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Sample records for atr wg-mox fuel

  1. AFC-1 Fuel Rodlet Fission Power Deposition Validation in ATR

    SciTech Connect

    G. S. Chang; M. A. Lillo; D. J. Utterbeck

    2008-11-01

    One of the viable options of long-term geological disposal of the nuclear power reactors generated spent fuel is to extract plutonium, the minor actinides (MA) and potentially long-lived fission products from the spent fuel and transmute them into short-lived or stable radionuclides in an appropriate reactor for the reduction of the radiological toxicity of the nuclear waste stream. An important component of that technology will be a non-fertile / low-fertile actinide transmutation fuel form containing the plutonium, neptunium, americium (and possibly curium) isotopes to be transmuted. Such advanced fuel forms, especially ones enriched in the long-life minor actinide (LLMA) elements (i.e., Np, Am, Cm), have minimal irradiation performance data available from which to establish a transmutation fuel form design. Recognizing these needs, an Advanced Fuel Cycle test series-1 (AFC-1) irradiation test on a variety of candidate fuel forms is now being conducted in Advanced Test Reactor (ATR) at the Idaho National Laboratory (INL). The first advanced fuel experiment (AFC-1) has been finalized and the test assembly analyzed for insertion and irradiation in ATR. The ATR core consists of a serpentine and rotationally symmetric fuel assembly about the z-axis of the core center. The plan view of the ATR core configuration is shown in Fig. 5, in Ref. 1. A cadmium filter with a 0.178 cm (0.045") thickness and 121.5 cm (48") in length, is currently used in the actinide-fuel capsule design for the East Flux Trap (EFT) position in ATR, to depress the linear heat generation rate (LHGR) lower than the project’s 330 W/cm limit for the experimental fuel rodlets. The LHGR is proportional to the fission power deposited in the fuel rodlets from the neutron fissions. The fraction of the fission power generated from the neutron fission reactions deposited in the fuel rodlet is an important parameter for test assembly thermal analysis, which will be validated in this summary.

  2. Weapons-Grade MOX Fuel Burnup Characteristics in Advanced Test Reactor Irradiation

    SciTech Connect

    G. S. Chang

    2006-07-01

    Mixed oxide (MOX) test capsules prepared with weapons-derived plutonium have been irradiated to a burnup of 50 GWd/t. The MOX fuel was fabricated at Los Alamos National Laboratory (LANL) by a master-mix process and has been irradiated in the Advanced Test Reactor (ATR) at the Idaho National Laboratory (INL). Previous withdrawals of the same fuel have occurred at 9, 21, 30, 40, and 50 GWd/t. Oak Ridge National Laboratory (ORNL) manages this test series for the Department of Energy’s Fissile Materials Disposition Program (FMDP). A UNIX BASH (Bourne Again SHell) script CMO has been written and validated at the Idaho National Laboratory (INL) to couple the Monte Carlo transport code MCNP with the depletion and buildup code ORIGEN-2 (CMO). The new Monte Carlo burnup analysis methodology in this paper consists of MCNP coupling through CMO with ORIGEN-2(MCWO). MCWO is a fully automated tool that links the Monte Carlo transport code MCNP with the radioactive decay and burnup code ORIGEN-2. The fuel burnup analyses presented in this study were performed using MCWO. MCWO analysis yields time-dependent and neutron-spectrum-dependent minor actinide and Pu concentrations for the ATR small I-irradiation test position. The purpose of this report is to validate both the Weapons-Grade Mixed Oxide (WG-MOX) test assembly model and the new fuel burnup analysis methodology by comparing the computed results against the neutron monitor measurements and the irradiated WG-MOX post irradiation examination (PIE) data.

  3. Comparison of HEU and LEU Fuel Neutron Spectrum for ATR Fuel Element and ATR Flux-Trap Positions

    SciTech Connect

    G. S. Chang

    2008-10-01

    The Advanced Test Reactor (ATR) is a high power and high neutron flux research reactor operating in the United States. Powered with highly enriched uranium (HEU), the ATR has a maximum thermal power rating of 250 MWth. Because of the high total core power and high neutron flux, the ATR is an ideal candidate for assessing the feasibility of converting an HEU driven reactor to a low-enriched core. An optimized low-enriched uranium (LEU) (U-10Mo) core conversion case, which can meet the project requirements, has been selected. However, LEU contains a significant quantity of high density U-238 (80.3 wt.%), which will harden the neutron spectrum in the core region. Based on the reference ATR HEU and the optimized LEU full core plate-by-plate (PBP) models, the present work investigates and compares the neutron spectra differences in the fuel element (FE), Northeast flux trap (NEFT), Southeast flux trap (SEFT), and East flux trap (EFT) positions. A detailed PBP MCNP ATR core model was developed and validated for fuel cycle burnup comparison analysis. The current ATR core with HEU U 235 enrichment of 93.0wt.% was used as the reference model. Each HEU fuel element contains 19 fuel plates with a fuel meat thickness of 0.508 mm (20 mil). In this work, an optimized LEU (U-10Mo) core conversion case with a nominal fuel meat thickness of 0.330 mm (13 mil) and the U-235 enrichment of 19.7 wt.% was used to calculate the impact of the neutron spectrum in FE and FT positions. MCNP-calculated results show that the neutron spectrum in the LEU FE is slightly harder than in the HEU FE, as expected. However, when neutrons transport through water coolant and beryllium (Be), the neutrons are thermalized to an equilibrium neutron spectrum as a function of water volume fraction in the investigated FT positions. As a result, the neutron spectrum differences of the HEU and LEU in the NEFT, SEFT, and EFT are negligible. To demonstrate that the LEU core fuel cycle performance can meet the

  4. Analysis of the ATR fuel element swaging process

    SciTech Connect

    Richins, W.D.; Miller, G.K.

    1995-12-01

    This report documents a detailed evaluation of the swaging process used to connect fuel plates to side plates in Advanced Test Reactor (ATR) fuel elements. The swaging is a mechanical process that begins with fitting a fuel plate into grooves in the side plates. Once a fuel plate is positioned, a lip on each of two side plate grooves is pressed into the fuel plate using swaging wheels to form the joints. Each connection must have a specified strength (measured in terms, of a pullout force capacity) to assure that these joints do not fail during reactor operation. The purpose of this study is to analyze the swaging process and associated procedural controls, and to provide recommendations to assure that the manufacturing process produces swaged connections that meet the minimum strength requirement. The current fuel element manufacturer, Babcock and Wilcox (B&W) of Lynchburg, Virginia, follows established procedures that include quality inspections and process controls in swaging these connections. The procedures have been approved by Lockheed Martin Idaho Technologies and are designed to assure repeatability of the process and structural integrity of each joint. Prior to July 1994, ATR fuel elements were placed in the Hydraulic Test Facility (HTF) at the Idaho National Engineering Laboratory (AGNAIL), Test Reactor Area (TRA) for application of Boehmite (an aluminum oxide) film and for checking structural integrity before placement of the elements into the ATR. The results presented in this report demonstrate that the pullout strength of the swaged connections is assured by the current manufacturing process (with several recommended enhancements) without the need for- testing each element in the HTF.

  5. Methodology for the Weapons-Grade MOX Fuel Burnup Analysis in the Advanced Test Reactor

    SciTech Connect

    G. S. Chang

    2005-08-01

    A UNIX BASH (Bourne Again SHell) script CMO has been written and validated at the Idaho National Laboratory (INL) to couple the Monte Carlo transport code MCNP with the depletion and buildup code ORIGEN-2 (CMO). The new Monte Carlo burnup analysis methodology in this paper consists of MCNP coupling through CMO with ORIGEN-2, and is therefore called the MCWO. MCWO is a fully automated tool that links the Monte Carlo transport code MCNP with the radioactive decay and burnup code ORIGEN-2. MCWO is capable of handling a large number of fuel burnup and material loading specifications, Advanced Test Reactor (ATR) lobe powers, and irradiation time intervals. MCWO processes user input that specifies the system geometry, initial material compositions, feed/removal specifications, and other code-specific parameters. Calculated results from MCNP, ORIGEN-2, and data process module calculations are output in succession as MCWO executes. The principal function of MCWO is to transfer one-group cross-section and flux values from MCNP to ORIGEN-2, and then transfer the resulting material compositions (after irradiation and/or decay) from ORIGEN-2 back to MCNP in a repeated, cyclic fashion. The basic requirements of MCWO are a working MCNP input file and some additional input parameters; all interaction with ORIGEN-2 as well as other calculations are performed by CMO. This paper presents the MCWO-calculated results for the Reduced Enrichment Research and Test Reactor (RERTR) experiments RERTR-1 and RERTR-2 as well as the Weapons-Grade Mixed Oxide (WG-MOX) fuel testing in ATR. Calculations performed for the WG-MOX test irradiation, which is managed by the Oak Ridge National Laboratory (ORNL), supports the DOE Fissile Materials Disposition Program (FMDP). The MCWO-calculated results are compared with measured data.

  6. Irradiaton of Metallic and Oxide Fuels for Actinide Transmutation in the ATR

    SciTech Connect

    Heather J. MacLean; Steven L. Hayes

    2007-09-01

    Metallic fuels containing minor actinides and rare earth additions have been fabricated and are prepared for irradiation in the ATR, scheduled to begin during the summer of 2007. Oxide fuels containing minor actinides are being fabricated and will be ready for irradiation in ATR, scheduled to begin during the summer of 2008. Fabrication and irradiation of these fuels will provide detailed studies of actinide transmutation in support of the Global Nuclear Energy Partnership. These fuel irradiations include new fuel compositions that have never before been tested. Results from these tests will provide fundamental data on fuel irradiation performance and will advance the state of knowledge for transmutation fuels.

  7. MCWO - Linking MCNP And ORIGEN2 For Fuel Burnup Analysis

    SciTech Connect

    Gray S Chang

    2005-04-01

    The UNIX BASH (Bourne Again Shell) script MCWO has been developed at the Idaho National Engineering and Environment Laboratory (INEEL) to couple the Monte Carlo transport code MCNP with the depletion and buildup code ORIGEN2. MCWO is a fully automated tool that links the Monte Carlo transport code MCNP with the radioactive decay and burnup code ORIGEN2. MCWO can handle a large number of fuel burnup and material loading specifications, Advanced Test Reactor (ATR) powers, and irradiation time intervals. The program processes input from the user that specifies the system geometry, initial material compositions, feed/removal specifications, and other code-specific parameters. Calculated results from MCNP, ORIGEN2, and data process module calculations are then output successively as the code runs. The principal function of MCWO is to transfer one-group cross-section and flux values from MCNP to ORIGEN2, and then transfer the resulting material compositions (after irradiation and/or decay) from ORIGEN2 back to MCNP in a repeated, cyclic fashion. The basic requirement of the code is that the user have a working MCNP input file and other input parameters; all interaction with ORIGEN2 and other calculations are performed by UNIX BASH script MCWO. This paper presents the MCWO-calculated results of the RERTR-1 and -2 , and the Weapons-Grade Mixed Oxiide fuel (Wg-MOX) fuel experiments in ATR and compares the MCWO-calculated results with the measured data.

  8. ATR LEU Fuel and Burnable Absorber Neutronics Performance Optimization by Fuel Meat Thickness Variation

    SciTech Connect

    G. S. Chang

    2007-09-01

    The Advanced Test Reactor (ATR) is a high power density and high neutron flux research reactor operating in the United States. Powered with highly enriched uranium (HEU), the ATR has a maximum thermal power rating of 250 MWth. Because of the large test volumes located in high flux areas, the ATR is an ideal candidate for assessing the feasibility of converting an HEU driven reactor to a low-enriched core. The present work investigates the necessary modifications and evaluates the subsequent operating effects of this conversion. A detailed plate-by-plate MCNP ATR 1/8th core model was developed and validated for a fuel cycle burnup comparison analysis. Using the current HEU U 235 enrichment of 93.0 % as a baseline, an analysis can be performed to determine the low-enriched uranium (LEU) density and U-235 enrichment required in the fuel meat to yield an equivalent K-eff between the HEU core and the LEU core versus effective full power days (EFPD). The MCNP ATR 1/8th core model will be used to optimize the U-235 loading in the LEU core, such that the differences in K-eff and heat flux profile between the HEU and LEU core can be minimized. The depletion methodology MCWO was used to calculate K-eff versus EFPDs in this paper. The MCWO-calculated results for the LEU cases with foil (U-10Mo) types demonstrated adequate excess reactivity such that the K-eff versus EFPDs plot is similar to the reference ATR HEU case. Each HEU fuel element contains 19 fuel plates with a fuel meat thickness of 0.508 mm. In this work, the proposed LEU (U-10Mo) core conversion case with a nominal fuel meat thickness of 0.508 mm and the same U-235 enrichment (15.5 wt%) can be used to optimize the radial heat flux profile by varying the fuel plate thickness from 0.254 to 0.457 mm at the inner 4 fuel plates (1-4) and outer 4 fuel plates (16-19). In addition, a 0.7g of burnable absorber Boron-10 was added in the inner and outer plates to reduce the initial excess reactivity, and the inner/outer heat

  9. ATR LEU fuel and burnable absorber neutronics performance optimization by fuel meat thickness variation

    SciTech Connect

    Chang, G.S.

    2008-07-15

    The Advanced Test Reactor (ATR) is a high power density and high neutron flux research reactor operating in the United States. Powered with highly enriched uranium (HEU), the ATR has a maximum thermal power rating of 250 MWth. Because of the large test volumes located in high flux areas, the ATR is an ideal candidate for assessing the feasibility of converting an HEU driven reactor to a low-enriched core. The present work investigates the necessary modifications and evaluates the subsequent operating effects of this conversion. A detailed plate-by-plate MCNP ATR 1/8th core model was developed and validated for a fuel cycle burnup comparison analysis. Using the current HEU U-235 enrichment of 93.0 % as a baseline, an analysis can be performed to determine the low-enriched uranium (LEU) density and U-235 enrichment required in the fuel meat to yield an equivalent K-eff between the HEU core th and the LEU core versus effective full power days (EFPD). The MCNP ATR 1/8th core model will be used to optimize the U-235 loading in the LEU core, such that the differences in K-eff and heat flux profile between the HEU and LEU core can be minimized. The depletion methodology MCWO was used to calculate K-eff versus EFPDs in this paper. The MCWO-calculated results for the LEU cases with foil (U-10Mo) types demonstrated adequate excess reactivity such that the K-eff versus EFPDs plot is similar to the reference ATR HEU case. Each HEU fuel element contains 19 fuel plates with a fuel meat thickness of 0.508 mm. In this work, the proposed LEU (U-10Mo) core conversion case with a nominal fuel meat thickness of 0.381 mm and the same U-235 enrichment (19.7 wt%) can be used to optimize the radial heat flux profile by varying the fuel meat thickness from 0.191 mm (7.5 mil) to 0.343 mm (13.5 mil) at the inner 4 fuel plates (1-4) and outer 4 fuel plates (16-19). In addition, 0.8g of a burnable absorber, Boron-10, was added in the inner and outer plates to reduce the initial excess

  10. Diesel fuel processor for PEM fuel cells: Two possible alternatives (ATR versus SR)

    NASA Astrophysics Data System (ADS)

    Cutillo, A.; Specchia, S.; Antonini, M.; Saracco, G.; Specchia, V.

    There are large efforts in exploring the on-board reforming technologies, which would avoid the actual lack of hydrogen infrastructure and related safety issues. From this view point, the present work deals with the comparison between two different 10 kW e fuel processors (FP) systems for the production of hydrogen-rich fuel gas starting from diesel oil, based respectively on autothermal (ATR) and steam-reforming (SR) process and related CO clean-up technologies; the obtained hydrogen rich gas is fed to the PEMFC stack of an auxiliary power unit (APU). Based on a series of simulations with Matlab/Simulink, the two systems were compared in terms of FP and APU efficiency, hydrogen concentration fed to the FC, water balance and process scheme complexity. Notwithstanding a slightly higher process scheme complexity and a slightly more difficult water recovery, the FP based on the SR scheme, as compared to the ATR one, shows higher efficiency and larger hydrogen concentration for the stream fed to the PEMFC anode, which represent key issues for auxiliary power generation based on FCs as compared, e.g. to alternators.

  11. ATR LEU Monolithic Foil-Type Fuel with Integral Cladding Burnable Absorber – Neutronics Performance Evaluation

    SciTech Connect

    Gray Chang

    2012-03-01

    The Advanced Test Reactor (ATR), currently operating in the United States, is used for material testing at very high neutron fluxes. Powered with highly enriched uranium (HEU), the ATR has a maximum thermal power rating of 250 MWth. Because of the large test volumes located in high flux areas, the ATR is an ideal candidate for assessing the feasibility of converting HEU driven reactor cores to low-enriched uranium (LEU) cores. The burnable absorber - 10B, was added in the inner and outer plates to reduce the initial excess reactivity, and to improve the peak ratio of the inner/outer heat flux. The present work investigates the LEU Monolithic foil-type fuel with 10B Integral Cladding Burnable Absorber (ICBA) design and evaluates the subsequent neutronics operating effects of this proposed fuel designs. The proposed LEU fuel specification in this work is directly related to both the RERTR LEU Development Program and the Advanced Test Reactor (ATR) LEU Conversion Project at Idaho National Laboratory (INL).

  12. Validation of ATR Fission Power Deposition Fraction in HEU and LEU Fuel Plates

    SciTech Connect

    G. S. Chang

    2008-09-01

    The Advanced Test Reactor (ATR) is a high power (250 MW), high neutron flux research reactor operating in the United States. Powered with highly enriched uranium (HEU), the ATR has a maximum unperturbed thermal neutron flux rating of 1.0 x 1015 n/cm2–s. Because of its high power and large test volumes located in high flux areas, the ATR is an ideal candidate for assessing the feasibility of converting an HEU driven reactor to a low-enriched core. A detailed plate-by-plate MCNP ATR full core model has been developed and validated for the low-enriched uranium (LEU) fuel conversion feasibility study. Using this model, an analysis has been performed to determine the LEU density and U-235 enrichment required in the fuel meat to yield equivalent K-eff versus effective full power days (EFPDs) between the HEU and LEU cores. This model has also been used to optimize U-235 content of the LEU core, minimizing the differences in K-eff and heat flux profile between the HEU and LEU cores at 115 MW total core power for 125 EFPDs. The LEU core conversion feasibility study evaluated foil type (U-10Mo) fuel with the LEU reference design of 19.7 wt% U-235 enrichment. The LEU reference design has a fixed fuel meat thickness of 0.330 mm and can sustain the same operating cycle length as the HEU fuel. Heat flux and fission power density are parameters that are proportional to the fraction of fission power deposited in fuel. Thus, the accurate determination of the fraction of fission power deposited in the fuel is important to ATR nuclear safety. In this work, a new approach was developed and validated, the Tally Fuel Cells Only (TFCO) method. This method calculates and compares the fission power deposition fraction between HEU and LEU fuel plates. Due to the high density of the U-10Mo LEU fuel, the fission ?-energy deposition fraction is 37.12%, which is larger than the HEU’s ?-energy deposition fraction of 19.7%. As a result, the fuel decay heat cooling will need to be improved

  13. Cadmium Depletion Impacts on Hardening Neutron6 Spectrum for Advanced Fuel Testing in ATR

    SciTech Connect

    Gray S. Chang

    2011-05-01

    For transmuting long-lived isotopes contained in spent nuclear fuel into shorter-lived fission products effectively is in a fast neutron spectrum reactor. In the absence of a fast spectrum test reactor in the United States of America (USA), initial irradiation testing of candidate fuels can be performed in a thermal test reactor that has been modified to produce a test region with a hardened neutron spectrum. A test region is achieved with a Cadmium (Cd) filter which can harden the neutron spectrum to a spectrum similar (although still somewhat softer) to that of the liquid metal fast breeder reactor (LMFBR). A fuel test loop with a Cd-filter has been installed within the East Flux Trap (EFT) of the Advanced Test Reactor (ATR) at the Idaho National Laboratory (INL). A detailed comparison analyses between the cadmium (Cd) filter hardened neutron spectrum in the ATR and the LMFBR fast neutron spectrum have been performed using MCWO. MCWO is a set of scripting tools that are used to couple the Monte Carlo transport code MCNP with the isotope depletion and buildup code ORIGEN-2.2. The MCWO-calculated results indicate that the Cd-filter can effectively flatten the Rim-Effect and reduce the linear heat rate (LHGR) to meet the advanced fuel testing project requirements at the beginning of irradiation (BOI). However, the filtering characteristics of Cd as a strong absorber quickly depletes over time, and the Cd-filter must be replaced for every two typical operating cycles within the EFT of the ATR. The designed Cd-filter can effectively depress the LHGR in experimental fuels and harden the neutron spectrum enough to adequately flatten the Rim Effect in the test region.

  14. Status Report on the Fabrication of Fuel Cladding Chemical Interaction Test Articles for ATR Irradiations

    SciTech Connect

    Field, Kevin G.; Howard, Richard H.

    2015-09-28

    FeCrAl alloys are a promising new class of alloys for light water reactor (LWR) applications due to their superior oxidation and corrosion resistance in high temperature environments. The current R&D efforts have focused on the alloy composition and processing routes to generate nuclear grade FeCrAl alloys with optimized properties for enhanced accident tolerance while maintaining properties needed for normal operation conditions. Therefore, the composition and processing routes must be optimized to maintain the high temperature steam oxidation (typically achieved by increasing the Cr and Al content) while still exhibiting properties conducive to normal operation in a LWR (such as radiation tolerance where reducing Cr content is favorable). Within this balancing act is the addition of understanding the influence on composition and processing routes on the FeCrAl alloys for fuel-cladding chemical interactions (FCCI). Currently, limited knowledge exists on FCCI for the FeCrAl-UO2 clad-fuel system. To overcome the knowledge gaps on the FCCI for the FeCrAl-UO2 clad-fuel system a series of fueled irradiation tests have been developed for irradiation in the Advanced Test Reactor (ATR) housed at the Idaho National Laboratory (INL). The first series of tests has already been reported. These tests used miniaturized 17x17 PWR fuel geometry rodlets of second-generation FeCrAl alloys fueled with industrial Westinghouse UO2 fuel. These rodlets were encapsulated within a stainless steel housing.To provide high fidelity experiments and more robust testing, a new series of rodlets have been developed deemed the Accident Tolerant Fuel Experiment #1 Oak Ridge National Laboratory FCCI test (ATF-1 ORNL FCCI). The main driving factor, which is discussed in detail, was to provide a radiation environment where prototypical fuel-clad interface temperatures are met while still maintaining constant contact between industrial fuel and the candidate cladding alloys

  15. Gamma-Ray Simulated Spectrum Deconvolution of a LaBr₃ 1-in. x 1-in. Scintillator for Nondestructive ATR Fuel Burnup On-Site Predictions

    DOE PAGESBeta

    Navarro, Jorge; Ring, Terry A.; Nigg, David W.

    2015-03-01

    A deconvolution method for a LaBr₃ 1"x1" detector for nondestructive Advanced Test Reactor (ATR) fuel burnup applications was developed. The method consisted of obtaining the detector response function, applying a deconvolution algorithm to 1”x1” LaBr₃ simulated, data along with evaluating the effects that deconvolution have on nondestructively determining ATR fuel burnup. The simulated response function of the detector was obtained using MCNPX as well with experimental data. The Maximum-Likelihood Expectation Maximization (MLEM) deconvolution algorithm was selected to enhance one-isotope source-simulated and fuel- simulated spectra. The final evaluation of the study consisted of measuring the performance of the fuel burnup calibrationmore » curve for the convoluted and deconvoluted cases. The methodology was developed in order to help design a reliable, high resolution, rugged and robust detection system for the ATR fuel canal capable of collecting high performance data for model validation, along with a system that can calculate burnup and using experimental scintillator detector data.« less

  16. Gamma-Ray Simulated Spectrum Deconvolution of a LaBr₃ 1-in. x 1-in. Scintillator for Nondestructive ATR Fuel Burnup On-Site Predictions

    SciTech Connect

    Navarro, Jorge; Ring, Terry A.; Nigg, David W.

    2015-03-01

    A deconvolution method for a LaBr₃ 1"x1" detector for nondestructive Advanced Test Reactor (ATR) fuel burnup applications was developed. The method consisted of obtaining the detector response function, applying a deconvolution algorithm to 1”x1” LaBr₃ simulated, data along with evaluating the effects that deconvolution have on nondestructively determining ATR fuel burnup. The simulated response function of the detector was obtained using MCNPX as well with experimental data. The Maximum-Likelihood Expectation Maximization (MLEM) deconvolution algorithm was selected to enhance one-isotope source-simulated and fuel- simulated spectra. The final evaluation of the study consisted of measuring the performance of the fuel burnup calibration curve for the convoluted and deconvoluted cases. The methodology was developed in order to help design a reliable, high resolution, rugged and robust detection system for the ATR fuel canal capable of collecting high performance data for model validation, along with a system that can calculate burnup and using experimental scintillator detector data.

  17. A Feasibility Study to Determine Cooling Time and Burnup of ATR Fuel Using a Nondestructive Technique and Three Types of Gamma-ray Detectors

    SciTech Connect

    Jorge Navarro; Rahmat Aryaeinejad,; David W. Nigg

    2011-05-01

    A Feasibility Study to Determine Cooling Time and Burnup of ATR Fuel Using a Nondestructive Technique1 Rahmat Aryaeinejad, Jorge Navarro, and David W Nigg Idaho National Laboratory Abstract Effective and efficient Advanced Test Reactor (ATR) fuel management require state of the art core modeling tools. These new tools will need isotopic and burnup validation data before they are put into production. To create isotopic, burn up validation libraries and to determine the setup for permanent fuel scanner system a feasibility study was perform. The study consisted in measuring short and long cooling time fuel elements at the ATR canal. Three gamma spectroscopy detectors (HPGe, LaBr3, and HPXe) and two system configurations (above and under water) were used in the feasibility study. The first stage of the study was to investigate which detector and system configuration would be better suited for different scenarios. The second stage of the feasibility study was to create burnup and cooling time calibrations using experimental isotopic data collected and ORIGEN 2.2 burnup data. The results of the study establish that a better spectra resolution is achieve with an above the water configuration and that three detectors can be used in the permanent fuel scanner system for different situations. In addition it was conclude that a number of isotopic ratios and absolute measurements could be used to predict ATR fuel burnup and cooling times. 1This work was supported by the U.S. Depart¬ment of Energy (DOE) under Battelle Energy Alliance, LLC Contract No. DE-AC07-05ID14517.

  18. Fabrication, Inspection, and Test Plan for the Advanced Test Reactor (ATR) High-Power Mixed-Oxide (MOX) Fuel Irradiation Project

    SciTech Connect

    Wachs, G. W.

    1998-09-01

    The Department of Energy (DOE) Fissile Disposition Program (FMDP) has announced that reactor irradiation of Mixed-Oxide (MOX) fuel is one of the preferred alternatives for disposal of surplus weapons-usable plutonium (Pu). MOX fuel has been utilized domestically in test reactors and on an experimental basis in a number of Commercial Light Water Reactors (CLWRs). Most of this experience has been with Pu derived from spent low enriched uranium (LEU) fuel, known as reactor grade (RG) Pu. The High-Power MOX fuel test will be irradiated in the Advanced Test Reactor (ATR) to provide preliminary data to demonstrate that the unique properties of surplus weapons-derived or weapons-grade (WG) plutonium (Pu) do not compromise the applicability of this MOX experience base. The purpose of the high-power experiment, in conjunction with the currently ongoing average-power experiment at the ATR, is to contribute new information concerning the response of WG plutonium under more severe irradiation conditions typical of the peak power locations in commercial reactors. In addition, the high-power test will contribute experience with irradiation of gallium-containing fuel to the database required for resolution of generic CLWR fuel design issues. The distinction between "high-power" and "average-power" relates to the position within the nominal CLWR core. The high-power test project is subject to a number of requirements, as discussed in the Fissile Materials Disposition Program Light Water Reactor Mixed Oxide Fuel Irradiation High-Power Test Project Plan (ORNL/MD/LTR-125).

