta}-barrel with a novel fold (V. parahaemolyticus VPA1032).

  6. Intensity-based modified Doppler variance algorithm: application to phase instable and phase stable optical coherence tomography systems

    E-Print Network [OSTI]

    Liu, Gangjun; Chou, Lidek; Jia, Wangcun; Qi, Wenjuan; Choi, Bernard; Chen, Zhongping

    2011-01-01

    domain OCT system. A microelectromechanical systems (MEMS)instable situation. A microelectromechanical systems (MEMS)

  7. Proteogenomics : applications of mass spectrometry at the interface of genomics and proteomics

    E-Print Network [OSTI]

    Castellana, Natalie

    2012-01-01

    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. How Pseudo-Boolean Programming can help Genome Rearrangement Distance Computation

    E-Print Network [OSTI]

    Fertin, Guillaume

    How Pseudo-Boolean Programming can help Genome Rearrangement Distance Computation S vialette@lri.fr Abstract. Computing genomic distances between whole genomes is a fundamental problem in comparative genomics. Recent researches have resulted in different genomic distance definitions: number

  9. Genomic definition of species. Revision 2

    SciTech Connect (OSTI)

    Crkvenjakov, R.; Drmanac, R.

    1993-03-01

    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.

  10. Electron Beam Instability in Left-Handed Media

    E-Print Network [OSTI]

    Yury P. Bliokh; Sergey Savel'ev; Franco Nori

    2008-04-08

    We predict that two electron beams can develop an instability when passing through a slab of left-handed media (LHM). This instability, which is inherent only for LHM, originates from the backward Cherenkov radiation and results in a self-modulation of the beams and radiation of electromagnetic waves. These waves leave the sample via the rear surface of the slab (the beam injection plane) and form two shifted bright circles centered at the beams. A simulated spectrum of radiation has well-separated lines on top of a broad continuous spectrum, which indicates dynamical chaos in the system. The radiation intensity and its spectrum can be controlled either by the beams' current or by the distance between the two beams.

  11. Resonant Dampers for Parametric Instabilities in Gravitational Wave Detectors

    E-Print Network [OSTI]

    Gras, Slawek; Barsotti, Lisa; Evans, Matthew

    2015-01-01

    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.

  12. Stabilization of beam-weibel instability by equilibrium density ripples

    SciTech Connect (OSTI)

    Mishra, S. K. Kaw, Predhiman; Das, A.; Sengupta, S.; Ravindra Kumar, G.

    2014-01-15

    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. Extensional Instability in Electro-Osmotic Microflows of Polymer Solutions

    E-Print Network [OSTI]

    R. M. Bryce; M. R. Freeman

    2010-02-24

    Fluid transport in microfluidic systems typically is laminar due to the low Reynolds number characteristic of the flow. The inclusion of suspended polymers imparts elasticity to fluids, allowing instabilities to be excited when substantial polymer stretching occurs. For high molecular weight polymer chains we find that flow velocities achievable by standard electro-osmotic pumping are sufficient to excite extensional instabilities in dilute polymer solutions. We observe a dependence in measured fluctuations on polymer concentration which plateaus at a threshold corresponding to the onset of significant molecular crowding in macromolecular solutions; plateauing occurs well below the overlap concentration. Our results show that electro-osmotic flows of complex fluids are disturbed from the steady regime, suggesting potential for enhanced mixing and requiring care in modeling the flow of complex liquids such as biopolymer suspensions.

  14. Laplace-Fourier analysis and instabilities of a gainy slab

    E-Print Network [OSTI]

    Hågenvik, Hans Olaf

    2015-01-01

    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.

  15. Hydrodynamic instabilities in shear flows of cohesive granular particles

    E-Print Network [OSTI]

    Kuniyasu Saitoh; Satoshi Takada; Hisao Hayakawa

    2015-05-15

    We extend the dynamic van der Waals model introduced by A. Onuki [Phys. Rev. Lett. 94, 054501 (2005)] to the description of cohesive granular flows under a plane shear to study their hydrodynamic instabilities. Numerically solving the dynamic van der Waals model, we observe various heterogeneous structures of the density in steady states, where the viscous heating is balanced with the energy dissipation caused by inelastic collisions. Based on the linear stability analysis, we find that the spatial structures are determined by the mean volume fraction, the applied shear rate, and the inelasticity, where the instability is triggered if the system is thermodynamically unstable, i.e. the pressure, $p$, and the volume fraction, $\\phi$, satisfy $\\partial p/\\partial\\phi<0$.

  16. Spontaneous azimuthal breakout and instability at the circular hydraulic jump

    E-Print Network [OSTI]

    Ray, Arnab K; Basu, Abhik; Bhattacharjee, Jayanta K

    2015-01-01

    We consider a shallow, two-dimensional flow of a liquid in which the radial and the azimuthal dynamics are coupled to each other. The steady and radial background flow of this system creates an axially symmetric circular hydraulic jump. On this background we apply time-dependent perturbations of the matter flow rate and the azimuthal flow velocity, with the latter strongly localized at the hydraulic jump. The perturbed variables depend spatially on both the radial and azimuthal coordinates. Linearization of the perturbations gives a coupled system of wave equations. The characteristic equations extracted from these wave equations show that under a marginally stable condition a spontaneous breaking of axial symmetry occurs at the position of the hydraulic jump. Departure from the marginal stability shows further that a linear instability develops in the azimuthal direction, resulting in an azimuthal transport of liquid at the hydraulic jump. The time for the growth of azimuthal instability is scaled by viscosi...

  17. Transposable elements and genetic instabilities in crop plants

    SciTech Connect (OSTI)

    Burr, B.; Burr, F.

    1981-04-10

    Transposable elements have long been associated with certain unstable loci in maize and have been intensively studied by McClintock and others. It is known that a transposable element can control the expression of the structural genes at the locus where it resides. These controlling elements in maize are now beginning to be studied at the molecular level. Using recombinant molecular probes we have been able to describe the changes induced by the controlling element Ds at the shrunken locus. Ds elements appear to be large and dissimilar insertions into the wild-type locus - two elements actually map within the transcribed region of the gene. Genetic instabilities have been described in other economically important plants but the bases for these phenomena have not been understood. We believe that it is likely that some of these instabilities are the result of transposable element activity much as in the case of maize.

  18. Inviscid helical magnetorotational instability in cylindrical Taylor-Couette flow

    E-Print Network [OSTI]

    Priede, J?nis

    2011-01-01

    This paper presents the analysis of helical magnetorotational instability (HMRI) in the inviscid limit, which is relevant for astrophysical conditions. The inductionless approximation defined by zero magnetic Prandtl number is adopted to distinguish the HMRI from the standard MRI in the cylindrical Taylor-Couette flow subject to a helical magnetic field. Using a Chebyshev collocation method convective and absolute instability thresholds are computed in terms of the MHD interaction parameter depending on the helicity of magnetic field and the velocity profile. It is found that the extension of self-sustained HMRI modes beyond the Rayleigh limit does not reach the astrophysically relevant Keplerian rotation profile not only in the narrow- but also the finite-gap approximation. The Keppler limit can be attained only by the convective HMRI mode provided that the boundaries are perfectly conducting. However, this mode is not self-sustained and, thus, unobservable without a permanent excitation because it is only c...

  19. 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.; Hager, J. D.; Betti, R.; Hu, S. X.; Delettrez, J.; Meyerhofer, D. D.

    2013-05-15

    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.

  20. Instability-driven electromagnetic fields in coronal plasmas

    SciTech Connect (OSTI)

    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.

    2013-04-15

    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.