  19. Safety Assurance for ATR Irradiations

    SciTech Connect

    S. Blaine Grover

    2006-10-01

    The Advanced Test Reactor (ATR) located at the Idaho National Laboratory (INL) is the world’s premiere test reactor for performing high fluence, large volume, irradiation test programs. The ATR has many capabilities and a wide variety of tests are performed in this truly one of a kind reactor, including isotope production, simple self-contained static capsule experiments, instrumented/controlled experiments, and loop testing under pressurized water conditions. Along with the five pressurized water loops, ATR may also have gas (temperature controlled) lead experiments, fuel boosted fast flux experiments, and static sealed capsules all in the core at the same time. In addition, any or all of these tests may contain fuel or moderating materials that can affect reactivity levels in the ATR core. Therefore the safety analyses required to ensure safe operation of each experiment as well as the reactor itself are complex. Each test has to be evaluated against stringent reactor control safety criteria, as well as the effects it could have on adjacent tests and the reactor as well as the consequences of those effects. The safety analyses of each experiment are summarized in a document entitled the Experiment Safety Assurance Package (ESAP). The ESAP references and employs the results of the reactor physics, thermal, hydraulic, stress, seismic, vibration, and all other analyses necessary to ensure the experiment can be irradiated safely in the ATR. The requirements for reactivity worth, chemistry compatibilities, pressure limitations, material issues, etc. are all specified in the Technical Safety Requirements and the Upgraded Final Safety Analysis Report (UFSAR) for the ATR. This paper discusses the ESAP process, types of analyses, types of safety requirements and the approvals necessary to ensure an experiment can be safely irradiated in the ATR.

  20. A feasibility study to determine cooling time and burnup of ATR fuel using a nondestructive technique and three types of gamma-ray detectors

    SciTech Connect

    Navarro, J.; Aryaeinejad, R.; Nigg, D.W.

    2011-07-01

    The goal of this work was to perform a feasibility study and establish measurement techniques to determine the burnup of the Advanced Test Reactor (ATR) fuels at the Idaho National Laboratory (INL). Three different detectors of high purity germanium (HPGe), lanthanum bromide (LaBr{sub 3}), and high pressure xenon (HPXe) in two detection system configurations of below and above the water pool were used in this study. The last two detectors were used for the first time in fuel burnup measurements. The results showed that a better quality spectra can be achieved with the above the water pool configuration. Both short and long cooling time fuels were investigated in order to determine which measurement technique, absolute or fission product ratio, is better suited in each scenario and also to establish what type of detector should be used in each case for the best burnup measurement. The burnup and cooling time calibrations were established using experimental absolute activities or isotopic ratios and ORIGEN burnup calculations. A method was developed to do burnup and cooling time calibrations using fission isotopes activities without the need to know the exact geometry. (authors)

  1. Irradiation Planning for Fully-Ceramic Micro-encsapsulated fuel in ATR at LWR-relevant conditions: year-end report on FY-2011

    SciTech Connect

    Abderrafi M. Ougouag; R. Sonat Sen; Michael A. Pope; Brian Boer

    2011-09-01

    This report presents the estimation of required ATR irradiation levels for the DB-FCM fuel design (fueled with Pu and MAs). The fuel and assembly designs are those considered in a companion report [R. S. Sen et al., FCR&D-2011- 00037 or INL/EXT-11-23269]. These results, pertaining to the DB-FCM fuel, are definitive in as much as the design of said fuel is definitive. In addition to the work performed, as required, for DB-FCM fuel, work has started in a preliminary fashion on single-cell UO2 and UN fuels. These latter activities go beyond the original charter of this project and although the corresponding work is incomplete, significant progress has been achieved. However, in this context, all that has been achieved is only preliminary because the corresponding fuel designs are neither finalized nor optimized. In particular, the UO2 case is unlikely to result in a viable fuel design if limited to enrichment at or under 20 weight % in U-235. The UN fuel allows reasonable length cycles and is likely to make an optimal design possible. Despite being limited to preliminary designs and offering only preliminary conclusions, the irradiation planning tasks for UO2 and UN fuels that are summarized in this report are useful to the overall goal of devising and deploying FCM-LWR fuel since the methods acquired and tested in this project and the overall procedure for planning will be available for planning tests for the finalized fuel design. Indeed, once the fuel design is finalized and the expected burnup level is determined, the methodology that has been assembled will allow the prompt finalization of the neutronic planning of the irradiation experiment and would provide guidance on the expected experimental performance of the fuel. Deviations from the expected behavior will then have to be analyzed and the outcome of the analysis may be corrections or modifications for the assessment models as well as, possibly, fuel design modifications, and perhaps even variation of

  2. ATR neutron spectral characterization

    SciTech Connect

    Rogers, J.W.; Anderl, R.A.

    1995-11-01

    The Advanced Test Reactor (ATR) at INEL provides intense neutron fields for irradiation-effects testing of reactor material samples, for production of radionuclides used in industrial and medical applications, and for scientific research. Characterization of the neutron environments in the irradiation locations of the ATR has been done by means of neutronics calculations and by means of neutron dosimetry based on the use of neutron activation monitors that are placed in the various irradiation locations. The primary purpose of this report is to present the results of an extensive characterization of several ATR irradiation locations based on neutron dosimetry measurements and on least-squares-adjustment analyses that utilize both neutron dosimetry measurements and neutronics calculations. This report builds upon the previous publications, especially the reference 4 paper. Section 2 provides a brief description of the ATR and it tabulates neutron spectral information for typical irradiation locations, as derived from the more historical neutron dosimetry measurements. Relevant details that pertain to the multigroup neutron spectral characterization are covered in section 3. This discussion includes a presentation on the dosimeter irradiation and analyses and a development of the least-squares adjustment methodology, along with a summary of the results of these analyses. Spectrum-averaged cross sections for neutron monitoring and for displacement-damage prediction in Fe, Cr, and Ni are given in section 4. In addition, section4 includes estimates of damage generation rates for these materials in selected ATR irradiation locations. In section 5, the authors present a brief discussion of the most significant conclusions of this work and comment on its relevance to the present ATR core configuration. Finally, detailed numerical and graphical results for the spectrum-characterization analyses in each irradiation location are provided in the Appendix.

  3. PUREX new substation ATR

    SciTech Connect

    Nelson, D.E.

    1997-05-12

    This document is the acceptance test report (ATR) for the New PUREX Main and Minisubstations. It covers the factory and vendor acceptance and commissioning test reports. Reports are presented for the Main 5 kV substation building, the building fire system, switchgear, and vacuum breaker; the minisubstation control building and switch gear; commissioning test; electrical system and loads inspection; electrical utilities transformer and cable; and relay setting changes based on operational experience.

  4. 78 FR 65183 - Airworthiness Directives; ATR-GIE Avions de Transport Régional Airplanes

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-31

    ...We are adopting a new airworthiness directive (AD) for certain ATR--GIE Avions de Transport R[eacute]gional Model ATR72-101, -201, - 102, -202, -211, -212, and -212A airplanes. This AD was prompted by reports of airplane incidents and accidents that have occurred because of low-level fuel tank situations and fuel starvation that resulted in engine flameouts. This AD requires installing a fuel......

  5. HEATR project: ATR algorithm parallelization

    NASA Astrophysics Data System (ADS)

    Deardorf, Catherine E.

    1998-09-01

    High Performance Computing (HPC) Embedded Application for Target Recognition (HEATR) is a project funded by the High Performance Computing Modernization Office through the Common HPC Software Support Initiative (CHSSI). The goal of CHSSI is to produce portable, parallel, multi-purpose, freely distributable, support software to exploit emerging parallel computing technologies and enable application of scalable HPC's for various critical DoD applications. Specifically, the CHSSI goal for HEATR is to provide portable, parallel versions of several existing ATR detection and classification algorithms to the ATR-user community to achieve near real-time capability. The HEATR project will create parallel versions of existing automatic target recognition (ATR) detection and classification algorithms and generate reusable code that will support porting and software development process for ATR HPC software. The HEATR Team has selected detection/classification algorithms from both the model- based and training-based (template-based) arena in order to consider the parallelization requirements for detection/classification algorithms across ATR technology. This would allow the Team to assess the impact that parallelization would have on detection/classification performance across ATR technology. A field demo is included in this project. Finally, any parallel tools produced to support the project will be refined and returned to the ATR user community along with the parallel ATR algorithms. This paper will review: (1) HPCMP structure as it relates to HEATR, (2) Overall structure of the HEATR project, (3) Preliminary results for the first algorithm Alpha Test, (4) CHSSI requirements for HEATR, and (5) Project management issues and lessons learned.

  6. Multiple Irradiation Capsule Experiment (MICE)-3B Irradiation Test of Space Fuel Specimens in the Advanced Test Reactor (ATR) - Close Out Documentation for Naval Reactors (NR) Information

    SciTech Connect

    M. Chen; CM Regan; D. Noe

    2006-01-09

    Few data exist for UO{sub 2} or UN within the notional design space for the Prometheus-1 reactor (low fission rate, high temperature, long duration). As such, basic testing is required to validate predictions (and in some cases determine) performance aspects of these fuels. Therefore, the MICE-3B test of UO{sub 2} pellets was designed to provide data on gas release, unrestrained swelling, and restrained swelling at the upper range of fission rates expected for a space reactor. These data would be compared with model predictions and used to determine adequacy of a space reactor design basis relative to fission gas release and swelling of UO{sub 2} fuel and to assess potential pellet-clad interactions. A primary goal of an irradiation test for UN fuel was to assess performance issues currently associated with this fuel type such as gas release, swelling and transient performance. Information learned from this effort may have enabled use of UN fuel for future applications.

  7. 78 FR 42898 - Airworthiness Directives; ATR-GIE Avions de Transport Régional Airplanes

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-18

    ...We propose to adopt a new airworthiness directive (AD) for certain ATR-GIE Avions de Transport R[eacute]gional Model ATR72-101, - 201, -102, -202, -211, -212, and -212A airplanes. This proposed AD was prompted by reports of airplane incidents and accidents that have occurred because of low-level fuel tank situations and fuel starvation that resulted in engine flameouts. This proposed AD would......

  8. LWRS ATR Irradiation Testing Readiness Status

    SciTech Connect

    Kristine Barrett

    2012-09-01

    The Light Water Reactor Sustainability (LWRS) Program was established by the U.S. Department of Energy Office of Nuclear Energy (DOE-NE) to develop technologies and other solutions that can improve the reliability, sustain the safety, and extend the life of the current reactors. The LWRS Program is divided into four R&D Pathways: (1) Materials Aging and Degradation; (2) Advanced Light Water Reactor Nuclear Fuels; (3) Advanced Instrumentation, Information and Control Systems; and (4) Risk-Informed Safety Margin Characterization. This report describes an irradiation testing readiness analysis in preparation of LWRS experiments for irradiation testing at the Idaho National Laboratory (INL) Advanced Test Reactor (ATR) under Pathway (2). The focus of the Advanced LWR Nuclear Fuels Pathway is to improve the scientific knowledge basis for understanding and predicting fundamental performance of advanced nuclear fuel and cladding in nuclear power plants during both nominal and off-nominal conditions. This information will be applied in the design and development of high-performance, high burn-up fuels with improved safety, cladding integrity, and improved nuclear fuel cycle economics

  9. Safety significance of ATR (Advanced Test Reactor) passive safety response attributes

    SciTech Connect

    Atkinson, S.A.

    1989-01-01

    The Advanced Test Reactor (ATR) at the Idaho National Engineering Laboratory was designed with some passive safety response attributes which contribute to the safety posture of the facility. The three passive safety attributes being evaluated in the paper are: (1) In-core and in-vessel natural convection cooling, (2) a passive heat sink capability of the ATR primary coolant system (PCS) for the transfer of decay power from the uninsulated piping to the confinement, and (3) gravity feed of emergency coolant makeup. The safety significance of the ATR passive safety response attributes is that the reactor can passively respond for most transients, given a reactor scram, to provide adequate decay power removal and a significant time for operator action should the normal active heat removal systems and their backup systems both fail. The ATR Interim Level 1 Probabilistic Risk Assessment (PRA) model ands results were used to evaluate the significance to ATR fuel damage frequency (or probability) of the above three passive response attributes. The results of the evaluation indicate that the first attribute is a major safety characteristic of the ATR. The second attribute has a noticeable but only minor safety significance. The third attribute has no significant influence on the ATR Level 1 PRA because of the diversity and redundancy of the ATR firewater injection system (emergency coolant system). 8 refs., 4 figs., 1 tab.

  10. Fabrication Report for the AFC-2A and AFC-2B Capsule Irradiations in the ATR

    SciTech Connect

    Timothy A. Hyde

    2007-10-01

    This document provides a general narrative description of the AFC-2A and 2B fuel fabrication processes for the AFC 2A and AFC 2B fuel irradiation experiments fabricated at the Idaho National Laboratory’s Materials and Fuels Complex (MFC) for irradiation in the Advanced Test Reactor (ATR).

  11. An informative confidence metric for ATR.

    SciTech Connect

    Bow, Wallace Johnston Jr.; Richards, John Alfred; Bray, Brian Kenworthy

    2003-03-01

    Automatic or assisted target recognition (ATR) is an important application of synthetic aperture radar (SAR). Most ATR researchers have focused on the core problem of declaration-that is, detection and identification of targets of interest within a SAR image. For ATR declarations to be of maximum value to an image analyst, however, it is essential that each declaration be accompanied by a reliability estimate or confidence metric. Unfortunately, the need for a clear and informative confidence metric for ATR has generally been overlooked or ignored. We propose a framework and methodology for evaluating the confidence in an ATR system's declarations and competing target hypotheses. Our proposed confidence metric is intuitive, informative, and applicable to a broad class of ATRs. We demonstrate that seemingly similar ATRs may differ fundamentally in the ability-or inability-to identify targets with high confidence.

  12. Validation of HELIOS for ATR Core Follow Analyses

    SciTech Connect

    Bays, Samuel E.; Swain, Emily T.; Crawford, Douglas S.; Nigg, David W.

    2015-03-01

    This work summarizes the validation analyses for the HELIOS code to support core design and safety assurance calculations of the Advanced Test Reactor (ATR). Past and current core safety assurance is performed by the PDQ-7 diffusion code; a state of the art reactor physics simulation tool from the nuclear industry’s earlier days. Over the past twenty years, improvements in computational speed have enabled the use of modern neutron transport methodologies to replace the role of diffusion theory for simulation of complex systems, such as the ATR. More exact methodologies have enabled a paradigm-shift away from highly tuned codes that force compliance with a bounding safety envelope, and towards codes regularly validated against routine measurements. To validate HELIOS, the 16 ATR operational cycles from late-2009 to present were modeled. The computed power distribution was compared against data collected by the ATR’s on-line power surveillance system. It was found that the ATR’s lobe-powers could be determined with ±10% accuracy. Also, the ATR’s cold startup shim configuration for each of these 16 cycles was estimated and compared against the reported critical position from the reactor log-book. HELIOS successfully predicted criticality within the tolerance set by the ATR startup procedure for 13 out of the 16 cycles. This is compared to 12 times for PDQ (without empirical adjustment). These findings, as well as other insights discussed in this report, suggest that HELIOS is highly suited for replacing PDQ for core safety assurance of the ATR. Furthermore, a modern verification and validation framework has been established that allows reactor and fuel performance data to be computed with a known degree of accuracy and stated uncertainty.

  13. Molecular Pathways: Targeting ATR in Cancer Therapy.

    PubMed

    Karnitz, Larry M; Zou, Lee

    2015-11-01

    The human ATR gene encodes a kinase that is activated by DNA damage and replication stress as a central transducer of a checkpoint signaling pathway. Once activated, ATR phosphorylates multiple substrates, including the kinase Chk1, to regulate cell-cycle progression, replication fork stability, and DNA repair. These events promote cell survival during replication stress and in cells with DNA damage. Accordingly, there has been the tantalizing possibility that ATR inhibitors would be therapeutically useful, especially if they were more effective in tumor versus normal cells. Indeed, multiple studies have demonstrated that alterations that promote tumorigenesis, such as defects in the ATM-p53 pathway, constitutive oncogene activation, and acquisition of the alternative lengthening of telomeres pathway, render tumor cells sensitive to ATR inhibitor monotherapy and/or increase the synergy between ATR inhibitors and genotoxic chemotherapies. Now, nearly two decades after the discovery of ATR, two highly selective and potent ATR inhibitors, AZD6738 and VX-970, are in early-phase clinical trials either as monotherapies or paired with a variety of genotoxic chemotherapies. These trials will generate important insights into the effects of ATR inhibition in humans and the potential role of inhibiting this kinase in the treatment of human malignancies. PMID:26362996

  14. EVALUATION OF LVDTS FOR USE IN ATR IRRADIATION EXPERIMENTS

    SciTech Connect

    D. L. Knudson; J. L. Rempe

    2009-04-01

    New materials are being considered for fuel, cladding, and structures in next generation and existing nuclear reactors. Such materials can experience significant dimensional changes during high temperature irradiation. Currently, these changes are determined by repeatedly irradiating a specimen for a defined period of time in the Advanced Test Reactor (ATR) and then removing it from the reactor for evaluation. The time and labor to remove, examine, and return irradiated samples for each measurement makes this approach very expensive. In addition, such techniques provide limited data and may disturb the phenomena of interest. To address these issues, the Idaho National Laboratory (INL) recently initiated efforts to evaluate candidate linear variable differential transducers (LVDTs) for use during high temperature irradiation experiments in typical ATR test locations. Two nuclear grade LVDTs are under consideration – a smaller diameter design qualified for temperatures up to 350 °C and a larger design with capabilities to 500 °C. Calibration and long duration performance evaluations are underway for temperatures up to 600 ºC. This paper presents results from these evaluations, which will ultimately lead to recommendations for an improved design for use in the ATR.

  15. AGR-2 Data Qualification Report for ATR Cycle 154B

    SciTech Connect

    Binh Pham; Jeff Einerson

    2014-01-01

    This report provides the data qualification status of Advanced Gas Reactor-2 (AGR-2) fuel irradiation experimental data from Advanced Test Reactor (ATR) Cycle 154B as recorded in the Nuclear Data Management and Analysis System (NDMAS). This is the last cycle of AGR-2 irradiation, as the test train was pulled from the ATR core during the outage portion of ATR Cycle 155A. The AGR-2 data streams addressed in this report include thermocouple (TC) temperatures, sweep gas data (flow rates including new Fission Product Monitoring (FPM) downstream flows from Fission Product Monitoring System (FPMS) detectors, pressure, and moisture content), and FPMS data (release rates and release-to-birth rate ratios [R/Bs]) for each of the six capsules in the AGR-2 experiment. The final data qualification status for these data streams is determined by a Data Review Committee (DRC) comprised of AGR technical leads, Sitewide Quality Assurance (QA), and NDMAS analysts. The Data Review Committee reviewed the data acquisition process, considered whether the data met the requirements for data collection as specified in QA-approved Very High Temperature Reactor (VHTR) data collection plans, examined the results of NDMAS data testing and statistical analyses, and confirmed the qualification status of the data as given in this report.

  16. 76 FR 47520 - Airworthiness Directives; ATR-GIE Avions de Transport Régional Model ATR42 and ATR72 Airplanes

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-05

    ... continued.airworthiness@atr.fr ; Internet http://www.aerochain.com . You may review copies of the referenced... 12866; 2. Is not a ``significant rule'' under the DOT Regulatory Policies and Procedures (44 FR 11034... Transport R gional Model ATR42 and ATR72 Airplanes AGENCY: Federal Aviation Administration (FAA),...

  17. Cascaded automatic target recognition (Cascaded ATR)

    NASA Astrophysics Data System (ADS)

    Walls, Bradley

    2010-04-01

    The global war on terror has plunged US and coalition forces into a battle space requiring the continuous adaptation of tactics and technologies to cope with an elusive enemy. As a result, technologies that enhance the intelligence, surveillance, and reconnaissance (ISR) mission making the warfighter more effective are experiencing increased interest. In this paper we show how a new generation of smart cameras built around foveated sensing makes possible a powerful ISR technique termed Cascaded ATR. Foveated sensing is an innovative optical concept in which a single aperture captures two distinct fields of view. In Cascaded ATR, foveated sensing is used to provide a coarse resolution, persistent surveillance, wide field of view (WFOV) detector to accomplish detection level perception. At the same time, within the foveated sensor, these detection locations are passed as a cue to a steerable, high fidelity, narrow field of view (NFOV) detector to perform recognition level perception. Two new ISR mission scenarios, utilizing Cascaded ATR, are proposed.

  18. Vanadium irradiation at ATR - neutronics aspects

    SciTech Connect

    Gomes, I.C.; Smith, D.L.

    1995-04-01

    Calculations were performed to estimate damage and transmutation rates in vanadium irradiated in the ATR (Advanced Test Reactor) located in Idaho. The main focuses of the study are to evaluate the transmutation of vanadium to chromium and to explore ways to design the irradiation experiment to avoid excessive transmutation. It was found that the A-hole of ATR produces damage rate of {approximately} 0.2%/dpa of vanadium to chromium. A thermal neutron filter can be incorporated into the design to reduce the vanadium-to-chromium transmutation rate to low levels. A filter 1-2 mm thick of gadolinium or hafnium can be used.

  19. Focusing and matching properties of the ATR transfer line

    SciTech Connect

    Tsoupas, N.; Fischer, W.; Kewisch, J.; MacKay, W.W.; Peggs, S.; Pilat, F.; Tepikian, S.; Wei, J.

    1997-07-01

    The AGS to RHIC (AtR) beam transfer line has been constructed and will be used to transfer beam bunches from the AGS machine into the RHIC machine which is presently under construction at BNL. The original design of the AtR line has been modified. This article will present the optics of the various sections of the existing AtR beam line, as well as the matching capabilities of the AtR line to the RHIC machine.

  20. Overview of the ATR Power Supplies

    NASA Astrophysics Data System (ADS)

    Bruno, D.; Soukas, A.; Toldo, F.; Lambiase, B.

    1997-05-01

    The AGS to RHIC transfer Line (ATR) transports a variety of beams from the Alternating Gradient Synchrotron (AGS) which gets its input from the Booster Synchrotron. In turn, the Booster receives input beams from either a Tandem Van de Graaff (heavy ions) or a Linac(protons). The AGS extracts beam bunches, up to a rate of 30 Hertz, to the ATR which will eventually feed the Relativistic Heavy Ion Collider (RHIC) starting with the sextant test in January of 1996. The ATR is made up of the upgraded U line and the new W, X and Y lines. A test in 1995 transported beam to the end of the W line. During normal operation, a pulsed switching magnet at the end of the W line will bend the beam into the X line or the Y line so that the two rings in RHIC are filled with counter rotating beams. The ATR line is comprised of 80 power supplies (PS's), 17 of which are upgraded AGS PS's. The remaining 63 PS's were newly purchased. These PS's range from bipolar 600 watt linear type trim magnet PS's to 1 Megawatt, thyristor, dipole PS's. Results of the commissioning runs will be presented, as well as descriptions of regulation, filtering, and analog and digital controls.

  1. Overview of the ATR power supplies

    SciTech Connect

    Bruno, D.; Soukas, A.; Toldo, F.; Lambiase, R.F.

    1997-07-01

    The AGS to RHIC transfer line (ATR) transports a variety of beams from the Alternating Gradient Synchrotron (AGS) which gets its input from the Booster Synchrotron. In turn, the Booster receives input beams from either a Tandem Van de Graaff (heavy ions) or a Linac (protons). The AGS extracts beam bunches, up to a rate of 30 Hertz, to the ATR which feeds the Relativistic Heavy Ion Collider (RHIC) starting with the sextant test in January of 1997. The ATR is made up of the upgraded U line and the new W, X, and Y lines. A test in 1995 transported beam to the end of the W line. During normal operation, a pulsed switching magnet at the end of the W line will bend the beam into the X line or the Y line so that the two storage rings in RHIC are filled with counter rotating beams. The ATR line is comprised of 80 power supplies (PS`s), 17 of which are upgraded AGS PS`s. The remaining 63 PS`s were newly purchased. These PS`s range from bipolar 600 watt linear type trim magnet PS`s to 1 Megawatt, thyristor, dipole PS`s. Results of the commissioning runs will be presented, as well as descriptions of regulation, filtering, and analog and digital controls.

  2. Neutron spectrum studies in the ATR (Advanced Test Reactor)

    SciTech Connect

    Rogers, J.W.; Anderl, R.A.; Putnam, M.H.

    1990-01-01

    The Advanced Test Reactor (ATR) at the Idaho National Engineering Laboratory (INEL) has been and currently is used to provide irradiation fields to study the effects of intense radiation on samples of reactor materials. These samples include fuel, cladding, control and structural materials. The ATR is also used to irradiate target materials for the production of radionuclides used in industrial and medical applications as well as for scientific research. Routine monitoring of the thermal'' and fast'' neutron levels have been conducted during every operational cycle since its startup in 1970. The routine neutron dosimetry has been primarily accomplished using the {sup 59}Co(n,{gamma}){sup 60}Co reaction for thermal'' neutrons and the {sup 58}Ni(n,p) {sup 58}Co reaction for fast'' neutrons as described in ASTM standard methods E261, E262, and E264. Neutron spectrum studies have now been conducted in the epithermal and fast neutron energy ranges for the various capsule irradiation test facilities and the routine neutron monitoring locations. 7 refs., 5 figs., 1 tab.

  3. MIR-ATR sensor for process monitoring

    NASA Astrophysics Data System (ADS)

    Geörg, Daniel; Schalk, Robert; Methner, Frank-Jürgen; Beuermann, Thomas

    2015-06-01

    A mid-infrared attenuated total reflectance (MIR-ATR) sensor has been developed for chemical reaction monitoring. The optical setup of the compact and low-priced sensor consists of an IR emitter as light source, a zinc selenide (ZnSe) ATR prism as boundary to the process, and four thermopile detectors, each equipped with an optical bandpass filter. The practical applicability was tested during esterification of ethanol and formic acid to ethyl formate and water as a model reaction with subsequent distillation. For reference analysis, a Fourier transform mid-infrared (FT-MIR) spectrometer with diamond ATR module was applied. On-line measurements using the MIR-ATR sensor and the FT-MIR spectrometer were performed in a bypass loop. The sensor was calibrated by multiple linear regression in order to link the measured absorbance in the four optical channels to the analyte concentrations. The analytical potential of the MIR-ATR sensor was demonstrated by simultaneous real-time monitoring of all four chemical substances involved in the esterification and distillation process. The temporal courses of the sensor signals are in accordance with the concentration values achieved by the commercial FT-MIR spectrometer. The standard error of prediction for ethanol, formic acid, ethyl formate, and water were 0.38 mol L  -  1, 0.48 mol L  -  1, 0.38 mol L  -  1, and 1.12 mol L  -  1, respectively. A procedure based on MIR spectra is presented to simulate the response characteristics of the sensor if the transmission ranges of the filters are varied. Using this tool analyte specific bandpass filters for a particular chemical reaction can be identified. By exchanging the optical filters, the sensor can be adapted to a wide range of processes in the chemical, pharmaceutical, and beverage industries.

  4. The distribution of atrazine (ATR) and ATR metabolites in the Wistar rat following gestational/lactational exposures

    EPA Science Inventory

    Gestational/lactational exposure to ATR is reported to alter reproductive/developmental function, yet our understanding of the transfer of ATR and/or its metabolites from the dam to the fetus/offspring is limited. Previously we examined the lactational transfer of CI4-ATR, but sp...

  5. ATR LEU Monothlic and Dispersed with 10B Loading Minimization Design – Neutronics Performance Analysis

    SciTech Connect

    G. S. Chang

    2001-10-01

    The Advanced Test Reactor (ATR), currently operating in the United States, is used for material testing at very high neutron fluxes. Powered with highly enriched uranium (HEU), the ATR has a maximum thermal power rating of 250 MWth. Because of the large test volumes located in high flux areas, the ATR is an ideal candidate for assessing the feasibility of converting HEU driven reactor cores to low-enriched uranium (LEU) cores. The present work investigates the optimized LEU Monolithic and Dispersed fuel with 10B loading minimization design and evaluates the subsequent neutronics operating effects of these optimized fuel designs. The MCNP ATR 1/8th core model was used to optimize the 235U and minimize the 10B loading in the LEU core, such that the differences in K-eff and heat flux profiles between the HEU and LEU cores were minimized. The fuel depletion methodology MCWO was used to calculate K eff versus effective full power days (EFPD) in this paper. The MCWO-calculated results for the optimized LEU Monolithic and Dispersed fuel cases demonstrated adequate excess reactivity such that the K-eff versus EFPD plot is similar to the ATR reference HEU case study. Each HEU fuel element contains 19 fuel plates with a fuel meat thickness of 0.508 mm (20 mil). In this work, the proposed LEU Monolithic (U-10Mo) core conversion case with nominal fuel meat thickness of 0.330 mm (13 mil) and 235U enrichment of 19.7 wt% is used to optimize the radial heat flux profile by varying the fuel meat thickness. The proposed LEU fuel meat varies from 0.203 mm (8.0 mil) to 0.254 mm (10.0 mil) at the inner four fuel plates (1-4) and outer four fuel plates (16-19). In addition, an optimized LEU dispersed (U7Mo) case with all the fuel meat thickness of 0.635 mm (25 mil) was also proposed. Then, for both Monolithic and dispersed cases, a burnable absorber – 10B, was added in the inner and outer plates to reduce the initial excess reactivity, and the higher to average ratio of the inner

  6. Function of the ATR N-terminal domain revealed by an ATM/ATR chimera

    SciTech Connect

    Chen Xinping; Zhao Runxiang; Glick, Gloria G.; Cortez, David . E-mail: david.cortez@vanderbilt.edu

    2007-05-01

    The ATM and ATR kinases function at the apex of checkpoint signaling pathways. These kinases share significant sequence similarity, phosphorylate many of the same substrates, and have overlapping roles in initiating cell cycle checkpoints. However, they sense DNA damage through distinct mechanisms. ATR primarily senses single stranded DNA (ssDNA) through its interaction with ATRIP, and ATM senses double strand breaks through its interaction with Nbs1. We determined that the N-terminus of ATR contains a domain that binds ATRIP. Attaching this domain to ATM allowed the fusion protein (ATM*) to bind ATRIP and associate with RPA-coated ssDNA. ATM* also gained the ability to localize efficiently to stalled replication forks as well as double strand breaks. Despite having normal kinase activity when tested in vitro and being phosphorylated on S1981 in vivo, ATM* is defective in checkpoint signaling and does not complement cellular deficiencies in either ATM or ATR. These data indicate that the N-terminus of ATR is sufficient to bind ATRIP and to promote localization to sites of replication stress.

  7. ATR promotes cilia signalling: links to developmental impacts.

    PubMed

    Stiff, Tom; Casar Tena, Teresa; O'Driscoll, Mark; Jeggo, Penny A; Philipp, Melanie

    2016-04-15

    Mutations in ATR(ataxia telangiectasia and RAD3-related) cause Seckel syndrome (ATR-SS), a microcephalic primordial dwarfism disorder. Hitherto, the clinical manifestation of ATR deficiency has been attributed to its canonical role in DNA damage response signalling following replication fork stalling/collapse. Here, we show that ATR regulates cilia-dependent signalling in a manner that can be uncoupled from its function during replication. ATR-depleted or patient-derived ATR-SS cells form cilia of slightly reduced length but are dramatically impaired in cilia-dependent signalling functions, including growth factor and Sonic hedgehog signalling. To better understand the developmental impact of ATR loss of function, we also used zebrafish as a model. Zebrafish embryos depleted of Atr resembled ATR-SS morphology, showed a modest but statistically significant reduction in cilia length and other morphological features indicative of cilia dysfunction. Additionally, they displayed defects in left-right asymmetry including ambiguous expression of southpaw, incorrectly looped hearts and randomized localization of internal organs including the pancreas, features typically conferred by cilia dysfunction. Our findings reveal a novel role for ATR in cilia signalling distinct from its canonical function during replication and strengthen emerging links between cilia function and development. PMID:26908596

  8. ATR promotes cilia signalling: links to developmental impacts

    PubMed Central

    Stiff, Tom; Casar Tena, Teresa; O'Driscoll, Mark; Jeggo, Penny A.; Philipp, Melanie

    2016-01-01

    Mutations in ATR (ataxia telangiectasia and RAD3-related) cause Seckel syndrome (ATR-SS), a microcephalic primordial dwarfism disorder. Hitherto, the clinical manifestation of ATR deficiency has been attributed to its canonical role in DNA damage response signalling following replication fork stalling/collapse. Here, we show that ATR regulates cilia-dependent signalling in a manner that can be uncoupled from its function during replication. ATR-depleted or patient-derived ATR-SS cells form cilia of slightly reduced length but are dramatically impaired in cilia-dependent signalling functions, including growth factor and Sonic hedgehog signalling. To better understand the developmental impact of ATR loss of function, we also used zebrafish as a model. Zebrafish embryos depleted of Atr resembled ATR-SS morphology, showed a modest but statistically significant reduction in cilia length and other morphological features indicative of cilia dysfunction. Additionally, they displayed defects in left-right asymmetry including ambiguous expression of southpaw, incorrectly looped hearts and randomized localization of internal organs including the pancreas, features typically conferred by cilia dysfunction. Our findings reveal a novel role for ATR in cilia signalling distinct from its canonical function during replication and strengthen emerging links between cilia function and development. PMID:26908596

  9. 75 FR 8476 - Airworthiness Directives; ATR-GIE Avions de Transport Régional Model ATR42 and ATR72 Airplanes

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-25

    ..., amendment 39-16159 (75 FR 221, January 5, 2010), on December 28, 2009. That AD applies to certain portable...'' under the DOT Regulatory Policies and Procedures (44 FR 11034, February 26, 1979); and 3. Will not have... Transport R gional Model ATR42 and ATR72 Airplanes AGENCY: Federal Aviation Administration (FAA),...

  10. Independent Review of AFC 2A, 2B, and 2E ATR Irradiation Tests

    SciTech Connect

    M. Cappiello; R. Hobbins; K. Penny; L. Walters

    2014-01-01

    As part of the Department of Energy Advanced Fuel Cycle program, a series of fuels development irradiation tests have been performed in the Advanced Test Reactor (ATR) at the Idaho National Laboratory. These tests are providing excellent data for advanced fuels development. The program is focused on the transmutation of higher actinides which best can be accomplished in a sodium-cooled fast reactor. Because a fast test reactor is no longer available in the US, a special test vehicle is used to achieve near-prototypic fast reactor conditions (neutron spectra and temperature) for use in ATR (a water-cooled thermal reactor). As part of the testing program, there were many successful tests of advanced fuels including metals and ceramics. Recently however, there have been three experimental campaigns using metal fuels that experienced failure during irradiation. At the request of the program, an independent review committee was convened to review the post-test analyses performed by the fuels development team, to assess the conclusions of the team for the cause of the failures, to assess the adequacy and completeness of the analyses, to identify issues that were missed, and to make recommendations for improvements in the design and operation of future tests. Although there is some difference of opinion, the review committee largely agreed with the conclusions of the fuel development team regarding the cause of the failures. For the most part, the analyses that support the conclusions are sufficient.

  11. AGR-3/4 Final Data Qualification Report for ATR Cycles 151A through 155B-1

    SciTech Connect

    Pham, Binh T.

    2015-03-01

    This report provides the qualification status of experimental data for the entire Advanced Gas Reactor 3/4 (AGR 3/4) fuel irradiation. AGR-3/4 is the third in a series of planned irradiation experiments conducted in the Advanced Test Reactor (ATR) at Idaho National Laboratory (INL) for the AGR Fuel Development and Qualification Program, which supports development of the advanced reactor technology under the INL ART Technology Development Office (TDO). The main objective of AGR-3/4 irradiation is to provide a known source of fission products for subsequent transport through compact matrix and structural graphite materials due to the presence of designed-to-fail fuel particles. Full power irradiation of the AGR 3/4 test began on December 14, 2011 (ATR Cycle 151A), and was completed on April 12, 2014 (end of ATR Cycle 155B) after 369.1 effective full power days of irradiation. The AGR-3/4 test was in the reactor core for eight of the ten ATR cycles between 151A and 155B. During the unplanned outage cycle, 153A, the experiment was removed from the ATR northeast flux trap (NEFT) location and stored in the ATR canal. This was to prevent overheating of fuel compacts due to higher than normal ATR power during the subsequent Powered Axial Locator Mechanism cycle, 153B. The AGR 3/4 test was inserted back into the ATR NEFT location during the outage of ATR Cycle 154A on April 26, 2013. Therefore, the AGR-3/4 irradiation data received during these 2 cycles (153A and 153B) are irrelevant and their qualification status isnot included in this report. Additionally, during ATR Cycle 152A the ATR core ran at low power for a short enough duration that the irradiation data are not used for physics and thermal calculations. However, the qualification status of irradiation data for this cycle is still covered in this report. As a result, this report includes data from 8 ATR Cycles: 151A, 151B, 152A, 152B, 154A, 154B, 155A, and 155B, as recorded in the Nuclear Data Management and

  12. Utilizing feedback in adaptive SAR ATR systems

    NASA Astrophysics Data System (ADS)

    Horsfield, Owen; Blacknell, David

    2009-05-01

    Existing SAR ATR systems are usually trained off-line with samples of target imagery or CAD models, prior to conducting a mission. If the training data is not representative of mission conditions, then poor performance may result. In addition, it is difficult to acquire suitable training data for the many target types of interest. The Adaptive SAR ATR Problem Set (AdaptSAPS) program provides a MATLAB framework and image database for developing systems that adapt to mission conditions, meaning less reliance on accurate training data. A key function of an adaptive system is the ability to utilise truth feedback to improve performance, and it is this feature which AdaptSAPS is intended to exploit. This paper presents a new method for SAR ATR that does not use training data, based on supervised learning. This is achieved by using feature-based classification, and several new shadow features have been developed for this purpose. These features allow discrimination of vehicles from clutter, and classification of vehicles into two classes: targets, comprising military combat types, and non-targets, comprising bulldozers and trucks. The performance of the system is assessed using three baseline missions provided with AdaptSAPS, as well as three additional missions. All performance metrics indicate a distinct learning trend over the course of a mission, with most third and fourth quartile performance levels exceeding 85% correct classification. It has been demonstrated that these performance levels can be maintained even when truth feedback rates are reduced by up to 55% over the course of a mission.

  13. Advanced miniature processing handware for ATR applications

    NASA Technical Reports Server (NTRS)

    Chao, Tien-Hsin (Inventor); Daud, Taher (Inventor); Thakoor, Anikumar (Inventor)

    2003-01-01

    A Hybrid Optoelectronic Neural Object Recognition System (HONORS), is disclosed, comprising two major building blocks: (1) an advanced grayscale optical correlator (OC) and (2) a massively parallel three-dimensional neural-processor. The optical correlator, with its inherent advantages in parallel processing and shift invariance, is used for target of interest (TOI) detection and segmentation. The three-dimensional neural-processor, with its robust neural learning capability, is used for target classification and identification. The hybrid optoelectronic neural object recognition system, with its powerful combination of optical processing and neural networks, enables real-time, large frame, automatic target recognition (ATR).

  14. MOX and MOX with 237Np/241Am Inert Fission Gas Generation Comparison in ATR

    SciTech Connect

    G. S. Chang; M. Robel; W. J. Carmack; D. J. Utterbeck

    2006-06-01

    The treatment of spent fuel produced in nuclear power generation is one of the most important issues to both the nuclear community and the general public. One of the viable options to long-term geological disposal of spent fuel is to extract plutonium, minor actinides (MA), and potentially long-lived fission products from the spent fuel and transmute them into short-lived or stable radionuclides in currently operating light-water reactors (LWR), thus reducing the radiological toxicity of the nuclear waste stream. One of the challenges is to demonstrate that the burnup-dependent characteristic differences between Reactor-Grade Mixed Oxide (RG-MOX) fuel and RG-MOX fuel with MA Np-237 and Am 241 are minimal, particularly, the inert gas generation rate, such that the commercial MOX fuel experience base is applicable. Under the Advanced Fuel Cycle Initiative (AFCI), developmental fuel specimens in experimental assembly LWR-2 are being tested in the northwest (NW) I-24 irradiation position of the Advanced Test Reactor (ATR). The experiment uses MOX fuel test hardware, and contains capsules with MOX fuel consisting of mixed oxide manufactured fuel using reactor grade plutonium (RG-Pu) and mixed oxide manufactured fuel using RG-Pu with added Np/Am. This study will compare the fuel neutronics depletion characteristics of Case-1 RG-MOX and Case-2 RG-MOX with Np/Am.

  15. Fuel processing device

    DOEpatents

    Ahluwalia, Rajesh K.; Ahmed, Shabbir; Lee, Sheldon H. D.

    2011-08-02

    An improved fuel processor for fuel cells is provided whereby the startup time of the processor is less than sixty seconds and can be as low as 30 seconds, if not less. A rapid startup time is achieved by either igniting or allowing a small mixture of air and fuel to react over and warm up the catalyst of an autothermal reformer (ATR). The ATR then produces combustible gases to be subsequently oxidized on and simultaneously warm up water-gas shift zone catalysts. After normal operating temperature has been achieved, the proportion of air included with the fuel is greatly diminished.

  16. Towards universal enrichment nanocoating for IR-ATR waveguides.

    PubMed

    Giammarco, James; Zdyrko, Bogdan; Petit, Laeticia; Musgraves, J David; Hu, Juejun; Agarwal, Anu; Kimerling, Lionel; Richardson, Kathleen; Luzinov, Igor

    2011-08-28

    Polymer multilayered nanocoating capable of concentrating various chemical substances at IR-ATR waveguide surfaces is described. The coating affinity to an analyte played a pivotal role in sensitivity enhancement of the IR-ATR measurements, since the unmodified waveguide did not show any analyte detection. PMID:21734984

  17. ATR FTIR Mapping of Leather Fiber Panels

    NASA Astrophysics Data System (ADS)

    Tondi, G.; Grünewald, T.; Petutschnigg, A.; Schnabel, T.

    2015-01-01

    Leather fiber panels are very promising materials for many applications, not only for the easy availability of the constituents but also for their outstanding fi re-retardant properties. These innovative composite panels can be an excellent material for building insulation, and in recent times, the interest of industries in this composite board has considerably arisen. For this reason the discrimination of the components in the leather fiber panels is becoming fundamental in order to ensure their homogeneous properties. A method to characterize the surface of these materials is then required. An ATR FTIR mapping system for the leather fiber panels has been performed with a Perkin-Elmer microscope coupled with a Frontier FTIR spectrometer. The system has successfully allowed transforming the optical image to a chemical one. This technique can be considered as a right tool for routine controls of the surface quality, especially when the leather shavings cannot be optically distinguished.

  18. ATR task and training requirements analysis

    SciTech Connect

    Gertman, D.I.; Blackman, H.S.; Gilmore, W.E. II; French, D.L.

    1983-05-01

    Task analysis techniques were used to assist in identifying improvements needed in the training curriculum for selected positions at the Advanced Test Reactor (ATR). Six positions were examined - Experiment Power Reactor Operator, Experiment (EPRO-Ex); Experiment Power Reactor Operator, Console (EPRO-Co); Senior Reactor Engineer (SRE); Assistant Shift Supervisor (AS); Shift Supervisor (SS); and Process Control Operator (PCO). A complete position task listing and a core of tasks defined in terms of (a) level of difficulty to perform, (b) severity of consequence if performed improperly, and (c) associated error probability were identified for each position. The systems, academic, and administrative knowledge needed by job incumbents to perform each task was noted. Strategies for teaching the knowledge associated with these tasks are presented.

  19. ATR inhibition rewires cellular signaling networks induced by replication stress.

    PubMed

    Wagner, Sebastian A; Oehler, Hannah; Voigt, Andrea; Dalic, Denis; Freiwald, Anja; Serve, Hubert; Beli, Petra

    2016-02-01

    The slowing down or stalling of replication forks is commonly known as replication stress and arises from multiple causes such as DNA lesions, nucleotide depletion, RNA-DNA hybrids, and oncogene activation. The ataxia telangiectasia and Rad3-related kinase (ATR) plays an essential role in the cellular response to replication stress and inhibition of ATR has emerged as therapeutic strategy for the treatment of cancers that exhibit high levels of replication stress. However, the cellular signaling induced by replication stress and the substrate spectrum of ATR has not been systematically investigated. In this study, we employed quantitative MS-based proteomics to define the cellular signaling after nucleotide depletion-induced replication stress and replication fork collapse following ATR inhibition. We demonstrate that replication stress results in increased phosphorylation of a subset of proteins, many of which are involved in RNA splicing and transcription and have previously not been associated with the cellular replication stress response. Furthermore, our data reveal the ATR-dependent phosphorylation following replication stress and discover novel putative ATR target sites on MCM6, TOPBP1, RAD51AP1, and PSMD4. We establish that ATR inhibition rewires cellular signaling networks induced by replication stress and leads to the activation of the ATM-driven double-strand break repair signaling. PMID:26572502

  20. ATR-mediated regulation of nuclear and cellular plasticity.

    PubMed

    Kidiyoor, Gururaj Rao; Kumar, Amit; Foiani, Marco

    2016-08-01

    ATR (Ataxia Telangiectasia and Rad3-related) is a member of the Phosphatidylinositol 3-kinase-related kinases (PIKKs) family, amongst six other vertebrate proteins known so far. ATR is indispensable for cell survival and its essential role is in sensing DNA damage and initiating appropriate repair responses. In this review we highlight emerging and recent observations connecting ATR to alternative roles in controlling the nuclear envelope, nucleolus, centrosome and other organelles in response to both internal and external stress conditions. We propose that ATR functions control cell plasticity by sensing structural deformations of different cellular components, including DNA and initiating appropriate repair responses, most of which are yet to be understood completely. PMID:27283761

  1. Infrared ATR: a probe for cellular activation

    NASA Astrophysics Data System (ADS)

    Timlin, Jerilyn A.; Martin, Laura E.; Alam, M. Kathleen; Haaland, David M.; Garrison, Kristen; Lyons, C. Richard; Hjelle, Brian

    2002-02-01

    We employ infrared spectroscopy (IR) with attenuated total reflectance (ATR) as a sampling technique to monitor live and dried RAW cells (a murine macrophage cell line) during activation with g-interferon and lipopolysaccharide. By comparing the spectra of activated cells at various time points to the spectra of healthy control cells, we identify spectral bands associated with nucleic acids that are markers for the cell activation process. These spectral changes are slight and can be complicated with the normal metabolic changes that occur within cells. We will discuss the use of data pretreatment strategies to accurately correct for the contribution of the buffer to the live cell spectra. We find the standard background correction method inadequate for concentrated solutions of cells. Data presented shows the severe effect incorrect background subtraction has on the cell spectra. We report a more accurate correction for phosphate buffer spectral contribution using an interactive subtraction of the buffer spectrum. We will show classification of dried control and activated macrophage cell spectra using partial-least squares analysis with multiplicative scatter correction.

  2. ATR-IR spectroscopy as applied to nucleic acid films

    NASA Astrophysics Data System (ADS)

    Stepanyugin, Andriy V.; Samijlenko, Svitlana P.; Martynenko, Olena I.; Hovorun, Dmytro M.

    2005-07-01

    For the first time the ATR technique was applied to obtain IR absorption spectra of DNA and RNA dry films. There was worked out procedure of the nucleic acid removal from germanium plate, which obviously was a main obstacle to application of ATR-IR spectroscopy to nucleic acids. This technique of IR spectroscopy was applied to confirmation of RNA tropism of aurin tricarboxylic acid observed by molecular biological methods.

  3. ATR National Scientific User Facility 2009 Annual Report

    SciTech Connect

    Todd R. Allen; Mitchell K. Meyer; Frances Marshall; Mary Catherine Thelen; Jeff Benson

    2010-11-01

    This report describes activities of the ATR NSUF from FY-2008 through FY-2009 and includes information on partner facilities, calls for proposals, users week and education programs. The report also contains project information on university research projects that were awarded by ATR NSUF in the fiscal years 2008 & 2009. This research is university-proposed researcher under a user facility agreement. All intellectual property from these experiments belongs to the university per the user agreement.

  4. Recent applications of ATR FTIR spectroscopy and imaging to proteins.

    PubMed

    Glassford, Stefanie E; Byrne, Bernadette; Kazarian, Sergei G

    2013-12-01

    Attenuated Total Reflection (ATR) Fourier Transform Infrared (FTIR) spectroscopy is a label-free, non-destructive analytical technique that can be used extensively to study a wide variety of different molecules in a range of different conditions. The aim of this review is to discuss and highlight the recent advances in the applications of ATR FTIR spectroscopic imaging to proteins. It briefly covers the basic principles of ATR FTIR spectroscopy and ATR FTIR spectroscopic imaging as well as their advantages to the study of proteins compared to other techniques and other forms of FTIR spectroscopy. It will then go on to examine the advances that have been made within the field over the last several years, particularly the use of ATR FTIR spectroscopy for the understanding and development of protein interaction with surfaces. Additionally, the growing potential of Surface Enhanced Infrared Spectroscopy (SEIRAS) within this area of applications will be discussed. The review includes the applications of ATR FTIR imaging to protein crystallisation and for high-throughput studies, highlighting the future potential of the technology within the field of protein structural studies and beyond. PMID:23928299

  5. Assessment of COTS IR image simulation tools for ATR development

    NASA Astrophysics Data System (ADS)

    Seidel, Heiko; Stahl, Christoph; Bjerkeli, Frode; Skaaren-Fystro, Paal

    2005-05-01

    Following the tendency of increased use of imaging sensors in military aircraft, future fighter pilots will need onboard artificial intelligence e.g. ATR for aiding them in image interpretation and target designation. The European Aeronautic Defence and Space Company (EADS) in Germany has developed an advanced method for automatic target recognition (ATR) which is based on adaptive neural networks. This ATR method can assist the crew of military aircraft like the Eurofighter in sensor image monitoring and thereby reduce the workload in the cockpit and increase the mission efficiency. The EADS ATR approach can be adapted for imagery of visual, infrared and SAR sensors because of the training-based classifiers of the ATR method. For the optimal adaptation of these classifiers they have to be trained with appropriate and sufficient image data. The training images must show the target objects from different aspect angles, ranges, environmental conditions, etc. Incomplete training sets lead to a degradation of classifier performance. Additionally, ground truth information i.e. scenario conditions like class type and position of targets is necessary for the optimal adaptation of the ATR method. In Summer 2003, EADS started a cooperation with Kongsberg Defence & Aerospace (KDA) from Norway. The EADS/KDA approach is to provide additional image data sets for training-based ATR through IR image simulation. The joint study aims to investigate the benefits of enhancing incomplete training sets for classifier adaptation by simulated synthetic imagery. EADS/KDA identified the requirements of a commercial-off-the-shelf IR simulation tool capable of delivering appropriate synthetic imagery for ATR development. A market study of available IR simulation tools and suppliers was performed. After that the most promising tool was benchmarked according to several criteria e.g. thermal emission model, sensor model, targets model, non-radiometric image features etc., resulting in a

  6. FLUX SENSOR EVALUATIONS AT THE ATR CRITICAL FACILITY

    SciTech Connect

    Troy Unruh; Joy Rempe; David Nigg; George Imel; Jason Harris; Eric Bonebrake

    2010-11-01

    The Advanced Test Reactor (ATR) and the ATR Critical (ATRC) facilities lack real-time methods for detecting thermal neutron flux and fission reaction rates for irradiation capsules. Direct measurements of the actual power deposited into a test are now possible without resorting to complicated correction factors. In addition, it is possible to directly measure minor actinide fission reaction rates and to provide time-dependent monitoring of the fission reaction rate or fast/thermal flux during transient testing. A joint Idaho State University /Idaho National Laboratory ATR National Scientific User Facility (ATR NSUF) project was recently initiated to evaluate new real-time state-of-the-art in-pile flux detection sensors. Initially, the project is comparing the accuracy, response time, and long duration performance of French Atomic Energy Commission (CEA)-developed miniature fission chambers, specialized self-powered neutron detectors (SPNDs) by the Argentinean National Energy Commission (CNEA), specially developed commercial SPNDs, and back-to-back fission (BTB) chambers developed by Argonne National Laboratory (ANL). As discussed in this paper, specialized fixturing and software was developed by INL to facilitate these joint ISU/INL evaluations. Calculations were performed by ISU to assess the performance of and reduce uncertainties in flux detection sensors and compare data obtained from these sensors with existing integral methods employed at the ATRC. Ultimately, project results will be used to select the detector that can provide the best online regional ATRC power measurement. It is anticipated that project results may offer the potential to increase the ATRC’s current power limit and its ability to perform low-level irradiation experiments. In addition, results from this effort will provide insights about the viability of using these detectors in the ATR. Hence, this effort complements current activities to improve ATR software tools, computational

  7. Homeostatic regulation of meiotic DSB formation by ATM/ATR

    SciTech Connect

    Cooper, Tim J.; Wardell, Kayleigh; Garcia, Valerie; Neale, Matthew J.

    2014-11-15

    Ataxia–telangiectasia mutated (ATM) and RAD3-related (ATR) are widely known as being central players in the mitotic DNA damage response (DDR), mounting responses to DNA double-strand breaks (DSBs) and single-stranded DNA (ssDNA) respectively. The DDR signalling cascade couples cell cycle control to damage-sensing and repair processes in order to prevent untimely cell cycle progression while damage still persists [1]. Both ATM/ATR are, however, also emerging as essential factors in the process of meiosis; a specialised cell cycle programme responsible for the formation of haploid gametes via two sequential nuclear divisions. Central to achieving accurate meiotic chromosome segregation is the introduction of numerous DSBs spread across the genome by the evolutionarily conserved enzyme, Spo11. This review seeks to explore and address how cells utilise ATM/ATR pathways to regulate Spo11-DSB formation, establish DSB homeostasis and ensure meiosis is completed unperturbed.

  8. ATR NATIONAL SCIENTIFIC USER FACILITY INSTRUMENTATION ENHANCEMENT EFFORTS

    SciTech Connect

    Joy L. Rempe; Mitchell K. Meyer

    2009-04-01

    A key component of the Advanced Test Reactor (ATR) National Scientific User Facility (NSUF) effort is to enhance instrumentation techniques available to users conducting irradiation tests in this unique facility. In particular, development of sensors capable of providing ‘real-time’ measurements of key irradiation parameters is emphasized because of their potential to offer increased fidelity data and reduced post-test examination costs. This paper describes the strategy for identifying new instrumentation needed for ATR irradiations and the program underway to develop and evaluate new sensors to address these needs. Accomplishments from this program are illustrated by describing several new sensors now available to users of the ATR NSUF. In addition, progress is reported on current research efforts to provide users improved in-pile instrumentation.

  9. Robust SAR ATR via set-valued classifiers: new results

    NASA Astrophysics Data System (ADS)

    Hoffman, John R.; Mahler, Ronald P. S.; Ravichandran, Ravi B.; Mehra, Raman K.; Musick, Stanton H.

    2003-08-01

    "Robust identification" in SAR ATR refers to the problem of determining target identity despite the confounding effects of "extended operating conditions" (EOCs). EOC"s are statistically uncharacterizable SAR intensity-signature variations caused by mud, dents, turret articulations, etc. This paper describes a robust ATR approach based on the idea of (1) hedging against EOCs by attaching "random error bars" (random intervals) to each value of the image likelihood function; (2) constructing a "generalized likelihood function" from them; and (3) using a set-valued, MLE-like approach to robustly estimate target type. We compare three such classifiers, showing that they outperform conventional approaches under EOC conditions.

  10. Design and implementation of an embedded software system for ATR

    NASA Astrophysics Data System (ADS)

    Wang, Yuehuan; Li, Shiyong

    2011-11-01

    This paper has designed and realized a coarse-grained, unbalanced, modularized parallel embedded software system for ATR. According to the characteristics of ATR algorithms, some control modules such as system monitoring, task assignment and hierarchical algorithm modules are realized in our system. There are different design principles for different modules. The task assignment module combines different modules into clusters based on mutually exclusive modules, and assigns them to different processors. The principle of combination is the minimum variance of load on different processors. The system satisfies the requirement of real-time performance due to this reasonable strategy for task assignment, with the flexibility and scalability significantly improved.

  11. ATR spectra on boundary with mixture containing organic substances

    NASA Astrophysics Data System (ADS)

    Schelokov, R. V.; Yatsishen, V. V.

    2005-02-01

    The problem of not destroying diagnostics and dosing of radiation at laser therapy is one of important in medicine. Therefore the purpose of our work is development of method ATR for diagnostics and researches in biomedicine. In this work as objects of consideration were: a mixture of nicotine with water, a mixture of an ascorbic acid with water and surface lesions of an eye cornea by a herpes virus. Results of our consideration are the ATR spectra defined at different concentration of organic substances and virions.

  12. ATR mediates a checkpoint at the nuclear envelope in response to mechanical stress.

    PubMed

    Kumar, Amit; Mazzanti, Michele; Mistrik, Martin; Kosar, Martin; Beznoussenko, Galina V; Mironov, Alexandre A; Garrè, Massimiliano; Parazzoli, Dario; Shivashankar, G V; Scita, Giorgio; Bartek, Jiri; Foiani, Marco

    2014-07-31

    ATR controls chromosome integrity and chromatin dynamics. We have previously shown that yeast Mec1/ATR promotes chromatin detachment from the nuclear envelope to counteract aberrant topological transitions during DNA replication. Here, we provide evidence that ATR activity at the nuclear envelope responds to mechanical stress. Human ATR associates with the nuclear envelope during S phase and prophase, and both osmotic stress and mechanical stretching relocalize ATR to nuclear membranes throughout the cell cycle. The ATR-mediated mechanical response occurs within the range of physiological forces, is reversible, and is independent of DNA damage signaling. ATR-defective cells exhibit aberrant chromatin condensation and nuclear envelope breakdown. We propose that mechanical forces derived from chromosome dynamics and torsional stress on nuclear membranes activate ATR to modulate nuclear envelope plasticity and chromatin association to the nuclear envelope, thus enabling cells to cope with the mechanical strain imposed by these molecular processes. PMID:25083873

  13. Hydraulic Shuttle Irradiation System (HSIS) Recently Installed in the Advanced Test Reactor (ATR)

    SciTech Connect

    A. Joseph Palmer; Gerry L. McCormick; Shannon J. Corrigan

    2010-06-01

    a Readiness Assessment in November 2009. The HSIS is a key component of the ATR National Scientific User Facility (NSUF) operated by Battelle Energy Alliance, LLC and is available to a wide variety of university researchers for nuclear fuels and materials experiments as well as medical isotope research and production.

  14. USE OF SILICON CARBIDE MONITORS IN ATR IRRADIATION TESTING

    SciTech Connect

    K. L. Davis; B. Chase; T. Unruh; D. Knudson; J. L. Rempe

    2012-07-01

    In April 2007, the Department of Energy (DOE) designated the Advanced Test Reactor (ATR) a National Scientific User Facility (NSUF) to advance US leadership in nuclear science and technology. By attracting new users from universities, laboratories, and industry, the ATR will support basic and applied nuclear research and development and help address the nation's energy security needs. In support of this new program, the Idaho National Laboratory (INL) has developed in-house capabilities to fabricate, test, and qualify new and enhanced temperature sensors for irradiation testing. Although most efforts emphasize sensors capable of providing real-time data, selected tasks have been completed to enhance sensors provided in irradiation locations where instrumentation leads cannot be included, such as drop-in capsule and Hydraulic Shuttle Irradiation System (HSIS) or 'rabbit' locations. For example, silicon carbide (SiC) monitors are now available to detect peak irradiation temperatures between 200°C and 800°C. Using a resistance measurement approach, specialized equipment installed at INL's High Temperature Test Laboratory (HTTL) and specialized procedures were developed to ensure that accurate peak irradiation temperature measurements are inferred from SiC monitors irradiated at the ATR. Comparison examinations were completed by INL to demonstrate this capability, and several programs currently rely on SiC monitors for peak temperature detection. This paper discusses the use of SiC monitors at the ATR, the process used to evaluate them at the HTTL, and presents representative measurements taken using SiC monitors.

  15. ATR inhibition preferentially targets homologous recombination-deficient tumor cells.

    PubMed

    Krajewska, M; Fehrmann, R S N; Schoonen, P M; Labib, S; de Vries, E G E; Franke, L; van Vugt, M A T M

    2015-06-01

    Homologous recombination (HR) is required for faithful repair of double-strand DNA breaks. Defects in HR repair cause severe genomic instability and challenge cellular viability. Paradoxically, various cancers are HR defective and have apparently acquired characteristics to survive genomic instability. We aimed to identify these characteristics to uncover therapeutic targets for HR-deficient cancers. Cytogenetic analysis of 1143 ovarian cancers showed that the degree of genomic instability was correlated to amplification of replication checkpoint genes ataxia telangiectasia and Rad3-related kinase (ATR) and CHEK1. To test whether genomic instability leads to increased reliance on replication checkpoint signaling, we inactivated Rad51 to model HR-related genomic instability. Rad51 inactivation caused defective HR repair and induced aberrant replication dynamics. Notably, inhibition of Rad51 led to increased ATR/checkpoint kinase-1 (Chk1)-mediated replication stress signaling. Importantly, inhibition of ATR or Chk1 preferentially killed HR-deficient cancer cells. Combined, our data show that defective HR caused by Rad51 inhibition results in differential sensitivity for ATR and Chk1 inhibitors, implicating replication checkpoint kinases as potential drug targets for HR-defective cancers. PMID:25174396

  16. 30 CFR 75.209 - Automated Temporary Roof Support (ATRS) systems.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Automated Temporary Roof Support (ATRS) systems... Automated Temporary Roof Support (ATRS) systems. (a) Except in anthracite mines and as specified in paragraphs (b) and (c) of this section, an ATRS system shall be used with roof bolting machines...

  17. 30 CFR 75.209 - Automated Temporary Roof Support (ATRS) systems.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Automated Temporary Roof Support (ATRS) systems... Automated Temporary Roof Support (ATRS) systems. (a) Except in anthracite mines and as specified in paragraphs (b) and (c) of this section, an ATRS system shall be used with roof bolting machines...

  18. 30 CFR 75.209 - Automated Temporary Roof Support (ATRS) systems.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Automated Temporary Roof Support (ATRS) systems... Automated Temporary Roof Support (ATRS) systems. (a) Except in anthracite mines and as specified in paragraphs (b) and (c) of this section, an ATRS system shall be used with roof bolting machines...

  19. 30 CFR 75.209 - Automated Temporary Roof Support (ATRS) systems.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Automated Temporary Roof Support (ATRS) systems... Automated Temporary Roof Support (ATRS) systems. (a) Except in anthracite mines and as specified in paragraphs (b) and (c) of this section, an ATRS system shall be used with roof bolting machines...

  20. 30 CFR 75.209 - Automated Temporary Roof Support (ATRS) systems.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Automated Temporary Roof Support (ATRS) systems... Automated Temporary Roof Support (ATRS) systems. (a) Except in anthracite mines and as specified in paragraphs (b) and (c) of this section, an ATRS system shall be used with roof bolting machines...

  1. Integrate knowledge acquisition with target recognition through closed-loop ATR

    NASA Astrophysics Data System (ADS)

    Yu, Ssu-Hsin; McLaughlin, Pat; Zatezalo, Aleksandar; Hsiao, Kai-yuh; Boskovic, Jovan

    2015-05-01

    Automatic Target Recognition (ATR) algorithm performance is highly dependent on the sensing conditions under which the input data is collected. Open-loop fly-bys often produce poor results due to less than ideal measurement conditions. In addition, ATR algorithms must be extremely complicated to handle the diverse range of inputs with a resulting reduction in overall performance and increase in complexity. Our approach, closed-loop ATR (CL-ATR), focuses on improving the quality of information input to the ATR algorithms by optimizing motion, sensor settings and team (vehicle-vehicle-human) collaboration to dramatically improve classification accuracy. By managing the data collection guided by predicted ATR performance gain, we increase the information content of the data and thus dramatically improve ATR performance with existing ATR algorithms. CL-ATR has two major functions; first, an ATR utility function, which represents the performance sensitivity of ATR produced classification labels as a function of parameters that correlate to vehicle/sensor states. This utility function is developed off-line and is often available from the original ATR study as a confusion matrix, or it can be derived through simulation without direct access to the inner working of the ATR algorithm. The utility function is inserted into our CLATR framework to autonomously control the vehicle/sensor. Second, an on-board planner maps the utility function into vehicle position and sensor collection plans. Because we only require the utility function on-board, we can activate any ATR algorithm onto a unmanned aerial vehicle (UAV) platform no matter how complex. This pairing of ATR performance profiles with vehicle/sensor controls creates a unique and powerful active perception behavior.

  2. The SUMO (Small Ubiquitin-like Modifier) Ligase PIAS3 Primes ATR for Checkpoint Activation.

    PubMed

    Wu, Ching-Shyi; Zou, Lee

    2016-01-01

    The maintenance of genomic stability relies on the concerted action of DNA repair and DNA damage signaling pathways. The PIAS (protein inhibitor of activated STAT) family of SUMO (small ubiquitin-like modifier) ligases has been implicated in DNA repair, but whether it plays a role in DNA damage signaling is still unclear. Here, we show that the PIAS3 SUMO ligase is important for activation of the ATR (ataxia telangiectasia and Rad3 related)-regulated DNA damage signaling pathway. PIAS3 is the only member of the PIAS family that is indispensable for ATR activation. In response to different types of DNA damage and replication stress, PIAS3 plays multiple roles in ATR activation. In cells treated with camptothecin (CPT), PIAS3 contributes to formation of DNA double-stranded breaks. In UV (ultraviolet light)- or HU (hydroxyurea)-treated cells, PIAS3 is required for efficient ATR autophosphorylation, one of the earliest events during ATR activation. Although PIAS3 is dispensable for ATRIP (ATR-interacting protein) SUMOylation and the ATR-ATRIP interaction, it is required for maintaining the basal kinase activity of ATR prior to DNA damage. In the absence of PIAS3, ATR fails to display normal kinase activity after DNA damage, which accompanies with reduced phosphorylation of ATR substrates. Together, these results suggest that PIAS3 primes ATR for checkpoint activation by sustaining its basal kinase activity, revealing a new function of the PIAS family in DNA damage signaling. PMID:26565033

  3. Analyzing the ATR-mediated checkpoint using Xenopus egg extracts

    PubMed Central

    Lupardus, Patrick J.; Van, Christopher; Cimprich, Karlene A.

    2009-01-01

    Our knowledge of cell cycle events such as DNA replication and mitosis has been advanced significantly through the use of Xenopus egg extracts as a model system. More recently, Xenopus extracts have been used to investigate the cellular mechanisms that ensure accurate and complete duplication of the genome, processes otherwise known as the DNA damage and replication checkpoints. Here we describe several Xenopus extract methods that have advanced the study of the ATR-mediated checkpoints. These include a protocol for the preparation of nucleoplasmic extract (NPE), which is a soluble extract system useful for studying nuclear events such as DNA replication and checkpoints. In addition, we describe several key assays for studying checkpoint activation as well as methods for using small DNA structures to activate ATR. PMID:17189864

  4. Recent ATR and fusion algorithm improvements for multiband sonar imagery

    NASA Astrophysics Data System (ADS)

    Aridgides, Tom; Fernández, Manuel

    2009-05-01

    An improved automatic target recognition processing string has been developed. The overall processing string consists of pre-processing, subimage adaptive clutter filtering, normalization, detection, data regularization, feature extraction, optimal subset feature selection, feature orthogonalization and classification processing blocks. The objects that are classified by the 3 distinct ATR strings are fused using the classification confidence values and their expansions as features, and using "summing" or log-likelihood-ratio-test (LLRT) based fusion rules. The utility of the overall processing strings and their fusion was demonstrated with new high-resolution three-frequency band sonar imagery. The ATR processing strings were individually tuned to the corresponding three-frequency band data, making use of the new processing improvement, data regularization; this improvement entails computing the input data mean, clipping the data to a multiple of its mean and scaling it, prior to feature extraction and resulted in a 3:1 reduction in false alarms. Two significant fusion algorithm improvements were made. First, a nonlinear exponential Box-Cox expansion (consisting of raising data to a to-be-determined power) feature LLRT fusion algorithm was developed. Second, a repeated application of a subset Box-Cox feature selection / feature orthogonalization / LLRT fusion block was utilized. It was shown that cascaded Box-Cox feature LLRT fusion of the ATR processing strings outperforms baseline "summing" and single-stage Box-Cox feature LLRT algorithms, yielding significant improvements over the best single ATR processing string results, and providing the capability to correctly call the majority of targets while maintaining a very low false alarm rate.

  5. Neutronics analysis of the DHCE experiment in ATR-ITV

    SciTech Connect

    Gomes, I.C.; Smith, D.L.; Tsai, H.

    1997-08-01

    The preliminary analysis of the DHCE experiments in the ITV and ATR was performed and its was concluded that such a vehicle is suitable for this kind of experiment. It is recommended to place an extra filter material in the thermocouple sleeve (such as B-10), to improve the helium to dpa ratio profile during irradiation. Also, it was concluded that a preliminary estimation of period of time for replacement of the external filter would be around 5 dps`s.

  6. A SAR ATR algorithm based on coherent change detection

    SciTech Connect

    Harmony, D.W.

    2000-12-01

    This report discusses an automatic target recognition (ATR) algorithm for synthetic aperture radar (SAR) imagery that is based on coherent change detection techniques. The algorithm relies on templates created from training data to identify targets. Objects are identified or rejected as targets by comparing their SAR signatures with templates using the same complex correlation scheme developed for coherent change detection. Preliminary results are presented in addition to future recommendations.

  7. Clipping service: ATR-based SAR image compression

    NASA Astrophysics Data System (ADS)

    Rodkey, David L.; Welby, Stephen P.; Hostetler, Larry D.

    1996-06-01

    Future wide area surveillance systems such as the Tier II+ and Tier III- unmanned aerial vehicles (UAVs) will be gathering cast amounts of high resolution SAR data for transmission to ground stations and subsequent analysis by image interpreters to provide critical and timely information to field commanders. This extremely high data rate presents two problems. First, wide bandwidth data link channels which would be needed to transmit this high data rate presents two problems. First, wide bandwidth data link channels which would be needed to transmit this imagery to a ground station are both expensive and difficult to obtain. Second, the volume of data which is generated by the system will quickly saturate any human-based analysis system without some degree of computer assistance. The ARPA sponsored clipping service program seeks to apply automatic target recognition (ATR) technology to perform 'intelligent' data compression on this imagery in a way which will provide a product on the ground that preserves essential information for further processing either by the military analyst or by a ground-based ATR system. An ATR system on board the UAV would examine the imagery data stream in real time determining regions of interest. Imagery from those regions would be transmitted to the ground in a manner which preserved most or all of the information contained in the original image. The remainder of the imagery would be transmitted to the ground with lesser fidelity. This paper presents system analysis deriving the operational requirements for the clipping service system and examines candidate architectures.

  8. Simulator of IRST system with ATR embedded functions

    NASA Astrophysics Data System (ADS)

    Sozzi, B.; Fossati, E.; Barani, G.; Santini, N.; Ondini, A.; Colombi, G.; Quaranta, C.

    2010-04-01

    This paper presents a soft-real time simulator for IRST (InfraRed Search and Track) systems with ATR (Automatic Target Recognition) embedded functions to test airborne applications performance. The IR camera model includes detector, optics, available Field-of-Regard, etc., and it is integrated with the motion platform local stabilization system to consider all factors impacting IR images. The atmosphere contributions are taken into account by means of a link to ModTran computer program. Sensor simulation allows derivation and assessment of IR Figures of Merit (NEI, NETD, SNR...). IR signatures of targets derive both from data collected in specific trial campaigns and from laboratory built models. The simulation of the scan procedure takes into account different policies (ground points paths or defined angular volume) and different platform motion strategies (continuous or step steering scan). The scan process includes Kalman technique to face unexpected variations of aircraft motion. Track and ATR processors are simulated and run consistently on the output of the sensor model. The simulator functions are developed in MatLab and SIMULINK and then exported in C code to be integrated in soft real-time environment. The use of this simulator supports the definition and design of the IRST systems especially for the evaluation of the most demanding operative requirements. An application of this simulator is for the NEURON UCAV (Unmanned Combat Air Vehicle) technological demonstrator, which accommodates on board both IRST and ATR tasks.

  9. Clamping the Mec1/ATR checkpoint kinase into action.

    PubMed

    Majka, Jerzy; Burgers, Peter M J

    2007-05-15

    The yeast checkpoint protein kinase Mec1, the ortholog of human ATR, is the essential upstream regulator of the cell cycle checkpoint in response to DNA damage and to stalling of DNA replication forks. The activity of Mec1/ATR is not directly regulated by the DNA substrates that signal checkpoint activation. Rather the signal appears to be transduced to Mec1 by factors that interact with the signaling DNA substrates. One of these factors, the DNA damage checkpoint clamp Rad17-Mec3-Ddc1 (human 9-1-1) is loaded onto gapped DNA resulting from the partial repair of DNA damage, and the Ddc1 subunit of this complex activates Mec1. In vertebrate cells, the TopBP1 protein (Cut5 in S. pombe and Dpb11 in S. cervisiae) that is also required for establishment of the replication fork, functions during replication fork dysfunction to activate ATR. Both mechanisms of activation generally upregulate the kinase activity towards all downstream targets. PMID:17495536

  10. ATR pathway inhibition is synthetically lethal in cancer cells with ERCC1 deficiency

    PubMed Central

    Mohni, Kareem N.; Kavanaugh, Gina M.; Cortez, David

    2014-01-01

    The DNA damage response kinase ATR and its effector kinase CHEK1 are required for cancer cells to survive oncogene-induced replication stress. ATR inhibitors exhibit synthetic lethal interactions with deficiencies in the DNA damage response enzymes ATM and XRCC1 and with overexpression of the cell cycle kinase Cyclin E. Here we report a systematic screen to identify synthetic lethal interactions with ATR-pathway targeted drugs, rationalized by their predicted therapeutic utility in the oncology clinic. We found that reduced function in the ATR pathway itself provided the strongest synthetic lethal interaction. In addition, we found that loss of the structure specific-endonuclease ERCC1-XPF (ERCC4) is synthetic lethal with ATR pathway inhibitors. ERCC1-deficient cells exhibited elevated levels of DNA damage, which was increased further by ATR inhibition. When treated with ATR or CHEK1 inhibitors, ERCC1-deficient cells arrested in S phase and failed to complete cell cycle transit even after drug removal. Notably, triple-negative breast cancer cells and non-small cell lung cancer cells depleted of ERCC1 exhibited increased sensitivity to ATR-pathway targeted drugs. Overall, we concluded that ATR pathway-targeted drugs may offer particular utility in cancers with reduced ATR pathway function or reduced levels of ERCC4 activity. PMID:24662920

  11. ATR-101 disrupts mitochondrial functions in adrenocortical carcinoma cells and in vivo.

    PubMed

    Cheng, Yunhui; Kerppola, Raili Emilia; Kerppola, Tom Klaus

    2016-04-01

    Adrenocortical carcinoma (ACC) generally has poor prognosis. Existing treatments provide limited benefit for most patients with locally advanced or metastatic tumors. We investigated the mechanisms for the cytotoxicity, xenograft suppression, and adrenalytic activity of ATR-101 (PD132301-02), a prospective agent for ACC treatment. Oral administration of ATR-101 inhibited the establishment and impeded the growth of ACC-derived H295R cell xenografts in mice. ATR-101 induced H295R cell apoptosis in culture and in xenografts. ATR-101 caused mitochondrial hyperpolarization, reactive oxygen release, and ATP depletion within hours after exposure, followed by cytochrome c release, caspase-3/7 activation, and membrane permeabilization. The increase in mitochondrial membrane potential occurred concurrently with the decrease in cellular ATP levels. When combined with ATR-101, lipophilic free radical scavengers suppressed the reactive oxygen release, and glycolytic precursors prevented the ATP depletion, abrogating ATR-101 cytotoxicity. ATR-101 directly inhibited F1F0-ATPase activity and suppressed ATP synthesis in mitochondrial fractions. ATR-101 administration to guinea pigs caused oxidized lipofuscin accumulation in thezona fasciculatalayer of the adrenal cortex, implicating reactive oxygen release in the adrenalytic effect of ATR-101. These results support the development of ATR-101 and other adrenalytic compounds for the treatment of ACC. PMID:26843528

  12. ATR pathway inhibition is synthetically lethal in cancer cells with ERCC1 deficiency.

    PubMed

    Mohni, Kareem N; Kavanaugh, Gina M; Cortez, David

    2014-05-15

    The DNA damage response kinase ATR and its effector kinase CHEK1 are required for cancer cells to survive oncogene-induced replication stress. ATR inhibitors exhibit synthetic lethal interactions, with deficiencies in the DNA damage response enzymes ATM and XRCC1 and with overexpression of the cell cycle kinase cyclin E. Here, we report a systematic screen to identify synthetic lethal interactions with ATR pathway-targeted drugs, rationalized by their predicted therapeutic utility in the oncology clinic. We found that reduced function in the ATR pathway itself provided the strongest synthetic lethal interaction. In addition, we found that loss of the structure-specific endonuclease ERCC1-XPF (ERCC4) is synthetic lethal with ATR pathway inhibitors. ERCC1-deficient cells exhibited elevated levels of DNA damage, which was increased further by ATR inhibition. When treated with ATR or CHEK1 inhibitors, ERCC1-deficient cells were arrested in S-phase and failed to complete cell-cycle transit even after drug removal. Notably, triple-negative breast cancer cells and non-small cell lung cancer cells depleted of ERCC1 exhibited increased sensitivity to ATR pathway-targeted drugs. Overall, we concluded that ATR pathway-targeted drugs may offer particular utility in cancers with reduced ATR pathway function or reduced levels of ERCC4 activity. PMID:24662920

  13. Problem set guidelines to facilitate ATR research, development, and performance assessments

    NASA Astrophysics Data System (ADS)

    Westerkamp, Lori A.; Wild, Thomas J.; Meredith, Donna; Morrison, S. A.; Mossing, John C.; Avent, Randy K.; Bergman, Annette; Bruckheim, Arthur; Castanon, David A.; Corbett, Francis J.; Hugo, Douglas; Hummel, Robert A.; Irvine, John M.; Merle, Bruce; Otto, Louis; Reynolds, Robert; Sadowski, Charles; Schachter, Bruce J.; Simonson, Katherine M.; Smit, Gene; Walters, Clarence P.

    2002-07-01

    In November of 2000, the Deputy Under Secretary of Defense for Science and Technology Sensor Systems (DUSD (S&T/SS)) chartered the ATR Working Group (ATRWG) to develop guidelines for sanctioned Problem Sets. Such Problem Sets are intended for development and test of ATR algorithms and contain comprehensive documentation of the data in them. A problem set provides a consistent basis to examine ATR performance and growth. Problem Sets will, in general, serve multiple purposes. First, they will enable informed decisions by government agencies sponsoring ATR development and transition. Problem Sets standardize the testing and evaluation process, resulting in consistent assessment of ATR performance. Second, they will measure and guide ATR development progress within this standardized framework. Finally, they quantify the state of the art for the community. Problem Sets provide clearly defined operating condition coverage. This encourages ATR developers to consider these critical challenges and allows evaluators to assess over them. Thus the widely distributed development and self-test portions, along with a disciplined methodology documented within the Problem Set, permit ATR developers to address critical issues and describe their accomplishments, while the sequestered portion permits government assessment of state-of-the-art and of transition readiness. This paper discusses the elements of an ATR problem set as a package of data and information that presents a standardized ATR challenge relevant to one or more scenarios. The package includes training and test data containing targets and clutter, truth information, required experiments, and a standardized analytical methodology to assess performance.

  14. Drugging ATR: progress in the development of specific inhibitors for the treatment of cancer.

    PubMed

    Foote, Kevin M; Lau, Alan; Nissink, J Willem M

    2015-01-01

    In this article, we review the ATR inhibitor field from initial pharmacological tools to first-generation clinical candidates with the potential to bring benefit to cancer patients. ATR is a critical part of the cell DNA-damage response. Over the past decade or more, compounds with weak ATR potency and low specificity have been used as tools in early studies to elucidate ATR pharmacology. More recently highly potent, selective and in vivo active ATR inhibitors have been developed enabling detailed preclinical in vitro and in vivo target assessment to be made. The published studies reveal the potential of ATR inhibitors for use as monotherapy or in combination with DNA-damaging agents. To date, VX-970 and AZD6738, have entered clinical assessment. PMID:26061106

  15. Requirement of ATR for maintenance of intestinal stem cells in aging Drosophila

    PubMed Central

    Pyo, Jung-Hoon; Jeon, Ho-Jun; Kim, Young-Shin; Yoo, Mi-Ae

    2015-01-01

    The stem cell genomic stability forms the basis for robust tissue homeostasis, particularly in high-turnover tissues. For the genomic stability, DNA damage response (DDR) is essential. This study was focused on the role of two major DDR-related factors, ataxia telangiectasia-mutated (ATM) and ATM- and RAD3-related (ATR) kinases, in the maintenance of intestinal stem cells (ISCs) in the adult Drosophila midgut. We explored the role of ATM and ATR, utilizing immunostaining with an anti-pS/TQ antibody as an indicator of ATM/ATR activation, γ-irradiation as a DNA damage inducer, and the UAS/GAL4 system for cell type-specific knockdown of ATM, ATR, or both during adulthood. The results showed that the pS/TQ signals got stronger with age and after oxidative stress. The pS/TQ signals were found to be more dependent on ATR rather than on ATM in ISCs/enteroblasts (EBs). Furthermore, an ISC/EB-specific knockdown of ATR, ATM, or both decreased the number of ISCs and oxidative stress-induced ISC proliferation. The phenotypic changes that were caused by the ATR knockdown were more pronounced than those caused by the ATM knockdown; however, our data indicate that ATR and ATM are both needed for ISC maintenance and proliferation; ATR seems to play a bigger role than does ATM. PMID:26000719

  16. Advanced Test Reactor National Scientific User Facility (ATR NSUF) Monthly Report October 2014

    SciTech Connect

    Dan Ogden

    2014-10-01

    Advanced Test Reactor National Scientific User Facility (ATR NSUF) Monthly Report October 2014 Highlights • Rory Kennedy, Dan Ogden and Brenden Heidrich traveled to Germantown October 6-7, for a review of the Infrastructure Management mission with Shane Johnson, Mike Worley, Bradley Williams and Alison Hahn from NE-4 and Mary McCune from NE-3. Heidrich briefed the group on the project progress from July to October 2014 as well as the planned path forward for FY15. • Jim Cole gave two invited university seminars at Ohio State University and University of Florida, providing an overview of NSUF including available capabilities and the process for accessing facilities through the peer reviewed proposal process. • Jim Cole and Rory Kennedy co-chaired the NuMat meeting with Todd Allen. The meeting, sponsored by Elsevier publishing, was held in Clearwater, Florida, and is considered one of the premier nuclear fuels and materials conferences. Over 340 delegates attended with 160 oral and over 200 posters presented over 4 days. • Thirty-one pre-applications were submitted for NSUF access through the NE-4 Combined Innovative Nuclear Research Funding Opportunity Announcement. • Fourteen proposals were received for the NSUF Rapid Turnaround Experiment Summer 2014 call. Proposal evaluations are underway. • John Jackson and Rory Kennedy attended the Nuclear Fuels Industry Research meeting. Jackson presented an overview of ongoing NSUF industry research.

  17. Open source tools for ATR development and performance evaluation

    NASA Astrophysics Data System (ADS)

    Baumann, James M.; Dilsavor, Ronald L.; Stubbles, James; Mossing, John C.

    2002-07-01

    Early in almost every engineering project, a decision must be made about tools; should I buy off-the-shelf tools or should I develop my own. Either choice can involve significant cost and risk. Off-the-shelf tools may be readily available, but they can be expensive to purchase and to maintain licenses, and may not be flexible enough to satisfy all project requirements. On the other hand, developing new tools permits great flexibility, but it can be time- (and budget-) consuming, and the end product still may not work as intended. Open source software has the advantages of both approaches without many of the pitfalls. This paper examines the concept of open source software, including its history, unique culture, and informal yet closely followed conventions. These characteristics influence the quality and quantity of software available, and ultimately its suitability for serious ATR development work. We give an example where Python, an open source scripting language, and OpenEV, a viewing and analysis tool for geospatial data, have been incorporated into ATR performance evaluation projects. While this case highlights the successful use of open source tools, we also offer important insight into risks associated with this approach.

  18. Fuel cell technology for prototype logistic fuel cell mobile systems

    SciTech Connect

    Sederquist, R.A.; Garow, J.

    1995-08-01

    Under the aegis of the Advanced Research Project Agency`s family of programs to develop advanced technology for dual use applications, International Fuel Cells Corporation (IFC) is conducting a 39 month program to develop an innovative system concept for DoD Mobile Electric Power (MEP) applications. The concept is to integrate two technologies, the phosphoric acid fuel cell (PAFC) with an auto-thermal reformer (ATR), into an efficient fuel cell power plant of nominally 100-kilowatt rating which operates on logistic fuels (JP-8). The ATR fuel processor is the key to meeting requirements for MEP (including weight, volume, reliability, maintainability, efficiency, and especially operation on logistic fuels); most of the effort is devoted to ATR development. An integrated demonstration test unit culminates the program and displays the benefits of the fuel cell system, relative to the standard 100-kilowatt MEP diesel engine generator set. A successful test provides the basis for proceeding toward deployment. This paper describes the results of the first twelve months of activity during which specific program aims have remained firm.

  19. Corrosion of spent Advanced Test Reactor fuel

    SciTech Connect

    Lundberg, L.B.; Croson, M.L.

    1994-11-01

    The results of a study of the condition of spent nuclear fuel elements from the Advanced Test Reactor (ATR) currently being stored underwater at the Idaho National Engineering Laboratory (INEL) are presented. This study was motivated by a need to estimate the corrosion behavior of dried, spent ATR fuel elements during dry storage for periods up to 50 years. The study indicated that the condition of spent ATR fuel elements currently stored underwater at the INEL is not very well known. Based on the limited data and observed corrosion behavior in the reactor and in underwater storage, it was concluded that many of the fuel elements currently stored under water in the facility called ICPP-603 FSF are in a degraded condition, and it is probable that many have breached cladding. The anticipated dehydration behavior of corroded spent ATR fuel elements was also studied, and a list of issues to be addressed by fuel element characterization before and after forced drying of the fuel elements and during dry storage is presented.

  20. ATR CONTRIBUTES TO CELL CYCLE ARREST AND SURVIVAL AFTER CISPLATIN BUT NOT OXALIPLATIN1

    PubMed Central

    Lewis, Kriste A.; Lilly, Kia K.; Reynolds, Evelyn A.; Sullivan, William P.; Kaufmann, Scott H.; Cliby, William A.

    2009-01-01

    The DNA cross-linking agents cisplatin and oxaliplatin are widely used in the treatment of human cancer. Lesions produced by these agents are widely known to activate the G1 and G2 cell cycle checkpoints. Less is known about the role of the intra-S phase checkpoint in the response to these agents. In the present study, two different cell lines expressing a dominant negative kinase-dead (kd) version of the ATR (ataxia telangiectasia and rad3-related) kinase in an inducible fashion were examined for their responses to these two platinating agents and a variety of other DNA cross-linking drugs. Expression of the kdATR allele markedly sensitized the cells to cisplatin, but not oxaliplatin, as assessed by inhibition of colony formation, induction of apoptosis, and cell cycle analysis. Similar differences in survival were noted for melphalan (ATR-dependent) and 4-hydroperoxycyclophosphamide (4HC) (ATR-independent). Further experiments demonstrated that ATR function is not necessary for removal of Pt-DNA adducts. The predominant difference between the responses to the two platinum drugs was presence of a drug-specific ATR-dependent S phase arrest after cisplatin but not oxaliplatin. These results indicate that involvement of ATR in the response to DNA cross-linking agents is lesion specific. This observation might need to be taken into account in the development and use of ATR or Chk1 inhibitors. PMID:19372558

  1. 78 FR 58967 - Airworthiness Directives; ATR-GIE Avions de Transport Régional Airplanes

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-25

    ... 21 62 21; fax +33 (0) 5 62 21 67 18; email continued.airworthiness@atr.fr ; Internet http://www... Procedures (44 FR 11034, February 26, 1979); 3. Will not affect intrastate aviation in Alaska; and 4. Will...)5 62 21 69 41; email: techdesk@atr.fr . ] (1) If the inspection was done on or after the...

  2. ATR-FTIR Spectroscopy in the Undergraduate Chemistry Laboratory: Part I--Fundamentals and Examples

    ERIC Educational Resources Information Center

    Schuttlefield, Jennifer D.; Grassian, Vicki H.

    2008-01-01

    Attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy is a useful technique for measuring the infrared spectra of solids and liquids as well as probing adsorption on particle surfaces. Several examples of the use of FTIR-ATR spectroscopy in different undergraduate chemistry laboratory courses are presented here. These…

  3. Drosophila ATM and ATR checkpoint kinases control partially redundant pathways for telomere maintenance

    PubMed Central

    Bi, Xiaolin; Srikanta, Deepa; Fanti, Laura; Pimpinelli, Sergio; Badugu, RamaKrishna; Kellum, Rebecca; Rong, Yikang S.

    2005-01-01

    In higher eukaryotes, the ataxia telangiectasia mutated (ATM) and ATM and Rad3-related (ATR) checkpoint kinases play distinct, but partially overlapping, roles in DNA damage response. Yet their interrelated function has not been defined for telomere maintenance. We discover in Drosophila that the two proteins control partially redundant pathways for telomere protection: the loss of ATM leads to the fusion of some telomeres, whereas the loss of both ATM and ATR renders all telomeres susceptible to fusion. The ATM-controlled pathway includes the Mre11 and Nijmegen breakage syndrome complex but not the Chk2 kinase, whereas the ATR-regulated pathway includes its partner ATR-interacting protein but not the Chk1 kinase. This finding suggests that ATM and ATR regulate different molecular events at the telomeres compared with the sites of DNA damage. This compensatory relationship between ATM and ATR is remarkably similar to that observed in yeast despite the fact that the biochemistry of telomere elongation is completely different in the two model systems. We provide evidence suggesting that both the loading of telomere capping proteins and normal telomeric silencing requires ATM and ATR in Drosophila and propose that ATM and ATR protect telomere integrity by safeguarding chromatin architecture that favors the loading of telomere-elongating, capping, and silencing proteins. PMID:16203987

  4. Primary microcephaly, impaired DNA replication, and genomic instability caused by compound heterozygous ATR mutations.

    PubMed

    Mokrani-Benhelli, Houda; Gaillard, Laetitia; Biasutto, Patricia; Le Guen, Tangui; Touzot, Fabien; Vasquez, Nadia; Komatsu, Jun; Conseiller, Emmanuel; Pïcard, Capucine; Gluckman, Eliane; Francannet, Christine; Fischer, Alain; Durandy, Anne; Soulier, Jean; de Villartay, Jean-Pierre; Cavazzana-Calvo, Marina; Revy, Patrick

    2013-02-01

    Ataxia telangiectasia-mutated (ATM) and ataxia telangiectasia and Rad3-related (ATR) kinases are two key regulators of DNA-damage responses (DDR) that are mainly activated in response to DNA double-strand breaks and single-stranded DNA damages, respectively. Seckel syndrome, a rare genetic disorder characterized by a microcephaly and a markedly reduced body size, has been associated with defective ATR-dependent DNA damage signaling. However, the only human genetic ATR defect reported so far is a hypomorphic splicing mutation identified in five related individuals with Seckel syndrome. Here, we report the first case of primary microcephaly with compound heterozygous mutations in ATR: a 540 kb genomic deletion on one allele and a missense mutation leading to splice dysregulation on the other, which ultimately lead to a sharp decrease in ATR expression. DNA combing technology revealed a profound spontaneous alteration of several DNA replication parameters in patient's cells and FISH analyses highlighted the genomic instability caused by ATR deficiency. Collectively, our results emphasize the crucial role for ATR in the control of DNA replication, and reinforce the complementary and nonredundant contributions of ATM and ATR in human cells to face DNA damages and warrant genome integrity. PMID:23111928

  5. Method for fast start of a fuel processor

    DOEpatents

    Ahluwalia, Rajesh K.; Ahmed, Shabbir; Lee, Sheldon H. D.

    2008-01-29

    An improved fuel processor for fuel cells is provided whereby the startup time of the processor is less than sixty seconds and can be as low as 30 seconds, if not less. A rapid startup time is achieved by either igniting or allowing a small mixture of air and fuel to react over and warm up the catalyst of an autothermal reformer (ATR). The ATR then produces combustible gases to be subsequently oxidized on and simultaneously warm up water-gas shift zone catalysts. After normal operating temperature has been achieved, the proportion of air included with the fuel is greatly diminished.

  6. ARF and ATM/ATR cooperate in p53-mediated apoptosis upon oncogenic stress

    SciTech Connect

    Pauklin, Siim . E-mail: spauklin@ut.ee; Kristjuhan, Arnold; Maimets, Toivo; Jaks, Viljar

    2005-08-26

    Induction of apoptosis is pivotal for eliminating cells with damaged DNA or deregulated proliferation. We show that tumor suppressor ARF and ATM/ATR kinase pathways cooperate in the induction of apoptosis in response to elevated expression of c-myc, {beta}-catenin or human papilloma virus E7 oncogenes. Overexpression of oncogenes leads to the formation of phosphorylated H2AX foci, induction of Rad51 protein levels and ATM/ATR-dependent phosphorylation of p53. Inhibition of ATM/ATR kinases abolishes both induction of Rad51 and phosphorylation of p53, and remarkably reduces the level of apoptosis induced by co-expression of oncogenes and ARF. However, the induction of apoptosis is downregulated in p53-/- cells and does not depend on activities of ATM/ATR kinases, indicating that efficient induction of apoptosis by oncogene activation depends on coordinated action of ARF and ATM/ATR pathways in the regulation of p53.

  7. Thermal Analysis of Irradiation Experiments in the ATR

    SciTech Connect

    Paul Murray

    2012-09-01

    Reactor material testing in the INL's Advanced Test Reactor (ATR) involves modeling and simulation of each experiment to accurately determine the irradiation temperature. This paper describes thermal analysis of capsule experiments using gas gap temperature control and provides data on recent material tests that validate the modeling results. Static capsule experiments and lead-out capsule experiments are discussed. The source of temperature variation in capsule experiments and ways to mitigate these variations are also explained. Two examples of instrumented lead-out capsule experiments, TMIST-1 and UCSB-2, are presented. A comparison of measured and calculated temperatures is used to validate the thermal models and to ascertain the accuracy of the calculated temperature.

  8. Corrosion inhibitor film formation studied by ATR-FTIR

    SciTech Connect

    Campbell, S.; Jovancicevic, V.

    1999-11-01

    The development of an inhibitor film is essential for the effective performance of a corrosion inhibitor. The use of attenuated total reflection fourier transform infrared spectroscopy (ATR-FTIR) allows the development of inhibitor films on iron oxides to be monitored. For two distinct corrosion inhibitor chemistries, oleic imidazoline and phosphate ester, the film formation and corrosion processes are monitored on Fe{sub 3}O{sub 4} in a powdered form (a model surface). Additional data following on the physical and chemical properties are obtained using XPS and SEM techniques, which allows for a more complete characterization of the model inhibitor/oxide system. By the proper choice of system and measurement techniques, the complex phenomenon of corrosion inhibition may be analyzed directly.

  9. Deep convolutional neural networks for ATR from SAR imagery

    NASA Astrophysics Data System (ADS)

    Morgan, David A. E.

    2015-05-01

    Deep architectures for classification and representation learning have recently attracted significant attention within academia and industry, with many impressive results across a diverse collection of problem sets. In this work we consider the specific application of Automatic Target Recognition (ATR) using Synthetic Aperture Radar (SAR) data from the MSTAR public release data set. The classification performance achieved using a Deep Convolutional Neural Network (CNN) on this data set was found to be competitive with existing methods considered to be state-of-the-art. Unlike most existing algorithms, this approach can learn discriminative feature sets directly from training data instead of requiring pre-specification or pre-selection by a human designer. We show how this property can be exploited to efficiently adapt an existing classifier to recognise a previously unseen target and discuss potential practical applications.

  10. Wurfelspiel-based training data methods for ATR

    NASA Astrophysics Data System (ADS)

    Peterson, James K.

    2004-09-01

    A data object is constructed from a P by M Wurfelspiel matrix W by choosing an entry from each column to construct a sequence A0A1"AM-1. Each of the PM possibilities are designed to correspond to the same category according to some chosen measure. This matrix could encode many types of data. (1) Musical fragments, all of which evoke sadness; each column entry is a 4 beat sequence with a chosen A0A1A2 thus 16 beats long (W is P by 3). (2) Paintings, all of which evoke happiness; each column entry is a layer and a given A0A1A2 is a painting constructed using these layers (W is P by 3). (3) abstract feature vectors corresponding to action potentials evoked from a biological cell's exposure to a toxin. The action potential is divided into four relevant regions and each column entry represents the feature vector of a region. A given A0A1A2 is then an abstraction of the excitable cell's output (W is P by 4). (4) abstract feature vectors corresponding to an object such as a face or vehicle. The object is divided into four categories each assigned an abstract feature vector with the resulting concatenation an abstract representation of the object (W is P by 4). All of the examples above correspond to one particular measure (sad music, happy paintings, an introduced toxin, an object to recognize)and hence, when a Wurfelspiel matrix is constructed, relevant training information for recognition is encoded that can be used in many algorithms. The focus of this paper is on the application of these ideas to automatic target recognition (ATR). In addition, we discuss a larger biologically based model of temporal cortex polymodal sensor fusion which can use the feature vectors extracted from the ATR Wurfelspiel data.

  11. Project Description Advanced Fuel Cycle Initiative AFC-2A and AFC-2B Experiments

    SciTech Connect

    AFCI AFC-2A and AFC-2B Experiments Project Executi

    2007-03-01

    The proposed AFC-2A and AFC-2B irradiation experiments are a continuation of the AFC-1 fuel test series currently in progress in the ATR. This document discusses the experiments and the planned activities that will take place.

  12. AGR-3/4 Data Qualification Report for ATR Cycles 151A, 151B, 152A, 152B, 154A, and 154B

    SciTech Connect

    Binh T. Pham

    2014-02-01

    This data report provides the qualification status of Advanced Gas Reactor-3/4 (AGR-3/4) fuel irradiation experimental data from Advanced Test Reactor (ATR) Cycles 151A, 151B, 152A, 152B, 154A, and 154B, as recorded in the Nuclear Data Management and Analysis System (NDMAS). Of these cycles, ATR Cycle 152A is a low power cycle that occurred when the ATR core was briefly at low power. The irradiation data are not used for physics and thermal calculation, but the qualification status of these cycle data is still covered in this report. On the other hand, during ATR Cycles 153A (unplanned Outage cycle) and 153B (Power Axial Locator Mechanism [PALM] cycle), the AGR-3/4 was pulled out from the ATR core and stored in the canal to avoid being overheated. Therefore, qualification of the AGR-3/4 irradiation data from these 2 cycles was excluded in this report. By the end of ATR Cycle 154B, AGR-3/4 was irradiated for a total of 264.1 effective full power days. The AGR-3/4 data streams addressed in this report include thermocouple (TC) temperatures, sweep gas data (flow rates, pressure, and moisture content), and Fission Product Monitoring System (FPMS) data (release rates and release-to-birth rate ratios [R/Bs]) for each of the twelve capsules in the AGR-3/4 experiment. The final data qualification status for these data streams is determined by a Data Review Committee (DRC) composed of AGR technical leads, Sitewide Quality Assurance (QA), and NDMAS analysts. The DRC convened on February 12, 2014, reviewed the data acquisition process, and considered whether the data met the requirements for data collection as specified in QA-approved Very High Temperature Reactor (VHTR) Technology Development Office (TDO) data collection plans. The DRC also examined the results of NDMAS data testing and statistical analyses, and confirmed the qualification status of the data as given in this report.

  13. Quantitative monitoring of membrane permeation via in-situ ATR FT-IR spectroscopy

    NASA Astrophysics Data System (ADS)

    Beckingham, Bryan; Miller, Daniel

    Ion conducting membranes are of interest for various energy applications including fuel cells and artificial photosynthesis systems. Within the context of artificial photosynthesis, membranes are desired that facilitate the ion transport necessary to feed the electrochemical reactions while meeting various additional selectivity and permeability demands depending on the CO2 reduction products. Herein, we demonstrate the use of in-situ ATR FT-IR spectroscopy to quantitatively resolve the concentration of single and multicomponent mixtures of various CO2 reduction products including methanol, formate and acetate. We then apply this methodology to the in-situ monitoring of the permeation of single and multicomponent mixtures across commercially available membranes. Membrane permeabilities and selectivities calculated from the single component time-resolved concentration curves are compared to the multicomponent permeation experiments. This material is based upon work performed at the Joint Center for Artificial Photosynthesis, a DOE Energy Innovation Hub, supported through the Office of Science of the U.S. Department of Energy under Award Number DE-SC000493.

  14. Cancer-Specific Synthetic Lethality between ATR and CHK1 Kinase Activities.

    PubMed

    Sanjiv, Kumar; Hagenkort, Anna; Calderón-Montaño, José Manuel; Koolmeister, Tobias; Reaper, Philip M; Mortusewicz, Oliver; Jacques, Sylvain A; Kuiper, Raoul V; Schultz, Niklas; Scobie, Martin; Charlton, Peter A; Pollard, John R; Berglund, Ulrika Warpman; Altun, Mikael; Helleday, Thomas

    2016-01-12

    ATR and CHK1 maintain cancer cell survival under replication stress and inhibitors of both kinases are currently undergoing clinical trials. As ATR activity is increased after CHK1 inhibition, we hypothesized that this may indicate an increased reliance on ATR for survival. Indeed, we observe that replication stress induced by the CHK1 inhibitor AZD7762 results in replication catastrophe and apoptosis, when combined with the ATR inhibitor VE-821 specifically in cancer cells. Combined treatment with ATR and CHK1 inhibitors leads to replication fork arrest, ssDNA accumulation, replication collapse, and synergistic cell death in cancer cells in vitro and in vivo. Inhibition of CDK reversed replication stress and synthetic lethality, demonstrating that regulation of origin firing by ATR and CHK1 explains the synthetic lethality. In conclusion, this study exemplifies cancer-specific synthetic lethality between two proteins in the same pathway and raises the prospect of combining ATR and CHK1 inhibitors as promising cancer therapy. PMID:26748709

  15. RNF4 and PLK1 are required for replication fork collapse in ATR-deficient cells.

    PubMed

    Ragland, Ryan L; Patel, Sima; Rivard, Rebecca S; Smith, Kevin; Peters, Ashley A; Bielinsky, Anja-Katrin; Brown, Eric J

    2013-10-15

    The ATR-CHK1 axis stabilizes stalled replication forks and prevents their collapse into DNA double-strand breaks (DSBs). Here, we show that fork collapse in Atr-deleted cells is mediated through the combined effects the sumo targeted E3-ubiquitin ligase RNF4 and activation of the AURKA-PLK1 pathway. As indicated previously, Atr-deleted cells exhibited a decreased ability to restart DNA replication following fork stalling in comparison with control cells. However, suppression of RNF4, AURKA, or PLK1 returned the reinitiation of replication in Atr-deleted cells to near wild-type levels. In RNF4-depleted cells, this rescue directly correlated with the persistence of sumoylation of chromatin-bound factors. Notably, RNF4 repression substantially suppressed the accumulation of DSBs in ATR-deficient cells, and this decrease in breaks was enhanced by concomitant inhibition of PLK1. DSBs resulting from ATR inhibition were also observed to be dependent on the endonuclease scaffold protein SLX4, suggesting that RNF4 and PLK1 either help activate the SLX4 complex or make DNA replication fork structures accessible for subsequent SLX4-dependent cleavage. Thus, replication fork collapse following ATR inhibition is a multistep process that disrupts replisome function and permits cleavage of the replication fork. PMID:24142876

  16. Status of ATR-A1 irradiation experiment on vanadium alloys and low-activation steels

    SciTech Connect

    Tsai, H.; Strain, R.V.; Gomes, I.; Chung, H.; Smith, D.L.

    1997-04-01

    The ATR-A1 irradiation experiment in the Advanced Test Reactor (ATR) was a collaborative U.S./Japan effort to study at low temperatures the effects of neutron damage on vanadium alloys. The experiment also contained a limited quantity of low-activation ferritic steel specimens from Japan as part of the collaboration agreement. The irradiation was completed on May 5, 1996, as planned, after achieving an estimated neutron damage of 4.7 dpa in vanadium. The capsule has since been kept in the ATR water canal for the required radioactivity cool-down. Planning is underway for disassembly of the capsule and test specimen retrieval.

  17. Fabrication Control Plan for ORNL RH-LOCA ATF Test Specimens to be Irradiated in the ATR

    SciTech Connect

    Kevin G. Field; Richard Howard; Michael Teague

    2014-06-01

    The purpose of this fabrication plan is (1) to summarize the design of a set of rodlets that will be fabricated and then irradiated in the Advanced Test Reactor (ATR) and (2) provide requirements for fabrication and acceptance criteria for inspections of the Light Water Reactor (LWR) – Accident Tolerant Fuels (ATF) rodlet components. The functional and operational (F&OR) requirements for the ATF program are identified in the ATF Test Plan. The scope of this document only covers fabrication and inspections of rodlet components detailed in drawings 604496 and 604497. It does not cover the assembly of these items to form a completed test irradiation assembly or the inspection of the final assembly, which will be included in a separate INL final test assembly specification/inspection document. The controls support the requirements that the test irradiations must be performed safely and that subsequent examinations must provide valid results.

  18. 3D ladar ATR based on recognition by parts

    NASA Astrophysics Data System (ADS)

    Sobel, Erik; Douglas, Joel; Ettinger, Gil

    2003-09-01

    LADAR imaging is unique in its potential to accurately measure the 3D surface geometry of targets. We exploit this 3D geometry to perform automatic target recognition on targets in the domain of military and civilian ground vehicles. Here we present a robust model based 3D LADAR ATR system which efficiently searches through target hypothesis space by reasoning hierarchically from vehicle parts up to identification of a whole vehicle with specific pose and articulation state. The LADAR data consists of one or more 3D point clouds generated by laser returns from ground vehicles viewed from multiple sensor locations. The key to this approach is an automated 3D registration process to precisely align and match multiple data views to model based predictions of observed LADAR data. We accomplish this registration using robust 3D surface alignment techniques which we have also used successfully in 3D medical image analysis applications. The registration routine seeks to minimize a robust 3D surface distance metric to recover the best six-degree-of-freedom pose and fit. We process the observed LADAR data by first extracting salient parts, matching these parts to model based predictions and hierarchically constructing and testing increasingly detailed hypotheses about the identity of the observed target. This cycle of prediction, extraction, and matching efficiently partitions the target hypothesis space based on the distinctive anatomy of the target models and achieves effective recognition by progressing logically from a target's constituent parts up to its complete pose and articulation state.

  19. Adaptive SAR ATR problem set (AdaptSAPS)

    NASA Astrophysics Data System (ADS)

    Wise, Angela R.; Fitzgerald, Donna; Ross, Timothy D.

    2004-09-01

    A strong and growing interest in systems that adapt to changing circumstances was evident in panel discussions at the "Algorithms for SAR Imagery" Conference of the AeroSense Symposium in April 2003, with DARPA, Air Force, industry and academia participation. As a result, Conference Co-Chair Mr. Ed Zelnio suggested producing a dynamic model to create problem sets suitable for adaptive system research and development. Such a problem set provides a framework for the overall problem, including organization of operating conditions, performance measures and specific test cases. It is hoped that this AdaptSAPS framework will help provide the community with a more concrete base for discussing adaptation in SAR imagery exploitation. AdaptSAPS Version 1.0 was produced by the AFRL COMPASE and SDMS organizations and posted on 5 August 2003. AdaptSAPS consists of over a dozen MatLab programs that allow the user to create "missions" with SAR data of varying complexities and then present that test data one image at a time, first as unexploited imagery and then later with the exploitation results that an ATR could use for adaptation in an operational environment. AdaptSAPS keeps track of performance results and reports performance measures. This paper describes AdaptSAPS - its application process and possible improvements as a problem set.

  20. Hydrogen-Deuterium exchange monitored by ATR-FTIR spectroscopy

    NASA Astrophysics Data System (ADS)

    Poe, Brent; Del Vecchio, Alessandro; Cestelli Guidi, Mariangela

    2016-04-01

    Measuring the extent of isotopic exchange is a common means for the determination of self-diffusion coefficients in any type of medium (gas, liquid, amorphous solid, crystalline solid). For rapidly diffusing species such as hydrogen in condensed phases, real time methods involving vibrational spectroscopy can be used by taking advantage of the large relative mass difference between 1H and 2H, resulting in large differences in the band positions of their vibrational modes. We demonstrate rapid isotopic exchange between D2O liquid and H2O vapor using ATR (attenuated total reflectance) in a FTIR spectrometer. Over the course of a few minutes several spectra were acquired of a D2O droplet mounted on a diamond crystal. The progressive exchange reaction between the liquid phase and H2O from the atmosphere was monitored by measuring the decreasing absorbance of the D-O-D bending and O-D stretching bands and the increasing absorbance of the D-O-H and H-O-H bending and O-H stretching bands as functions of time. Our results offer some intriguing insights into the structural characteristics of water as inferred by this exchange process.

  1. Neutron dosimetry and damage calculations for the ATR-A1 irradiation

    SciTech Connect

    Greenwood, L.R.; Ratner, R.T.

    1998-09-01

    Neutron fluence measurements and radiation damage calculations are reported for the collaborative US/Japan ATR-A1 irradiation in the Advanced Test Reactor (ATR) at Idaho National Engineering Laboratory (INEL). The maximum total neutron fluence at midplane was 9.4 {times} 10{sup 21} n/cm{sup 2} (5.5 {times} 10{sup 21} n/cm{sup 2} above 0.1 MeV), resulting in about 4.6 dpa in vanadium.

  2. Cancer-Specific Synthetic Lethality between ATR and CHK1 Kinase Activities

    PubMed Central

    Sanjiv, Kumar; Hagenkort, Anna; Calderón-Montaño, José Manuel; Koolmeister, Tobias; Reaper, Philip M.; Mortusewicz, Oliver; Jacques, Sylvain A.; Kuiper, Raoul V.; Schultz, Niklas; Scobie, Martin; Charlton, Peter A.; Pollard, John R.; Berglund, Ulrika Warpman; Altun, Mikael; Helleday, Thomas

    2015-01-01

    Summary ATR and CHK1 maintain cancer cell survival under replication stress and inhibitors of both kinases are currently undergoing clinical trials. As ATR activity is increased after CHK1 inhibition, we hypothesized that this may indicate an increased reliance on ATR for survival. Indeed, we observe that replication stress induced by the CHK1 inhibitor AZD7762 results in replication catastrophe and apoptosis, when combined with the ATR inhibitor VE-821 specifically in cancer cells. Combined treatment with ATR and CHK1 inhibitors leads to replication fork arrest, ssDNA accumulation, replication collapse, and synergistic cell death in cancer cells in vitro and in vivo. Inhibition of CDK reversed replication stress and synthetic lethality, demonstrating that regulation of origin firing by ATR and CHK1 explains the synthetic lethality. In conclusion, this study exemplifies cancer-specific synthetic lethality between two proteins in the same pathway and raises the prospect of combining ATR and CHK1 inhibitors as promising cancer therapy. PMID:26748709

  3. Roles of ATR1 paralogs YMR279c and YOR378w in boron stress tolerance

    SciTech Connect

    Bozdag, Gonensin Ozan; Uluisik, Irem; Gulculer, Gulce Sila; Karakaya, Huseyin C.; Koc, Ahmet

    2011-06-17

    Highlights: {yields} ATR1 paralog YMR279c plays role in boron detoxification. {yields} YMR279c overexpression lowers cytoplasmic boron levels. {yields} ATR1 paralog YOR378w has no roles in boron stress response. -- Abstract: Boron is a necessary nutrient for plants and animals, however excess of it causes toxicity. Previously, Atr1 and Arabidopsis Bor1 homolog were identified as the boron efflux pump in yeast, which lower the cytosolic boron concentration and help cells to survive in the presence of toxic amount of boron. In this study, we analyzed ATR1 paralogs, YMR279c and YOR378w, to understand whether they participate in boron stress tolerance in yeast. Even though these genes share homology with ATR1, neither their deletion rendered cells boron sensitive nor their expression was significantly upregulated by boron treatment. However, expression of YMR279, but not YOR378w, from the constitutive GAPDH promoter on a high copy plasmid provided remarkable boron resistance by decreasing intracellular boron levels. Thus our results suggest the presence of a third boron exporter, YMR279c, which functions similar to ATR1 and provides boron resistance in yeast.

  4. Achilles Tendon Reflex (ATR) in response to short exposures of microgravity and hypergravity

    NASA Technical Reports Server (NTRS)

    Fujii, M.; Jaweed, M.

    1992-01-01

    Previous studies indicate that latency and amplitude of the Achilles tendon reflex (ATR) are reduced after exposure to microgravity for 28 days. The objective of this study was to quantitatively measure the latency of ATR during brief (20 sec) exposure to microgravity in KC-135 parabolic flights. Methods: The ATR was elicited in ten men during parabolic flight with the ankle held neutrally, planarflexed, and dorsiflexed. During flight, the ATR was elicited during the zero G and 1.8 G phases. Postflight testing was performed flying back to the airfield. Latencies to onset of the ATR were calculated and analyses of variance were performed to determine the effect of gravity and ankle position on latency. Result: The mean latencies for zero-G, 1.8-G and postflight with the ankle in the neutral position were 32.7 plus or minus 0.5 ms, and 33.1 plus or minus 0.7 ms respectively, which were not significantly different. There was a trend toward prolongation of latencies postflight. The mean latency for those who were motion sick was 32.1 plus or minus 0.1 ms compared to 34.0 plus or minus 0.3 ms for those who were not sick. Conclusions: These studies indicate that neither the level of gravity nor ankle position significantly affected the latency of the ATR.

  5. Coordinated regulation of XPA stability by ATR and HERC2 during nucleotide excision repair.

    PubMed

    Lee, T-H; Park, J-M; Leem, S-H; Kang, T-H

    2014-01-01

    ATR (ATM and Rad3-related) is an essential regulator of the nucleotide excision repair (NER) mechanism. For NER activation, ATR phosphorylates XPA, the rate-limiting factor in the NER pathway. However, the role of XPA phosphorylation at serine 196 by ATR has been elusive. Here we show that ATR-mediated XPA phosphorylation enhances XPA stability by inhibiting HERC2-mediated ubiquitination and subsequent degradation. We analyzed stabilization of XPA with substitutions of Ser 196 either to aspartate (S196D), a phosphomimetic mutation, or to alanine (S196A), a phosphodeficient mutation. Upon ultraviolet damage, ATR facilitated HERC2 dissociation from the XPA complex to induce XPA stabilization. However, this regulation was abrogated in S196A-complemented XPA-deficient cells due to persistent association of HERC2 with this XPA complex, resulting in enhanced ubiquitination of S196A. Conversely, the S196D substitution showed delayed degradation kinetics compared with the wild-type and less binding with HERC2, resulting in reduced ubiquitination of S196D. We also found that XPA phosphorylation enhanced the chromatin retention of XPA, the interaction with its binding partners following DNA damage. Taken together, our study presents a novel control mechanism in the NER pathway by regulating the steady-state level of XPA through posttranslational modifications by which ATR-mediated phosphorylation induces XPA stabilization by antagonizing HERC2-catalyzed XPA ubiquitination. PMID:23178497

  6. Gas Test Loop Booster Fuel Hydraulic Testing

    SciTech Connect

    Gas Test Loop Hydraulic Testing Staff

    2006-09-01

    The Gas Test Loop (GTL) project is for the design of an adaptation to the Advanced Test Reactor (ATR) to create a fast-flux test space where fuels and materials for advanced reactor concepts can undergo irradiation testing. Incident to that design, it was found necessary to make use of special booster fuel to enhance the neutron flux in the reactor lobe in which the Gas Test Loop will be installed. Because the booster fuel is of a different composition and configuration from standard ATR fuel, it is necessary to qualify the booster fuel for use in the ATR. Part of that qualification is the determination that required thermal hydraulic criteria will be met under routine operation and under selected accident scenarios. The Hydraulic Testing task in the GTL project facilitates that determination by measuring flow coefficients (pressure drops) over various regions of the booster fuel over a range of primary coolant flow rates. A high-fidelity model of the NW lobe of the ATR with associated flow baffle, in-pile-tube, and below-core flow channels was designed, constructed and located in the Idaho State University Thermal Fluids Laboratory. A circulation loop was designed and constructed by the university to provide reactor-relevant water flow rates to the test system. Models of the four booster fuel elements required for GTL operation were fabricated from aluminum (no uranium or means of heating) and placed in the flow channel. One of these was instrumented with Pitot tubes to measure flow velocities in the channels between the three booster fuel plates and between the innermost and outermost plates and the side walls of the flow annulus. Flow coefficients in the range of 4 to 6.5 were determined from the measurements made for the upper and middle parts of the booster fuel elements. The flow coefficient for the lower end of the booster fuel and the sub-core flow channel was lower at 2.3.

  7. AGR-2 Data Qualification Report for ATR Cycles 147A, 148A, 148B, and 149A

    SciTech Connect

    Michael L. Abbott; Keith A. Daum

    2011-08-01

    This report presents the data qualification status of fuel irradiation data from the first four reactor cycles (147A, 148A, 148B, and 149A) of the on-going second Advanced Gas Reactor (AGR-2) experiment as recorded in the NGNP Data Management and Analysis System (NDMAS). This includes data received by NDMAS from the period June 22, 2010 through May 21, 2011. AGR-2 is the second in a series of eight planned irradiation experiments for the AGR Fuel Development and Qualification Program, which supports development of the very high temperature gas-cooled reactor (VHTR) under the Next Generation Nuclear Plant (NGNP) Project. Irradiation of the AGR-2 test train is being performed at the Advanced Test Reactor (ATR) at the Idaho National Laboratory (INL) and is planned for 600 effective full power days (approximately 2.75 calendar years) (PLN-3798). The experiment is intended to demonstrate the performance of UCO (uranium oxycarbide) and UO2 (uranium dioxide) fuel produced in a large coater. Data qualification status of the AGR-1 experiment was reported in INL/EXT-10-17943 (Abbott et al. 2010).

  8. Untangling the ATR-CHEK1 network for prognostication, prediction and therapeutic target validation in breast cancer.

    PubMed

    Abdel-Fatah, Tarek M A; Middleton, Fiona K; Arora, Arvind; Agarwal, Devika; Chen, Tao; Moseley, Paul M; Perry, Christina; Doherty, Rachel; Chan, Stephen; Green, Andrew R; Rakha, Emad; Ball, Graham; Ellis, Ian O; Curtin, Nicola J; Madhusudan, Srinivasan

    2015-03-01

    ATR-CHEK1 signalling is critical for genomic stability. ATR-CHEK1 signalling may be deregulated in breast cancer and have prognostic, predictive and therapeutic significance. We investigated ATR, CHEK1 and phosphorylated CHEK1 (Ser345) protein (pCHEK1) levels in 1712 breast cancers. ATR and CHEK1 mRNA expression was evaluated in 1950 breast cancers. Pre-clinically, biological consequences of ATR gene knock down or ATR inhibition by the small molecule inhibitor (VE-821) were investigated in MCF7 and MDA-MB-231 breast cancer cell lines and in non-tumorigenic breast epithelial cells (MCF10A). High ATR and high cytoplasmic pCHEK1 levels were significantly associated with higher tumour stage, higher mitotic index, pleomorphism and lymphovascular invasion. In univariate analyses, high ATR and high cytoplasmic pCHEK1 levels were associated with poor breast cancer specific survival (BCSS). In multivariate analysis, high ATR level remains an independent predictor of adverse outcome. At the mRNA level, high CHEK1 remains associated with aggressive phenotypes including lymph node positivity, high grade, Her-2 overexpression, triple negative, aggressive molecular phenotypes and adverse BCSS. Pre-clinically, CHEK1 phosphorylation at serine(345) following replication stress was impaired in ATR knock down and in VE-821 treated breast cancer cells. Doxycycline inducible knockdown of ATR suppressed growth, which was restored when ATR was re-expressed. Similarly, VE-821 treatment resulted in a dose dependent suppression of cancer cell growth and survival (MCF7 and MDA-MB-231) but was less toxic in non-tumorigenic breast epithelial cells (MCF10A). We provide evidence that ATR and CHEK1 are promising biomarkers and rational drug targets for personalized therapy in breast cancer. PMID:25468710

  9. A cell-based screen identifies ATR inhibitors with synthetic lethal properties for cancer-associated mutations

    PubMed Central

    Toledo, Luis I.; Murga, Matilde; Zur, Rafal; Soria, Rebeca; Rodriguez, Antonio; Martinez, Sonia; Oyarzabal, Julen; Pastor, Joaquin; Bischoff, James R.; Fernandez-Capetillo, Oscar

    2016-01-01

    SUMMARY Oncogene activation has been shown to generate replication-born DNA damage, also known as replicative stress (RS). Notably, the ATR kinase –and not ATM- is the primary responder to RS. One limitation for the study of ATR is the lack of potent inhibitors. We here describe a cell-based screening strategy that has allowed us to identify compounds with ATR inhibitory activity in the nanomolar range. Pharmacological inhibition of ATR generates RS, leading to chromosomal breakage in the presence of conditions that stall replication forks. Moreover, ATR inhibition is particularly toxic for p53 deficient cells, this toxicity being exacerbated by RS-generating conditions such as the overexpression of cyclin E. Importantly, one of the compounds is NVP-BEZ235, a dual PI3K/mTOR inhibitor that is currently being tested for cancer chemotherapy, but which we now show is also very potent against ATM, ATR and DNA-PKcs. PMID:21552262

  10. 10 CFR 830 Major Modification Determination for Advanced Test Reactor LEU Fuel Conversion

    SciTech Connect

    Boyd D. Christensen; Michael A. Lehto; Noel R. Duckwitz

    2012-05-01

    The Advanced Test Reactor (ATR), located in the ATR Complex of the Idaho National Laboratory (INL), was constructed in the 1960s for the purpose of irradiating reactor fuels and materials. Other irradiation services, such as radioisotope production, are also performed at ATR. The ATR is fueled with high-enriched uranium (HEU) matrix (UAlx) in an aluminum sandwich plate cladding. The National Nuclear Security Administration Global Threat Reduction Initiative (GTRI) strategic mission includes efforts to reduce and protect vulnerable nuclear and radiological material at civilian sites around the world. Converting research reactors from using HEU to low-enriched uranium (LEU) was originally started in 1978 as the Reduced Enrichment for Research and Test Reactors (RERTR) Program under the U.S. Department of Energy (DOE) Office of Science. Within this strategic mission, GTRI has three goals that provide a comprehensive approach to achieving this mission: The first goal, the driver for the modification that is the subject of this determination, is to convert research reactors from using HEU to LEU. Thus the mission of the ATR LEU Fuel Conversion Project is to convert the ATR and Advanced Test Reactor Critical facility (ATRC) (two of the six U.S. High-Performance Research Reactors [HPRR]) to LEU fuel by 2017. The major modification criteria evaluation of the project pre-conceptual design identified several issues that lead to the conclusion that the project is a major modification.

  11. Attila{sup R} Modeling with Comparisons to Data, MCNP and MCNPX for the Advanced Test Reactor (ATR)

    SciTech Connect

    Lucas, D. Scott; LaPorta, Anthony; Hounshel, Derek A.

    2006-07-01

    The 3D neutron transport code Attila{sup R} has been used in a Laboratory Directed Research and Development (LDRD) project for the Advanced Test Reactor (ATR) at the Idaho National Laboratory (INL). The purpose is to examine the feasibility of replacing the current diffusion based Core Safety Analysis Methods with a neutron transport code. This is a discussion of the development of the Attila models, and their comparison to models from other codes and historical data from the ATR. Additional comparisons have been made to the ATR Critical Facility (ATRC), the low power version of ATR, used for physics testing. (authors)

  12. EVALUATION OF CORE PHYSICS ANALYSIS METHODS FOR CONVERSION OF THE INL ADVANCED TEST REACTOR TO LOW-ENRICHMENT FUEL

    SciTech Connect

    Mark DeHart; Gray S. Chang

    2012-04-01

    Computational neutronics studies to support the possible conversion of the ATR to LEU are underway. Simultaneously, INL is engaged in a physics methods upgrade project to put into place modern computational neutronics tools for future support of ATR fuel cycle and experiment analysis. A number of experimental measurements have been performed in the ATRC in support of the methods upgrade project, and are being used to validate the new core physics methods. The current computational neutronics work is focused on performance of scoping calculations for the ATR core loaded with a candidate LEU fuel design. This will serve as independent confirmation of analyses that have been performed previously, and will evaluate some of the new computational methods for analysis of a candidate LEU fuel for ATR.

  13. Advanced Test Reactor (ATR) Facility 10CFR830 Safety Basis Related to Facility Experiments

    SciTech Connect

    Tomberlin, Terry Alan

    2002-06-01

    The Idaho National Engineering and Environmental Laboratory (INEEL) Advanced Test Reactor (ATR), a DOE Category A reactor, was designed to provide an irradiation test environment for conducting a variety of experiments. The ATR Safety Analysis Report, determined by DOE to meet the requirements of 10 CFR 830, Subpart B, provides versatility in types of experiments that may be conducted. This paper addresses two general types of experiments in the ATR facility and how safety analyses for experiments are related to the ATR safety basis. One type of experiment is more routine and generally represents greater risks; therefore this type of experiment is addressed with more detail in the safety basis. This allows individual safety analyses for these experiments to be more routine and repetitive. The second type of experiment is less defined and is permitted under more general controls. Therefore, individual safety analyses for the second type of experiment tend to be more unique from experiment to experiment. Experiments are also discussed relative to "major modifications" and DOE-STD-1027-92. Application of the USQ process to ATR experiments is also discussed.

  14. Advanced Test Reactor (ATR) Facility 10CFR830 Safety Basis Related to Facility Experiments

    SciTech Connect

    Tomberlin, T.A.

    2002-06-19

    The Idaho National Engineering and Environmental Laboratory (INEEL) Advanced Test Reactor (ATR), a DOE Category A reactor, was designed to provide an irradiation test environment for conducting a variety of experiments. The ATR Safety Analysis Report, determined by DOE to meet the requirements of 10 CFR 830, Subpart B, provides versatility in types of experiments that may be conducted. This paper addresses two general types of experiments in the ATR facility and how safety analyses for experiments are related to the ATR safety basis. One type of experiment is more routine and generally represents greater risks; therefore this type of experiment is addressed with more detail in the safety basis. This allows individual safety analyses for these experiments to be more routine and repetitive. The second type of experiment is less defined and is permitted under more general controls. Therefore, individual safety analyses for the second type of experiment tend to be more unique from experiment to experiment. Experiments are also discussed relative to ''major modifications'' and DOE-STD-1027-92. Application of the USQ process to ATR experiments is also discussed.

  15. Structural elucidation and functional characterization of the Hyaloperonospora arabidopsidis effector protein ATR13.

    PubMed

    Leonelli, Lauriebeth; Pelton, Jeffery; Schoeffler, Allyn; Dahlbeck, Douglas; Berger, James; Wemmer, David E; Staskawicz, Brian

    2011-12-01

    The oomycete Hyaloperonospora arabidopsidis (Hpa) is the causal agent of downy mildew on the model plant Arabidopsis thaliana and has been adapted as a model system to investigate pathogen virulence strategies and plant disease resistance mechanisms. Recognition of Hpa infection occurs when plant resistance proteins (R-genes) detect the presence or activity of pathogen-derived protein effectors delivered to the plant host. This study examines the Hpa effector ATR13 Emco5 and its recognition by RPP13-Nd, the cognate R-gene that triggers programmed cell death (HR) in the presence of recognized ATR13 variants. Herein, we use NMR to solve the backbone structure of ATR13 Emco5, revealing both a helical domain and a disordered internal loop. Additionally, we use site-directed and random mutagenesis to identify several amino acid residues involved in the recognition response conferred by RPP13-Nd. Using our structure as a scaffold, we map these residues to one of two surface-exposed patches of residues under diversifying selection. Exploring possible roles of the disordered region within the ATR13 structure, we perform domain swapping experiments and identify a peptide sequence involved in nucleolar localization. We conclude that ATR13 is a highly dynamic protein with no clear structural homologues that contains two surface-exposed patches of polymorphism, only one of which is involved in RPP13-Nd recognition specificity. PMID:22194684

  16. Interplay between ATM and ATR in the regulation of common fragile site stability.

    PubMed

    Ozeri-Galai, E; Schwartz, M; Rahat, A; Kerem, B

    2008-04-01

    Common fragile sites are specific genomic loci that form constrictions and gaps on metaphase chromosomes under conditions that slow, but do not arrest, DNA replication. These sites have been shown to have a role in various chromosomal rearrangements in tumors. Different DNA damage response proteins were shown to regulate fragile site stability, including ataxia-telangiectasia and Rad3-related (ATR) and its effector Chk1. Here, we investigated the role of ataxia-telangiectasia mutated (ATM), the main transducer of DNA double-strand break (DSB) signal, in this regulation. We demonstrate that replication stress conditions, which induce fragile site expression, lead to DNA fragmentation and recruitment of phosphorylated ATM to nuclear foci at DSBs. We further show that ATM plays a role in maintaining fragile site stability, which is revealed only in the absence of ATR. However, the activation of ATM under these replication stress conditions is ATR independent. Following conditions that induce fragile site expression both ATR and ATM phosphorylate Chk1, suggesting that both proteins regulate fragile site expression probably via their effect on Chk1 activation. Our findings provide new insights into the interplay between ATR and ATM pathways in response to partial replication inhibition and in the regulation of fragile site stability. PMID:17934520

  17. Evaluation of shooting distance by AFM and FTIR/ATR analysis of GSR.

    PubMed

    Mou, Yongyan; Lakadwar, Jyoti; Rabalais, J Wayne

    2008-11-01

    The techniques of atomic force microscopy (AFM) and Fourier transform infrared attenuated total reflectance (FTIR/ATR) spectroscopy are applied to the analysis of gun-shot residue (GSR) to test their ability to determine shooting distance and discrimination of the powder manufacturers. AFM is a nondestructive technique that is capable of characterizing the shapes and size distributions of GSR particles with resolution down to less than a nanometer. This may be useful for estimation of the shooting distance. Our AFM images of GSR show that the size distribution of the particles is inversely proportional to the shooting distance. Discrimination of powder manufacturers is tested by FTIR/ATR investigation of GSR. Identifying the specific compounds in the GSR by FTIR/ATR was not possible because it is a mixture of the debris of several compounds that compose the residue. However, it is shown that the GSR from different cartridges has characteristic FTIR/ATR bands that may be useful in differentiating the powder manufacturers. It appears promising that the development of AFM and FTIR/ATR databases for various powder manufacturers may be useful in analysis and identification of GSR. PMID:18761553

  18. HORMAD2 is essential for synapsis surveillance during meiotic prophase via the recruitment of ATR activity.

    PubMed

    Kogo, Hiroshi; Tsutsumi, Makiko; Inagaki, Hidehito; Ohye, Tamae; Kiyonari, Hiroshi; Kurahashi, Hiroki

    2012-11-01

    Meiotic chromosome segregation requires homologous pairing, synapsis and crossover recombination during meiotic prophase. The checkpoint kinase ATR has been proposed to be involved in the quality surveillance of these processes, although the underlying mechanisms remain largely unknown. In our present study, we generated mice lacking HORMAD2, a protein that localizes to unsynapsed meiotic chromosomes. We show that this Hormad2 deficiency hampers the proper recruitment of ATR activity to unsynapsed chromosomes. Male Hormad2-deficient mice are infertile due to spermatocyte loss as a result of characteristic impairment of sex body formation; an ATR- and γH2AX-enriched repressive chromatin domain is formed, but is partially dissociated from the elongated sex chromosome axes. In contrast to males, Hormad2-deficient females are fertile. However, our analysis of Hormad2/Spo11 double-mutant females shows that the oocyte number is negatively correlated with the frequency of pseudo-sex body formation in a Hormad2 gene dosage-dependent manner. This result suggests that the elimination of Spo11-deficient asynaptic oocytes is associated with the HORMAD2-dependent pseudo-sex body formation that is likely initiated by local concentration of ATR activity in the absence of double-strand breaks. Our results thus show a HORMAD2-dependent quality control mechanism that recognizes unsynapsis and recruits ATR activity during mammalian meiosis. PMID:23039116

  19. ATR suppresses endogenous DNA damage and allows completion of homologous recombination repair.

    PubMed

    Brown, Adam D; Sager, Brian W; Gorthi, Aparna; Tonapi, Sonal S; Brown, Eric J; Bishop, Alexander J R

    2014-01-01

    DNA replication fork stalling or collapse that arises from endogenous damage poses a serious threat to genome stability, but cells invoke an intricate signaling cascade referred to as the DNA damage response (DDR) to prevent such damage. The gene product ataxia telangiectasia and Rad3-related (ATR) responds primarily to replication stress by regulating cell cycle checkpoint control, yet it's role in DNA repair, particularly homologous recombination (HR), remains unclear. This is of particular interest since HR is one way in which replication restart can occur in the presence of a stalled or collapsed fork. Hypomorphic mutations in human ATR cause the rare autosomal-recessive disease Seckel syndrome, and complete loss of Atr in mice leads to embryonic lethality. We recently adapted the in vivo murine pink-eyed unstable (pun) assay for measuring HR frequency to be able to investigate the role of essential genes on HR using a conditional Cre/loxP system. Our system allows for the unique opportunity to test the effect of ATR loss on HR in somatic cells under physiological conditions. Using this system, we provide evidence that retinal pigment epithelium (RPE) cells lacking ATR have decreased density with abnormal morphology, a decreased frequency of HR and an increased level of chromosomal damage. PMID:24675793

  20. Drosophila ATM and ATR have distinct activities in the regulation of meiotic DNA damage and repair.

    PubMed

    Joyce, Eric F; Pedersen, Michael; Tiong, Stanley; White-Brown, Sanese K; Paul, Anshu; Campbell, Shelagh D; McKim, Kim S

    2011-10-31

    Ataxia telangiectasia-mutated (ATM) and ataxia telangiectasia-related (ATR) kinases are conserved regulators of cellular responses to double strand breaks (DSBs). During meiosis, however, the functions of these kinases in DSB repair and the deoxyribonucleic acid (DNA) damage checkpoint are unclear. In this paper, we show that ATM and ATR have unique roles in the repair of meiotic DSBs in Drosophila melanogaster. ATR mutant analysis indicated that it is required for checkpoint activity, whereas ATM may not be. Both kinases phosphorylate H2AV (γ-H2AV), and, using this as a reporter for ATM/ATR activity, we found that the DSB repair response is surprisingly dynamic at the site of DNA damage. γ-H2AV is continuously exchanged, requiring new phosphorylation at the break site until repair is completed. However, most surprising is that the number of γ-H2AV foci is dramatically increased in the absence of ATM, but not ATR, suggesting that the number of DSBs is increased. Thus, we conclude that ATM is primarily required for the meiotic DSB repair response, which includes functions in DNA damage repair and negative feedback control over the level of programmed DSBs during meiosis. PMID:22024169

  1. AGR-2 Final Data Qualification Report for U.S. Capsules - ATR Cycles 147A Through 154B

    SciTech Connect

    Pham, Binh T; Einerson, Jeffrey J

    2014-07-01

    This report provides the data qualification status of AGR-2 fuel irradiation experimental data in four U.S. capsules from all 15 Advanced Test Reactor (ATR) Cycles 147A, 148A, 148B, 149A, 149B, 150A, 150B, 151A, 151B, 152A, 152B, 153A, 153B, 154A, and 154B, as recorded in the Nuclear Data Management and Analysis System (NDMAS). Thus, this report covers data qualification status for the entire AGR-2 irradiation and will replace four previously issued AGR-2 data qualification reports (e.g., INL/EXT-11-22798, INL/EXT-12-26184, INL/EXT-13-29701, and INL/EXT-13-30750). During AGR-2 irradiation, two cycles, 152A and 153A, occurred when the ATR core was briefly at low power, so AGR-2 irradiation data are not used for physics and thermal calculations. Also, two cycles, 150A and 153B, are Power Axial Locator Mechanism (PALM) cycles when the ATR power is higher than during normal cycles. During the first PALM cycle, 150A, the experiment was temporarily moved from the B-12 location to the ATR water canal and during the second PALM cycle, 153B, the experiment was temporarily moved from the B-12 location to the I-24 location to avoid being overheated. During the “Outage” cycle, 153A, seven flow meters were installed downstream from seven Fission Product Monitoring System (FPMS) monitors to measure flows from the monitors and these data are included in the NDMAS database. The AGR-2 data streams addressed in this report include thermocouple (TC) temperatures, sweep gas data (flow rates including new FPM downstream flows, pressure, and moisture content), and FPMS data (release rates and release-to-birth rate ratios [R/Bs]) for each of the four U.S. capsules in the AGR-2 experiment (Capsules 2, 3, 5, and 6). The final data qualification status for these data streams is determined by a Data Review Committee comprised of AGR technical leads, Very High Temperature Reactor (VHTR) Program Quality Assurance (QA), and NDMAS analysts. The Data Review Committee, which convened just

  2. Development of an LS-DYNA Model of an ATR42-300 Aircraft for Crash Simulation

    NASA Technical Reports Server (NTRS)

    Jackson, Karen E.; Fasanella, Edwin L.

    2004-01-01

    This paper describes the development of an LS-DYNA simulation of a vertical drop test of an ATR42-300 twin-turboprop high-wing commuter-class airplane. A 30-ft/s drop test of this aircraft was performed onto a concrete impact surface at the FAA Technical Center on July 30, 2003. The purpose of the test was to evaluate the structural response of a commuter-class aircraft when subjected to a severe, but survivable, impact. The aircraft was configured with crew and passenger seats, anthropomorphic test dummies, forward and aft luggage, instrumentation, and onboard data acquisition systems. The wings were filled with approximately 8,700 lb. of water to represent the fuel and the aircraft weighed a total of 33,200 lb. The model, which consisted of 57,643 nodes and 62,979 elements, was developed from direct measurements of the airframe geometry, over a period of approximately 8 months. The seats, dummies, luggage, fuel, and other ballast were represented using concentrated masses. Comparisons were made of the structural deformation and failure behavior of the airframe, as well as selected acceleration time history responses.

  3. 10 CFR 830 Major Modification Determination for Replacement of ATR Primary Coolant Pumps and Motors

    SciTech Connect

    Noel Duckwitz

    2011-05-01

    The continued safe and reliable operation of the ATR is critical to the Department of Energy (DOE) Office of Nuclear Energy (NE) mission. While ATR is safely fulfilling current mission requirements, a variety of aging and obsolescence issues challenge ATR engineering and maintenance personnel’s capability to sustain ATR over the long term. First documented in a series of independent assessments, beginning with an OA Environmental Safety and Health Assessment conducted in 2003, the issues were validated in a detailed Material Condition Assessment (MCA) conducted as a part of the ATR Life Extension Program in 2007.Accordingly, near term replacement of aging and obsolescent original ATR equipment has become important to ensure ATR capability in support of NE’s long term national missions. To that end, a mission needs statement has been prepared for a non-major system acquisition which is comprised of three interdependent subprojects. The first project will replace the existent diesel-electrical bus (E-3), switchgear, and the 50-year-old obsolescent marine diesels with commercial power that is backed with safety related emergency diesel generators, switchgear, and uninterruptible power supply (UPS). The second project, the subject of this major modification determination, will replace the four, obsolete, original primary coolant pumps (PCPs) and motors. Completion of this and the two other age-related projects (replacement of the ATR diesel bus [E-3] and switchgear and replacement of the existent emergency firewater injection system) will resolve major age-related operational issues plus make a significant contribution in sustaining the ATR safety and reliability profile. The major modification criteria evaluation of the project pre-conceptual design identified several issues that lead to the conclusion that the project is a major modification: 1. Evaluation Criteria #3 (Change of existing process). The proposed strategy for equipping the replacement PCPs with VFDs

  4. Esophago-gastric motility and nutritional management in a child with ATR-X syndrome.

    PubMed

    Watanabe, Toshihiko; Arai, Katsuhiro; Takahashi, Masataka; Ohno, Michinobu; Sato, Kaori; Fuchimoto, Yasushi; Wada, Takahiko; Ida, Shinobu; Kawahara, Hisayoshi; Kanamori, Yutaka

    2014-08-01

    X-linked alpha thalassemia mental retardation (ATR-X) syndrome is an X-linked recessive disorder that often involves gastrointestinal symptoms. Aspiration pneumonia related to gastroesophageal reflux has been reported as the major cause of death, but gastrointestinal function has not been well investigated. The present report describes a child with ATR-X syndrome who suffered from periodical episodes of refractory vomiting. We investigated the function of upper alimentary tract and found that esophago-gastric dysmotility and severe gastric volvulus were the major causes of gastrointestinal symptoms. This child was surgically treated with anterior gastropexy and jejunal alimentation through gastrostomy, and the symptoms were relieved with good weight gain. This report may provide insight into the gastrointestinal function and nutritional management in children with ATR-X syndrome. PMID:25252072

  5. Modeling the attenuated total reflectance infrared (ATR-FTIR) spectrum of apatite

    NASA Astrophysics Data System (ADS)

    Aufort, Julie; Ségalen, Loïc; Gervais, Christel; Brouder, Christian; Balan, Etienne

    2016-06-01

    Attenuated total reflectance (ATR) infrared spectra were measured on a synthetic and a natural fluorapatite sample. A modeling approach based on the computation of the Fresnel reflection coefficient between the ATR crystal and the powder sample was used to analyze the line shape of the spectra. The dielectric properties of the samples were related to those of pure fluorapatite using an effective medium approach, based on Maxwell-Garnett and Bruggeman models. The Bruggeman effective medium model leads to a very good agreement with the experimental data recorded on the synthetic fluorapatite sample. The poorer agreement observed on the natural sample suggests a more significant heterogeneity of the sample at a characteristic length scale larger than the mid-infrared characteristic wavelength, i.e., about 10 micrometers. The results demonstrate the prominent role of macroscopic electrostatic effects over fine details of the microscopic structure in determining the line shape of strong ATR bands.

  6. Status of ATR-A1 irradiation experiment on vanadium alloys and low-activation steels

    SciTech Connect

    Tsai, H.; Strain, R.V.; Gomes, I.; Smith, D.L.; Matsui, H.

    1996-10-01

    The ATR-A1 irradiation experiment was a collaborative U.S./Japan effort to study at low temperature the effects of neutron damage on vanadium alloys. The experiment also contained a limited quantity of low-activation ferritic steel specimens from Japan as part of the collaboration agreement. The irradiation started in the Advanced Test Reactor (ATR) on November 30, 1995, and ended as planned on May 5, 1996. Total exposure was 132.9 effective full power days (EFPDs) and estimated neutron damage in the vanadium was 4.7 dpa. The vehicle has been discharged from the ATR core and is scheduled to be disassembled in the next reporting period.

  7. Attenuated total reflection Fourier-transform infrared (ATR-FTIR) imaging of tissues and live cells.

    PubMed

    Andrew Chan, K L; Kazarian, Sergei G

    2016-03-29

    FTIR spectroscopic imaging is a label-free, non-destructive and chemically specific technique that can be utilised to study a wide range of biomedical applications such as imaging of biopsy tissues, fixed cells and live cells, including cancer cells. In particular, the use of FTIR imaging in attenuated total reflection (ATR) mode has attracted much attention because of the small, but well controlled, depth of penetration and corresponding path length of infrared light into the sample. This has enabled the study of samples containing large amounts of water, as well as achieving an increased spatial resolution provided by the high refractive index of the micro-ATR element. This review is focused on discussing the recent developments in FTIR spectroscopic imaging, particularly in ATR sampling mode, and its applications in the biomedical science field as well as discussing the future opportunities possible as the imaging technology continues to advance. PMID:26488803

  8. Depletion of ATR selectively sensitizes ATM-deficient human mammary epithelial cells to ionizing radiation and DNA-damaging agents

    PubMed Central

    Cui, Yuxia; Palii, Stela S; Innes, Cynthia L; Paules, Richard S

    2014-01-01

    DNA damage response (DDR) to double strand breaks is coordinated by 3 phosphatidylinositol 3-kinase-related kinase (PIKK) family members: the ataxia-telangiectasia mutated kinase (ATM), the ATM and Rad3-related (ATR) kinase and the catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs). ATM and ATR are central players in activating cell cycle checkpoints and function as an active barrier against genome instability and tumorigenesis in replicating cells. Loss of ATM function is frequently reported in various types of tumors, thus placing more reliance on ATR for checkpoint arrest and cell survival following DNA damage. To investigate the role of ATR in the G2/M checkpoint regulation in response to ionizing radiation (IR), particularly when ATM is deficient, cell lines deficient of ATM, ATR, or both were generated using a doxycycline-inducible lentiviral system. Our data suggests that while depletion of ATR or ATM alone in wild-type human mammary epithelial cell cultures (HME-CCs) has little effect on radiosensitivity or IR-induced G2/M checkpoint arrest, depletion of ATR in ATM-deficient cells causes synthetic lethality following IR, which correlates with severe G2/M checkpoint attenuation. ATR depletion also inhibits IR-induced autophagy, regardless of the ATM status, and enhances IR-induced apoptosis particularly when ATM is deficient. Collectively, our results clearly demonstrate that ATR function is required for the IR-induced G2/M checkpoint activation and subsequent survival of cells with ATM deficiency. The synthetic lethal interaction between ATM and ATR in response to IR supports ATR as a therapeutic target for improved anti-cancer regimens, especially in tumors with a dysfunctional ATM pathway. PMID:25483091

  9. ATR and transmission analysis of pigments by means of far infrared spectroscopy.

    PubMed

    Kendix, Elsebeth L; Prati, Silvia; Joseph, Edith; Sciutto, Giorgia; Mazzeo, Rocco

    2009-06-01

    In the field of FTIR spectroscopy, the far infrared (FIR) spectral region has been so far less investigated than the mid-infrared (MIR), even though it presents great advantages in the characterization of those inorganic compounds, which are inactive in the MIR, such as some art pigments, corrosion products, etc. Furthermore, FIR spectroscopy is complementary to Raman spectroscopy if the fluorescence effects caused by the latter analytical technique are considered. In this paper, ATR in the FIR region is proposed as an alternative method to transmission for the analyses of pigments. This methodology was selected in order to reduce the sample amount needed for analysis, which is a must when examining cultural heritage materials. A selection of pigments have been analyzed in both ATR and transmission mode, and the resulting spectra were compared with each other. To better perform this comparison, an evaluation of the possible effect induced by the thermal treatment needed for the preparation of the polyethylene pellets on the transmission spectra of the samples has been carried out. Therefore, pigments have been analyzed in ATR mode before and after heating them at the same temperature employed for the polyethylene pellet preparation. The results showed that while the heating treatment causes only small changes in the intensity of some bands, the ATR spectra were characterized by differences in both intensity and band shifts towards lower frequencies if compared with those recorded in transmission mode. All pigments' transmission and ATR spectra are presented and discussed, and the ATR method was validated on a real case study. PMID:19266186

  10. Increased Rrm2 gene dosage reduces fragile site breakage and prolongs survival of ATR mutant mice

    PubMed Central

    Specks, Julia; Barlow, Jacqueline H.; Ambrogio, Chiara; Desler, Claus; Vikingsson, Svante; Rodrigo-Perez, Sara; Green, Henrik; Rasmussen, Lene Juel; Murga, Matilde; Nussenzweig, André

    2015-01-01

    In Saccharomyces cerevisiae, absence of the checkpoint kinase Mec1 (ATR) is viable upon mutations that increase the activity of the ribonucleotide reductase (RNR) complex. Whether this pathway is conserved in mammals remains unknown. Here we show that cells from mice carrying extra alleles of the RNR regulatory subunit RRM2 (Rrm2TG) present supraphysiological RNR activity and reduced chromosomal breakage at fragile sites. Moreover, increased Rrm2 gene dosage significantly extends the life span of ATR mutant mice. Our study reveals the first genetic condition in mammals that reduces fragile site expression and alleviates the severity of a progeroid disease by increasing RNR activity. PMID:25838540

  11. 10 CFR 830 Major Modification Determination for the ATR Diesel Bus (E-3) and Switchgear Replacement

    SciTech Connect

    Noel Duckwtiz

    2011-05-01

    Near term replacement of aging and obsolescent original ATR equipment has become important to ensure ATR capability in support of NE’s long term national missions. To that end, a mission needs statement has been prepared for a non-major system acquisition which is comprised of three interdependent subprojects. The first project, subject of this determination, will replace the existent diesel-electrical bus (E-3) and associated switchgear. More specifically, INL proposes transitioning ATR to 100% commercial power with appropriate emergency backup to include: • Provide commercial power as the normal source of power to the ATR loads currently supplied by diesel-electric power. • Provide backup power to the critical ATR loads in the event of a loss of commercial power. • Replace obsolescent critical ATR power distribution equipment, e.g., switchgear, transformers, motor control centers, distribution panels. Completion of this and two other age-related projects (primary coolant pump and motor replacement and emergency firewater injection system replacement) will resolve major age related operational issues plus make a significant contribution in sustaining the ATR safety and reliability profile. The major modification criteria evaluation of the project pre-conceptual design identified several issues make the project a major modification: 1. Evaluation Criteria #2 (Footprint change). The addition of a new PC-4 structure to the ATR Facility to house safety-related SSCs requires careful attention to maintaining adherence to applicable engineering and nuclear safety design criteria (e.g., structural qualification, fire suppression) to ensure no adverse impacts to the safety-related functions of the housed equipment. 2. Evaluation Criteria #3 (Change of existing process). The change to the strategy for providing continuous reliable power to the safety-related emergency coolant pumps requires careful attention and analysis to ensure it meets a project primary object

  12. Effects of atrazine (ATR), deisopropylatrazine (DIA), Diaminochlorotriazine (DACT) on the hypothalamic-pituitary-adrenal (HPA) axis in female rats

    EPA Science Inventory

    We previously reported that a single dose of the herbicide ATR stimulated the HPA axis in the male rat while equimolar doses of its primary metabolite, DACT, had a minimal effect. In this study, we evaluated the effects of one or four daily doses of ATR, DACT, and an intermediat...

  13. ATR-FTIR Spectroscopy in the Undergraduate Chemistry Laboratory: Part II--A Physical Chemistry Laboratory Experiment on Surface Adsorption

    ERIC Educational Resources Information Center

    Schuttlefield, Jennifer D.; Larsen, Sarah C.; Grassian, Vicki H.

    2008-01-01

    Attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy is a useful technique for measuring the infrared spectra of solids and liquids as well as probing adsorption on particle surfaces. The use of FTIR-ATR spectroscopy in organic and inorganic chemistry laboratory courses as well as in undergraduate research was presented…

  14. EFFECTS OF ATRAZINE (ATR), DEISOPROPYLATRAZINE (DIA), AND DIAMINOCHLOROTRIAZINE (DACT) ON THE HYPOTHALAMIC-PITUITARY-ADRENAL (HPA) AXIS IN FEMALE RATS

    EPA Science Inventory

    Previously we reported that a single dose of ATR herbicide stimulated HPA axis activation in the male rat while its primary metabolite, DACT, did so to a lesser extent. In this study, we evaluated the effects of ATR, DACT, and an intermediate metabolite, DIA, on adrenocorticotrop...

  15. A synthetic lethal screen identifies ATR-inhibition as a novel therapeutic approach for POLD1-deficient cancers

    PubMed Central

    Hocke, Sandra; Guo, Yang; Job, Albert; Orth, Michael; Ziesch, Andreas; Lauber, Kirsten; De Toni, Enrico N; Gress, Thomas M.; Herbst, Andreas; Göke, Burkhard; Gallmeier, Eike

    2016-01-01

    The phosphoinositide 3-kinase-related kinase ATR represents a central checkpoint regulator and mediator of DNA-repair. Its inhibition selectively eliminates certain subsets of cancer cells in various tumor types, but the underlying genetic determinants remain enigmatic. Here, we applied a synthetic lethal screen directed against 288 DNA-repair genes using the well-defined ATR knock-in model of DLD1 colorectal cancer cells to identify potential DNA-repair defects mediating these effects. We identified a set of DNA-repair proteins, whose knockdown selectively killed ATR-deficient cancer cells. From this set, we further investigated the profound synthetic lethal interaction between ATR and POLD1. ATR-dependent POLD1 knockdown-induced cell killing was reproducible pharmacologically in POLD1-depleted DLD1 cells and a panel of other colorectal cancer cell lines by using chemical inhibitors of ATR or its major effector kinase CHK1. Mechanistically, POLD1 depletion in ATR-deficient cells caused caspase-dependent apoptosis without preceding cell cycle arrest and increased DNA-damage along with impaired DNA-repair. Our data could have clinical implications regarding tumor genotype-based cancer therapy, as inactivating POLD1 mutations have recently been identified in small subsets of colorectal and endometrial cancers. POLD1 deficiency might thus represent a predictive marker for treatment response towards ATR- or CHK1-inhibitors that are currently tested in clinical trials. PMID:26755646

  16. UPDATE ON MONOLITHIC FUEL FABRICATION METHODS

    SciTech Connect

    C. R. Clark; J. F. Jue; G. A. Moore; N. P. Hallinan; B. H. Park; D. E. Burkes

    2006-10-01

    Efforts to develop a viable monolithic research reactor fuel plate have continued at Idaho National Laboratory. These efforts have concentrated on both fabrication process refinement and scale-up to produce full sized fuel plates. Progress at INL has led to fabrication of hot isostatic pressed uranium-molybdenum bearing monolithic fuel plates. These miniplates are part of the RERTR-8 miniplate irradiation test. Further progress has also been made on friction stir weld processing which has been used to fabricate full size fuel plates which will be irradiated in the ATR and OSIRIS reactors.

  17. Assessment of Nuclear Fuels using Radiographic Thickness Measurement Method

    SciTech Connect

    Muhammad Abir; Fahima Islam; Hyoung Koo Lee; Daniel Wachs

    2014-11-01

    The Convert branch of the National Nuclear Security Administration (NNSA) Global Threat Reduction Initiative (GTRI) focuses on the development of high uranium density fuels for research and test reactors for nonproliferation. This fuel is aimed to convert low density high enriched uranium (HEU) based fuel to high density low enriched uranium (LEU) based fuel for high performance research reactors (HPRR). There are five U.S. reactors that fall under the HPRR category, including: the Massachusetts Institute of Technology Reactor (MITR), the National Bureau of Standards Reactor (NBSR), the Missouri University Research Reactor (UMRR), the Advanced Test Reactor (ATR), and the High Flux Isotope Reactor (HFIR). U-Mo alloy fuel phase in the form of either monolithic or dispersion foil type fuels, such as ATR Full-size In center flux trap Position (AFIP) and Reduced Enrichment for Research and Test Reactor (RERTR), are being designed for this purpose. The fabrication process1 of RERTR is susceptible to introducing a variety of fuel defects. A dependable quality control method is required during fabrication of RERTR miniplates to maintain the allowable design tolerances, therefore evaluating and analytically verifying the fabricated miniplates for maintaining quality standards as well as safety. The purpose of this work is to analyze the thickness of the fabricated RERTR-12 miniplates using non-destructive technique to meet the fuel plate specification for RERTR fuel to be used in the ATR.

  18. MATERNAL ATRAZINE (ATR) ALTERS HYPOTHALAMIC DOPAMINE (HYP-DA) AND SERUM PROLACTIN (SPRL) IN MALE PUPS

    EPA Science Inventory

    Maternal Atrazine (ATR) alters hypothalamic dopamine (HYP-DA) and serum prolactin (sPRL) in male pups. 1Christopher Langdale, 2Tammy Stoker and 2Ralph Cooper. 1 Dept. of Cell Biology, North Carolina State University College of Veterinary Medicine, Raleigh, NC. 2 Endocrinology ...

  19. Structural investigations of oriented membrane assemblies by FTIR-ATR spectroscopy

    NASA Astrophysics Data System (ADS)

    Fringeli, Urs Peter; Goette, Jeannette; Reiter, Gerald; Siam, Monira; Baurecht, Dieter

    1998-06-01

    In situ attenuated total reflection (ATR) Fourier transform (FT) spectroscopy is presented as an adequate tool for studying molecular structure and function of biomembranes. In this article emphasis was directed to the production of suitable model bilayer membranes for optimum mimicking of natural biomembranes, and to special FTIR ATR techniques to achieve enhanced selectivity as well as time resolved information on complex membrane assemblies. In this context, the preparation of supported bilayers according to the LB/vesicle method is presented and the use of such model membranes to build more complex assemblies, e.g. with creatine kinase, a surface bound enzyme, and alkaline phosphatase, a membrane anchored enzyme. A comprehensive summary of equations used for quantitative ATR spectroscopy is given and applied to determine the surface concentration and orientation of membrane bound molecules. The use of supported bilayers for drug membrane interaction studies is demonstrated by the local anesthetic dibucaine. Besides of structural information's, such studies result also thermodynamic date, such as adsorption isotherm and partition coefficient. A special ATR set-up for more precise background compensation is presented enabling the conversion of a single beam spectrometer into a pseudo double beam spectrometer. This optical component may be placed in the sample compartment of the spectrometer, and is referred to as single-beam-sample-reference (SBSR) attachment. Finally, a short theoretical introduction into time resolved modulation spectroscopy is given. Temperature modulated excitation of reversible conformational changes in the polypeptide poly-L-lysine and the enzyme RNase are shown as examples.

  20. Wee1 is required to sustain ATR/Chk1 signaling upon replicative stress

    PubMed Central

    Saini, Priyanka; Li, Yizhu; Dobbelstein, Matthias

    2015-01-01

    The therapeutic efficacy of nucleoside analogues, e.g. gemcitabine, against cancer cells can be augmented by inhibitors of checkpoint kinases, including Wee1, ATR, and Chk1. We have compared the chemosensitizing effect of these inhibitors in cells derived from pancreatic cancer, a tumor entity where gemcitabine is part of the first-line therapeutic regimens, and in osteosarcoma-derived cells. As expected, all three inhibitors rendered cancer cells more sensitive to gemcitabine, but Wee1 inhibition proved to be particularly efficient in this context. Investigating the reasons for this potent sensitizing effect, we found that Wee1 inhibition or knockdown not only blocked Wee1 activity, but also reduced the activation of ATR/Chk1 in gemcitabine-treated cells. Combination of several inhibitors revealed that Wee1 inhibition requires Cyclin-dependent kinases 1 and 2 (Cdk1/2) and Polo-like kinase 1 (Plk1) to reduce ATR/Chk1 activity. Through activation of Cdks and Plk1, Wee1 inhibition reduces Claspin and CtIP levels, explaining the impairment in ATR/Chk1 activity. Taken together, these results confer a consistent signaling pathway reaching from Wee1 inhibition to impaired Chk1 activity, mechanistically dissecting how Wee1 inhibitors not only dysregulate cell cycle progression, but also enhance replicative stress and chemosensitivity towards nucleoside analogues. PMID:25965828

  1. Multivariate analysis of ATR-FTIR spectra for assessment of oil shale organic geochemical properties

    USGS Publications Warehouse

    Washburn, Kathryn E.; Birdwell, Justin E.

    2013-01-01

    In this study, attenuated total reflectance (ATR) Fourier transform infrared spectroscopy (FTIR) was coupled with partial least squares regression (PLSR) analysis to relate spectral data to parameters from total organic carbon (TOC) analysis and programmed pyrolysis to assess the feasibility of developing predictive models to estimate important organic geochemical parameters. The advantage of ATR-FTIR over traditional analytical methods is that source rocks can be analyzed in the laboratory or field in seconds, facilitating more rapid and thorough screening than would be possible using other tools. ATR-FTIR spectra, TOC concentrations and Rock–Eval parameters were measured for a set of oil shales from deposits around the world and several pyrolyzed oil shale samples. PLSR models were developed to predict the measured geochemical parameters from infrared spectra. Application of the resulting models to a set of test spectra excluded from the training set generated accurate predictions of TOC and most Rock–Eval parameters. The critical region of the infrared spectrum for assessing S1, S2, Hydrogen Index and TOC consisted of aliphatic organic moieties (2800–3000 cm−1) and the models generated a better correlation with measured values of TOC and S2 than did integrated aliphatic peak areas. The results suggest that combining ATR-FTIR with PLSR is a reliable approach for estimating useful geochemical parameters of oil shales that is faster and requires less sample preparation than current screening methods.

  2. U-shaped fiber-optic ATR sensor enhanced by silver nanoparticles for continuous glucose monitoring.

    PubMed

    Li, Dachao; Yu, Songlin; Sun, Changyue; Zou, Chongwei; Yu, Haixia; Xu, Kexin

    2015-10-15

    An implantable U-shaped fiber ATR sensor enhanced by silver nanoparticles on cylindrical surface was presented for continuous glucose monitoring to overcome the drawbacks of traditional glucose sensing technique based on enzyme electrodes. A U-shaped structure was addressed to increase effective optical length at limited implantable space to enhance the sensitivity of fiber ATR sensor. A novel method to fabricate silver nanoparticles on cylindrical surface of U-shaped fiber ATR sensor based on chemical reduction of its silver halide material directly without any preliminary nanoparticles synthesis and following covalent bond or self-assembly was proposed. Five glucose absorption wavelengths in the mid-infrared band were employed for specific glucose monitoring. The experimental results indicate that the sensitivity and resolution of the silver-nanoparticle-enhanced U-shaped fiber-optic ATR sensor are approximately three times those of a conventional one. The high sensitivity and low-noise performance makes it promising for in vivo glucose monitoring in the future clinical applications. PMID:26022782

  3. ATM/ATR-mediated phosphorylation of PALB2 promotes RAD51 function.

    PubMed

    Ahlskog, Johanna K; Larsen, Brian D; Achanta, Kavya; Sørensen, Claus S

    2016-05-01

    DNA damage activates the ATM and ATR kinases that coordinate checkpoint and DNA repair pathways. An essential step in homology-directed repair (HDR) of DNA breaks is the formation of RAD51 nucleofilaments mediated by PALB2-BRCA2; however, roles of ATM and ATR in this critical step of HDR are poorly understood. Here, we show that PALB2 is markedly phosphorylated in response to genotoxic stresses such as ionizing radiation and hydroxyurea. This response is mediated by the ATM and ATR kinases through three N-terminal S/Q-sites in PALB2, the consensus target sites for ATM and ATR Importantly, a phospho-deficient PALB2 mutant is unable to support proper RAD51 foci formation, a key PALB2 regulated repair event, whereas a phospho-mimicking PALB2 version supports RAD51 foci formation. Moreover, phospho-deficient PALB2 is less potent in HDR than wild-type PALB2. Further, this mutation reveals a separation in PALB2 function, as the PALB2-dependent checkpoint response is normal in cells expressing the phospho-deficient PALB2 mutant. Collectively, our findings highlight a critical importance of PALB2 phosphorylation as a novel regulatory step in genome maintenance after genotoxic stress. PMID:27113759

  4. Dynamic generation of artificial HRSAR imagery for ATR development and cockpit simulation

    NASA Astrophysics Data System (ADS)

    Seidel, Heiko; Stahl, Christoph; Knappe, Peter; Hurst, Peter

    2004-09-01

    Following the tendency of increasingly using imaging sensors in military aircraft, future combat airplane pilots will need onboard artificial intelligence for aiding them in image interpretation and target designation. This document presents a system which is able to simulate high-resolution artificial SAR imagery and thereby facilitates automatic target recognition (ATR) algorithm development. The system provides a comprehensive interface that allows dynamically requesting imagery depending on the location and heading of a simulated carrier platform. Landscapes, structures and target signatures are generated based on digital terrain data and target models. An assessment of dissimilar database preparations for sensor simulation was done with respect to the different properties of SAR imaging compared to optical imaging. The document presents selected results for specific landscape elements. Post-processing algorithms for overcoming weaknesses of digital terrain databases and improving image realism are presented. Simulated sensor imagery is useful in a wide range of applications, two of which are training of ATR algorithms and sensor simulation in flight simulation environments. Using an existing ATR method as an example, the applicability and the influences of synthetic imagery on ATR training are shown and first approaches on how to validate the correctness of the imagery are explained. The integration of the system into a flight simulator in the context of interfacing and control topics serves as a concluding example.

  5. Potentiation of tumor responses to DNA damaging therapy by the selective ATR inhibitor VX-970.

    PubMed

    Hall, Amy B; Newsome, Dave; Wang, Yuxin; Boucher, Diane M; Eustace, Brenda; Gu, Yong; Hare, Brian; Johnson, Mac A; Milton, Sean; Murphy, Cheryl E; Takemoto, Darin; Tolman, Crystal; Wood, Mark; Charlton, Peter; Charrier, Jean-Damien; Furey, Brinley; Golec, Julian; Reaper, Philip M; Pollard, John R

    2014-07-30

    Platinum-based DNA-damaging chemotherapy is standard-of-care for most patients with lung cancer but outcomes remain poor. This has been attributed, in part, to the highly effective repair network known as the DNA-damage response (DDR). ATR kinase is a critical regulator of this pathway, and its inhibition has been shown to sensitize some cancer, but not normal, cells in vitro to DNA damaging agents. However, there are limited in vivo proof-of-concept data for ATR inhibition. To address this we profiled VX-970, the first clinical ATR inhibitor, in a series of in vitro and in vivo lung cancer models and compared it with an inhibitor of the downstream kinase Chk1. VX-970 markedly sensitized a large proportion of a lung cancer cell line and primary tumor panel in vitro to multiple DNA damaging drugs with clear differences to Chk1 inhibition observed. In vivo VX-970 blocked ATR activity in tumors and dramatically enhanced the efficacy of cisplatin across a panel of patient derived primary lung xenografts. The combination led to complete tumor growth inhibition in three cisplatin-insensitive models and durable tumor regression in a cisplatin-sensitive model. These data provide a strong rationale for the clinical evaluation of VX-970 in lung cancer patients. PMID:25010037

  6. Potentiation of tumor responses to DNA damaging therapy by the selective ATR inhibitor VX-970

    PubMed Central

    Boucher, Diane M.; Eustace, Brenda; Gu, Yong; Hare, Brian; Johnson, Mac A.; Milton, Sean; Murphy, Cheryl E.; Takemoto, Darin; Tolman, Crystal; Wood, Mark; Charlton, Peter; Charrier, Jean-Damien; Furey, Brinley; Golec, Julian; Reaper, Philip M.; Pollard, John R.

    2014-01-01

    Platinum-based DNA-damaging chemotherapy is standard-of-care for most patients with lung cancer but outcomes remain poor. This has been attributed, in part, to the highly effective repair network known as the DNA-damage response (DDR). ATR kinase is a critical regulator of this pathway, and its inhibition has been shown to sensitize some cancer, but not normal, cells in vitro to DNA damaging agents. However, there are limited in vivo proof-of-concept data for ATR inhibition. To address this we profiled VX-970, the first clinical ATR inhibitor, in a series of in vitro and in vivo lung cancer models and compared it with an inhibitor of the downstream kinase Chk1. VX-970 markedly sensitized a large proportion of a lung cancer cell line and primary tumor panel in vitro to multiple DNA damaging drugs with clear differences to Chk1 inhibition observed. In vivo VX-970 blocked ATR activity in tumors and dramatically enhanced the efficacy of cisplatin across a panel of patient derived primary lung xenografts. The combination led to complete tumor growth inhibition in three cisplatin-insensitive models and durable tumor regression in a cisplatin-sensitive model. These data provide a strong rationale for the clinical evaluation of VX-970 in lung cancer patients. PMID:25010037

  7. Distillate fuel-oil processing for phosphoric acid fuel-cell power plants

    SciTech Connect

    Ushiba, K. K.

    1980-02-01

    The current efforts to develop distillate oil-steam reforming processes are reviewed, and the applicability of these processes for integration with the fuel cell are discussed. The development efforts can be grouped into the following processing approaches: high-temperature steam reforming (HTSR); autothermal reforming (ATR); autothermal gasification (AG); and ultra desulfurization followed by steam reforming. Sulfur in the feed is a key problem in the process development. A majority of the developers consider sulfur as an unavoidable contaminant of distillate fuel and are aiming to cope with it by making the process sulfur-tolerant. In the HTSR development, the calcium aluminate catalyst developed by Toyo Engineering represents the state of the art. United Technology (UTC), Engelhard, and Jet Propulsion Laboratory (JPL) are also involved in the HTSR research. The ATR of distillate fuel is investigated by UTC and JPL. The autothermal gasification (AG) of distillate fuel is being investigated by Engelhard and Siemens AG. As in the ATR, the fuel is catalytically gasified utilizing the heat generated by in situ partial combustion of feed, however, the goal of the AG is to accomplish the initial breakdown of the feed into light gases and not to achieve complete conversion to CO and H/sub 2/. For the fuel-cell integration, a secondary reforming of the light gases from the AG step is required. Engelhard is currently testing a system in which the effluent from the AG section enters the steam-reforming section, all housed in a single vessel. (WHK)

  8. Linear deconvolution of ATR-IR spectra of mineral mixtures for planetary surface studies

    NASA Astrophysics Data System (ADS)

    Chemtob, S. M.; Glotch, T. D.; Rossman, G. R.

    2007-12-01

    Attenuated total reflectance (ATR) is an infrared spectroscopic method useful for compositional analysis of powdered samples. ATR-IR is frequently used for chemical phase ID, but is seldom used in geological studies. Because it is effective with small grain sizes, ATR-IR could be a powerful tool for in situ mineral identification on future planetary lander missions, especially for the analysis of fine-grained regoliths, atmospheric dust, and outcrop grindings. Here we test the ability of the ATR-IR technique to quantitatively determine the modal mineralogy of powdered mineral mixtures. Mixtures were prepared from four mineral endmembers - olivine (Fo90), plagioclase (An60), calcite and gypsum - in known volumetric proportions and in a variety of grain sizes. ATR spectra of mineral mixtures and endmembers were collected in the range 400-4000 cm-1. Spectra of mixtures were modeled using the deconvolution method of Rogers et al. (2006), modified so that a measured grain-size distribution (GSD) could be included as a weighted factor in the fit. The signal-to-noise ratio increased for each mineral with decreasing grain size. This is expected because finer grain sizes have a better contact with the ATR crystal. For mixtures of a single grain size, the deconvolution-modeled proportions generally matched actual proportions within 10-20%. Occasionally, the deconvolution model produced poor matches to actual mineralogy and observed spectral shape. To assess the effect of clinging fines, fine-grained (<10 μm) calcite and gypsum were added in increments from 0 to 30% to a mixture of coarsely particulate (74- 147 μm) olivine and plagioclase. The fine-grained components of these mixtures were strongly overrepresented in the model - possibly the result of non-ideal mixing and surface area dominating over volume in linear spectral addition. Increasing the weight of the GSD in the deconvolution model mitigated the overestimation of fines, but increased the RMS error of the

  9. ATR-Fourier-transform mid-infrared spectroscopy for determination of trans fatty acids in ground cereal products without oil extraction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    ATR-FTIR spectroscopy was investigated as a method for analysis of trans fatty acids (FA) in cereal products without oil extraction. Spectra were obtained with an ATR-FTIR spectrometer using ground samples pressed onto the diamond ATR surface and trans FA measured by a modification of AOAC Method 9...

  10. Protein phosphatase 5 is necessary for ATR-mediated DNA repair

    SciTech Connect

    Kang, Yoonsung; Cheong, Hyang-Min; Lee, Jung-Hee; Song, Peter I.; Lee, Kwang-Ho; Kim, Sang-Yong; Jun, Jae Yeoul; You, Ho Jin

    2011-01-07

    Research highlights: {yields} Serine/threonine protein phosphatase 5 (PP5) has been shown to participate in ataxia telangiectasia-mutated (ATM)- and ATR (ATM- and Rad3-related)-mediated checkpoint pathways, which plays an important role in the DNA damage response and maintenance of genomic stability. {yields} However, it is not clear exactly how PP5 participates in this process. {yields} Our results indicate that PP5 is more closely related with ATR-mediated pathway than ATM-mediated pathway in DNA damage repair. -- Abstract: Several recent studies have shown that protein phosphatase 5 (PP5) participates in cell cycle arrest after DNA damage, but its roles in DNA repair have not yet been fully characterized. We investigated the roles of PP5 in the repair of ultraviolet (UV)- and neocarzinostatin (NCS)-induced DNA damage. The results of comet assays revealed different repair patterns in UV- and NCS-exposed U2OS-PS cells. PP5 is only essential for Rad3-related (ATR)-mediated DNA repair. Furthermore, the phosphorylation of 53BP1 and BRCA1, important mediators of DNA damage repair, and substrates of ATR and ATM decreased in U2OS-PS cells exposed to UV radiation. In contrast, the cell cycle arrest proteins p53, CHK1, and CHK2 were normally phosphorylated in U2OS and U2OS-PS cells exposed to UV radiation or treated with NCS. In view of these results, we suggest that PP5 plays a crucial role in ATR-mediated repair of UV-induced DNA damage.

  11. Acute Transfusion Reactions (ATRs) in Intensive Care Unit (ICU): A Retrospective Study

    PubMed Central

    Kumar, Rajesh; Gupta, Manvi; Gupta, Varun; Kaur, Amarjit; Gupta, Sonia

    2014-01-01

    Background: Blood transfusion is a frequent and integral part of critical care. Although life saving, it can occasionally be unsafe and result in a spectrum of adverse events. Acute transfusion reactions (ATRs) are probably under diagnosed in critically ill patients due to confusion of the symptoms with the underlying disease. Aim: To analyze the incidence and spectrum of ATRs occuring in critically ill patients. Materials and Methods: This was a retrospective review conducted from 1st April 2011 till 31st March 2013. The ATRs related to the administration of blood components in the patients admitted in various Intensive Care Units (ICUs) were recorded, analyzed and classified on the basis of their clinical features and laboratory tests. Results: During the study period 98651 blood components were issued. Out of these 21971 were issued to various ICUs. A total of 225 transfusion reactions were reported from the various critical care departments during this period. The most frequent were Febrile Non Hemolytic Transfusion Reactions (FNHTR) 136 (60.4%), allergic reactions 70 (31.2%), hemolytic reactions 1(0.4%) and non specific reactions 18 (8%). The incidence of ATRs in our study was found to be 1.09% in adult ICUs and 0.36% in pediatric ICUs. Conclusions: Blood transfusion is a vital therapeutic procedure with a potential risk to already critical patients. So a strict vigilance has to be kept and each transfusion has to be monitored carefully with prompt recognition and treatment of ATRs. A rational use of these products considering their deleterious effects can decrease transfusion related morbidity and mortality in the critically ill patients. PMID:24701502

  12. Self-sustained operation of a kW e-class kerosene-reforming processor for solid oxide fuel cells

    NASA Astrophysics Data System (ADS)

    Yoon, Sangho; Bae, Joongmyeon; Kim, Sunyoung; Yoo, Young-Sung

    In this paper, fuel-processing technologies are developed for application in residential power generation (RPG) in solid oxide fuel cells (SOFCs). Kerosene is selected as the fuel because of its high hydrogen density and because of the established infrastructure that already exists in South Korea. A kerosene fuel processor with two different reaction stages, autothermal reforming (ATR) and adsorptive desulfurization reactions, is developed for SOFC operations. ATR is suited to the reforming of liquid hydrocarbon fuels because oxygen-aided reactions can break the aromatics in the fuel and steam can suppress carbon deposition during the reforming reaction. ATR can also be implemented as a self-sustaining reactor due to the exothermicity of the reaction. The kW e self-sustained kerosene fuel processor, including the desulfurizer, operates for about 250 h in this study. This fuel processor does not require a heat exchanger between the ATR reactor and the desulfurizer or electric equipment for heat supply and fuel or water vaporization because a suitable temperature of the ATR reformate is reached for H 2S adsorption on the ZnO catalyst beds in desulfurizer. Although the CH 4 concentration in the reformate gas of the fuel processor is higher due to the lower temperature of ATR tail gas, SOFCs can directly use CH 4 as a fuel with the addition of sufficient steam feeds (H 2O/CH 4 ≥ 1.5), in contrast to low-temperature fuel cells. The reforming efficiency of the fuel processor is about 60%, and the desulfurizer removed H 2S to a sufficient level to allow for the operation of SOFCs.

  13. Extended life aluminide fuel. Final report

    SciTech Connect

    Miller, L.G.; Beeston, J.M.

    1986-06-01

    As the price of fuel fabrication, shipment of both new and spent fuel, and fuel reprocessing continue to rise at a rapid rate, researchers look for alternate methods to keep reactor fuel costs within their limited funding. Extended fuel element lifetimes, without jeopardizing reactor safety, can reduce fuel costs by up to a factor of two. The Extended Life Aluminide (ELAF) program was started at the Idaho National Engineering Laboratory (INEL) as a joint project of the United States Department of Energy (DOE), the University of Missouri, and the Massachusetts Institute of Technology research reactors. Fuel plates of Advanced Test Reactor (ATR) type construction were fabricated at Atomics International and irradiated in the ATR at the INEL. Four fuel matrix compositions were tested (i.e., 50 vol% UAl/sub x/ cores for reference, and 40, 45 and 50 vol% UAl/sub 2/ cores). The 50 vol% UAl/sub 2/ cores contained up to 3 grams U-235 per cm/sup 3/ of core. Three plates of each composition were irradiated to peak burnup levels of 3 x 10/sup 21/ fission/cm/sup 3/ of core. The only observed damage was due to external corrosion at similar rates experienced by UAl/sub x/ fuel elements in test reactors.

  14. Decarbamoyl mitomycin C (DMC) activates p53-independent ataxia telangiectasia and rad3 related protein (ATR) chromatin eviction

    PubMed Central

    Xiao, Gu; Kue, Pao; Bhosle, Rahul; Bargonetti, Jill

    2015-01-01

    Interstrand crosslinks induce DNA replication fork stalling that in turn activates the ATR-dependent checkpoint and DNA repair on nuclear chromatin. Mitomycin C (MC) and Decarbamoyl Mitomycin C (DMC) induce different types of DNA crosslinks with DMC being a more cytotoxic agent. We previously reported that the novel DMC induced β–interstrand DNA crosslinks induce a p53-independent form of cell death. The p53-independent DMC cytotoxicity associates with the activation, and subsequent depletion, of Chk1. In this study we further dissect the novel DMC signal transduction pathway and asked how it influences chromatin-associated proteins. We found that treatment with DMC, but not MC, stimulated the disassociation of ATR from chromatin and re-localization of ATR to the cytoplasm. The chromatin eviction of ATR was coupled with the formation of nuclear Rad51 foci and the phosphorylation of Chk1. Furthermore, DMC but not MC, activated expression of gadd45α mRNA. Importantly, knocking down p53 via shRNA did not inhibit the DMC-induced disassociation of ATR from chromatin or reduce the activation of transcription of gadd45α. Our results suggest that DMC induces a p53-independent disassociation of ATR from chromatin that facilitates Chk1 checkpoint activation and Rad51 chromatin recruitment. Our findings provide evidence that ATR chromatin eviction in breast cancer cells is an area of study that should be focused on for inducing p53-independent cell death. PMID:25565400

  15. A Synthetic Lethal Screen Identifies DNA Repair Pathways that Sensitize Cancer Cells to Combined ATR Inhibition and Cisplatin Treatments

    PubMed Central

    Mohni, Kareem N.; Thompson, Petria S.; Luzwick, Jessica W.; Glick, Gloria G.; Pendleton, Christopher S.; Lehmann, Brian D.; Pietenpol, Jennifer A.; Cortez, David

    2015-01-01

    The DNA damage response kinase ATR may be a useful cancer therapeutic target. ATR inhibition synergizes with loss of ERCC1, ATM, XRCC1 and DNA damaging chemotherapy agents. Clinical trials have begun using ATR inhibitors in combination with cisplatin. Here we report the first synthetic lethality screen with a combination treatment of an ATR inhibitor (ATRi) and cisplatin. Combination treatment with ATRi/cisplatin is synthetically lethal with loss of the TLS polymerase ζ and 53BP1. Other DNA repair pathways including homologous recombination and mismatch repair do not exhibit synthetic lethal interactions with ATRi/cisplatin, even though loss of some of these repair pathways sensitizes cells to cisplatin as a single-agent. We also report that ATRi strongly synergizes with PARP inhibition, even in homologous recombination-proficient backgrounds. Lastly, ATR inhibitors were able to resensitize cisplatin-resistant cell lines to cisplatin. These data provide a comprehensive analysis of DNA repair pathways that exhibit synthetic lethality with ATR inhibitors when combined with cisplatin chemotherapy, and will help guide patient selection strategies as ATR inhibitors progress into the cancer clinic. PMID:25965342

  16. Conceptual design and selection of a biodiesel fuel processor for a vehicle fuel cell auxiliary power unit

    NASA Astrophysics Data System (ADS)

    Specchia, S.; Tillemans, F. W. A.; van den Oosterkamp, P. F.; Saracco, G.

    Within the European project BIOFEAT (biodiesel fuel processor for a fuel cell auxiliary power unit for a vehicle), a complete modular 10 kW e biodiesel fuel processor capable of feeding a PEMFC will be developed, built and tested to generate electricity for a vehicle auxiliary power unit (APU). Tail pipe emissions reduction, increased use of renewable fuels, increase of hydrogen-fuel economy and efficient supply of present and future APU for road vehicles are the main project goals. Biodiesel is the chosen feedstock because it is a completely natural and thus renewable fuel. Three fuel processing options were taken into account at a conceptual design level and compared for hydrogen production: (i) autothermal reformer (ATR) with high and low temperature shift (HTS/LTS) reactors; (ii) autothermal reformer (ATR) with a single medium temperature shift (MTS) reactor; (iii) thermal cracker (TC) with high and low temperature shift (HTS/LTS) reactors. Based on a number of simulations (with the AspenPlus® software), the best operating conditions were determined (steam-to-carbon and O 2/C ratios, operating temperatures and pressures) for each process alternative. The selection of the preferential fuel processing option was consequently carried out, based on a number of criteria (efficiency, complexity, compactness, safety, controllability, emissions, etc.); the ATR with both HTS and LTS reactors shows the most promising results, with a net electrical efficiency of 29% (LHV).

  17. Advanced Test Reactor National Scientific User Facility (ATR NSUF) Monthly Report November 2014

    SciTech Connect

    Soelberg, Renae

    2014-11-01

    Advanced Test Reactor National Scientific User Facility (ATR NSUF) Monthly Report November 2014 Highlights Rory Kennedy and Sarah Robertson attended the American Nuclear Society Winter Meeting and Nuclear Technology Expo in Anaheim, California, Nov. 10-13. ATR NSUF exhibited at the technology expo where hundreds of meeting participants had an opportunity to learn more about ATR NSUF. Dr. Kennedy briefed the Nuclear Engineering Department Heads Organization (NEDHO) on the workings of the ATR NSUF. • Rory Kennedy, James Cole and Dan Ogden participated in a reactor instrumentation discussion with Jean-Francois Villard and Christopher Destouches of CEA and several members of the INL staff. • ATR NSUF received approval from the NE-20 office to start planning the annual Users Meeting. The meeting will be held at INL, June 22-25. • Mike Worley, director of the Office of Innovative Nuclear Research (NE-42), visited INL Nov. 4-5. Milestones Completed • Recommendations for the Summer Rapid Turnaround Experiment awards were submitted to DOE-HQ Nov. 12 (Level 2 milestone due Nov. 30). Major Accomplishments/Activities • The University of California, Santa Barbara 2 experiment was unloaded from the GE-2000 at HFEF. The experiment specimen packs will be removed and shipped to ORNL for PIE. • The Terrani experiment, one of three FY 2014 new awards, was completed utilizing the Advanced Photon Source MRCAT beamline. The experiment investigated the chemical state of Ag and Pd in SiC shell of irradiated TRISO particles via X-ray Absorption Fine Structure (XAFS) spectroscopy. Upcoming Meetings/Events • The ATR NSUF program review meeting will be held Dec. 9-10 at L’Enfant Plaza. In addition to NSUF staff and users, NE-4, NE-5 and NE-7 representatives will attend the meeting. Awarded Research Projects Boise State University Rapid Turnaround Experiments (14-485 and 14-486) Nanoindentation and TEM work on the T91, HT9, HCM12A and 9Cr ODS specimens has been completed at

  18. IRRADIATION TESTING OF THE RERTR FUEL MINIPLATES WITH BURNABLE ABSORBERS IN THE ADVANCED TEST REACTOR

    SciTech Connect

    I. Glagolenko; D. Wachs; N. Woolstenhulme; G. Chang; B. Rabin; C. Clark; T. Wiencek

    2010-10-01

    Based on the results of the reactor physics assessment, conversion of the Advanced Test Reactor (ATR) at the Idaho National Laboratory (INL) can be potentially accomplished in two ways, by either using U-10Mo monolithic or U-7Mo dispersion type plates in the ATR fuel element. Both designs, however, would require incorporation of the burnable absorber in several plates of the fuel element to compensate for the excess reactivity and to flatten the radial power profile. Several different types of burnable absorbers were considered initially, but only borated compounds, such as B4C, ZrB2 and Al-B alloys, were selected for testing primarily due to the length of the ATR fuel cycle and fuel manufacturing constraints. To assess and compare irradiation performance of the U-Mo fuels with different burnable absorbers we have designed and manufactured 28 RERTR miniplates (20 fueled and 8 non-fueled) containing fore-mentioned borated compounds. These miniplates will be tested in the ATR as part of the RERTR-13 experiment, which is described in this paper. Detailed plate design, compositions and irradiations conditions are discussed.

  19. Enhanced Accident Tolerant LWR Fuels: Metrics Development

    SciTech Connect

    Shannon Bragg-Sitton; Lori Braase; Rose Montgomery; Chris Stanek; Robert Montgomery; Lance Snead; Larry Ott; Mike Billone

    2013-09-01

    The Department of Energy (DOE) Fuel Cycle Research and Development (FCRD) Advanced Fuels Campaign (AFC) is conducting research and development on enhanced Accident Tolerant Fuels (ATF) for light water reactors (LWRs). This mission emphasizes the development of novel fuel and cladding concepts to replace the current zirconium alloy-uranium dioxide (UO2) fuel system. The overall mission of the ATF research is to develop advanced fuels/cladding with improved performance, reliability and safety characteristics during normal operations and accident conditions, while minimizing waste generation. The initial effort will focus on implementation in operating reactors or reactors with design certifications. To initiate the development of quantitative metrics for ATR, a LWR Enhanced Accident Tolerant Fuels Metrics Development Workshop was held in October 2012 in Germantown, MD. This paper summarizes the outcome of that workshop and the current status of metrics development for LWR ATF.

  20. Achieving safety/risk goals for less ATR backup power upgrades

    SciTech Connect

    Atkinson, S.A.

    1995-10-01

    The Advanced Test Reactor probabilistic risk assessment for internal fire and flood events defined a relatively high risk for a total loss of electric power possibly leading to core damage. Backup power sources were disabled due to fire and flooding in the diesel generator area with propagation of the flooding to a common switchgear room. The ATR risk assessment was employed to define options for relocation of backup power system components to achieve needed risk reduction while minimizing costs. The risk evaluations were performed using sensitivity studies and importance measures. The risk-based evaluations of relocation options for backup power systems saved over $3 million from what might have been otherwise considered {open_quotes}necessary{close_quotes} for safety/risk improvement. The ATR experience shows that the advantages of a good risk assessment are to define risk significance, risk specifics, and risk solutions which enable risk goals to be achieved at the lowest cost.

  1. Phylogeny of cultivated and wild wheat species using ATR-FTIR spectroscopy

    NASA Astrophysics Data System (ADS)

    Demir, Pinar; Onde, Sertac; Severcan, Feride

    2015-01-01

    Within the last decade, an increasing amount of genetic data has been used to clarify the problems inherent in wheat taxonomy. The techniques for obtaining and analyzing these data are not only cumbersome, but also expensive and technically demanding. In the present study, we introduce infrared spectroscopy as a method for a sensitive, rapid and low cost phylogenetic analysis tool for wheat seed samples. For this purpose, 12 Triticum and Aegilops species were studied by Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) spectroscopy. Hierarchical cluster analysis and principal component analysis clearly revealed that the lignin band (1525-1505 cm-1) discriminated the species at the genus level. However, the species were clustered according to their genome commonalities when the whole spectra were used (4000-650 cm-1). The successful differentiation of Triticum and its closely related genus Aegilops clearly demonstrated the power of ATR-FTIR spectroscopy as a suitable tool for phylogenetic research.

  2. Alternative lengthening of telomeres renders cancer cells hypersensitive to ATR inhibitors.

    PubMed

    Flynn, Rachel Litman; Cox, Kelli E; Jeitany, Maya; Wakimoto, Hiroaki; Bryll, Alysia R; Ganem, Neil J; Bersani, Francesca; Pineda, Jose R; Suvà, Mario L; Benes, Cyril H; Haber, Daniel A; Boussin, Francois D; Zou, Lee

    2015-01-16

    Cancer cells rely on telomerase or the alternative lengthening of telomeres (ALT) pathway to overcome replicative mortality. ALT is mediated by recombination and is prevalent in a subset of human cancers, yet whether it can be exploited therapeutically remains unknown. Loss of the chromatin-remodeling protein ATRX associates with ALT in cancers. Here, we show that ATRX loss compromises cell-cycle regulation of the telomeric noncoding RNA TERRA and leads to persistent association of replication protein A (RPA) with telomeres after DNA replication, creating a recombinogenic nucleoprotein structure. Inhibition of the protein kinase ATR, a critical regulator of recombination recruited by RPA, disrupts ALT and triggers chromosome fragmentation and apoptosis in ALT cells. The cell death induced by ATR inhibitors is highly selective for cancer cells that rely on ALT, suggesting that such inhibitors may be useful for treatment of ALT-positive cancers. PMID:25593184

  3. An ATR-FTIR study of different phosphonic acids adsorbed onto boehmite

    NASA Astrophysics Data System (ADS)

    Zenobi, María C.; Luengo, Carina V.; Avena, Marcelo J.; Rueda, Elsa H.

    2010-04-01

    An ATR-FTIR study of the vibrational spectra of N,N-bis(2-hydroxyethyl) aminomethylphosphonic acid (BHAMP), 1-hydroxyethane-1,1'-diphosphonic acid (HEDP) and nitrilotris(methylenephosphonic acid) (NTMP) adsorbed onto boehmite is presented. The study was performed in the pH range from 5 to 9, and bands assignments are given in the 1200-900 cm -1 wavenumber range, where the bands associated with various P-O(H) vibrations can be found. The three phosphonic acids adsorb onto boehmite by forming inner-sphere surface complexes. ATR-FTIR data indicates the presence of both protonated and deprotonated mononuclear surface species. In all cases, the surface-bound ions undergo protonation reactions as pH is decreased. The results are in good agreement with previously proposed surface complexation models.

  4. An ATR-FTIR study of different phosphonic acids adsorbed onto boehmite.

    PubMed

    Zenobi, María C; Luengo, Carina V; Avena, Marcelo J; Rueda, Elsa H

    2010-04-01

    An ATR-FTIR study of the vibrational spectra of N,N-bis(2-hydroxyethyl) aminomethylphosphonic acid (BHAMP), 1-hydroxyethane-1,1'-diphosphonic acid (HEDP) and nitrilotris(methylenephosphonic acid) (NTMP) adsorbed onto boehmite is presented. The study was performed in the pH range from 5 to 9, and bands assignments are given in the 1200-900 cm(-1) wavenumber range, where the bands associated with various P-O(H) vibrations can be found. The three phosphonic acids adsorb onto boehmite by forming inner-sphere surface complexes. ATR-FTIR data indicates the presence of both protonated and deprotonated mononuclear surface species. In all cases, the surface-bound ions undergo protonation reactions as pH is decreased. The results are in good agreement with previously proposed surface complexation models. PMID:20129815

  5. Structure-Based Drug Design of Novel, Potent, and Selective Azabenzimidazoles (ABI) as ATR Inhibitors

    PubMed Central

    2014-01-01

    Compound 13 was discovered through morphing of the ATR biochemical HTS hit 1. The ABI series was potent and selective for ATR. Incorporation of a 6-azaindole afforded a marked increase in cellular potency but was associated with poor PK and hERG ion channel inhibition. DMPK experiments established that CYP P450 and AO metabolism in conjunction with Pgp and BCRP efflux were major causative mechanisms for the observed PK. The series also harbored the CYP3A4 TDI liability driven by the presence of both a morpholine and an indole moiety. Incorporation of an adjacent fluorine or nitrogen into the 6-azaindole addressed many of the various medicinal chemistry issues encountered. PMID:25589928

  6. Optimization of a Multi-Stage ATR System for Small Target Identification

    NASA Technical Reports Server (NTRS)

    Lin, Tsung-Han; Lu, Thomas; Braun, Henry; Edens, Western; Zhang, Yuhan; Chao, Tien- Hsin; Assad, Christopher; Huntsberger, Terrance

    2010-01-01

    An Automated Target Recognition system (ATR) was developed to locate and target small object in images and videos. The data is preprocessed and sent to a grayscale optical correlator (GOC) filter to identify possible regionsof- interest (ROIs). Next, features are extracted from ROIs based on Principal Component Analysis (PCA) and sent to neural network (NN) to be classified. The features are analyzed by the NN classifier indicating if each ROI contains the desired target or not. The ATR system was found useful in identifying small boats in open sea. However, due to "noisy background," such as weather conditions, background buildings, or water wakes, some false targets are mis-classified. Feedforward backpropagation and Radial Basis neural networks are optimized for generalization of representative features to reduce false-alarm rate. The neural networks are compared for their performance in classification accuracy, classifying time, and training time.

  7. Simultaneous quantification of verbenalin and verbascoside in Verbena officinalis by ATR-IR and NIR spectroscopy.

    PubMed

    Schönbichler, S A; Bittner, L K H; Pallua, J D; Popp, M; Abel, G; Bonn, G K; Huck, C W

    2013-10-01

    Attenuated-total-reflectance infrared spectroscopy (ATR-IR) and near-infrared diffuse reflectance spectroscopy (NIR) in hyphenation with multivariate analysis was utilized to quantify verbenalin and verbascoside in Verbena officinalis. A new high performance liquid chromatography (HPLC) method as a reference was established and validated. For both vibrational spectroscopic methods test-set and cross validation were performed. Different data-pre-treatments like SNV, 1st and 2nd derivative were applied to remove systematic errors and were evaluated. Quality parameters obtained for the test-set validation revealed that ATR-IR (verbenalin: R(2)=0.94, RPD=4.23; verbascoside: R(2)=0.93, RPD=3.63) has advantages over NIR (verbenalin: R(2)=0.91, RPD=3.75; verbascoside: R(2)=0.80, RPD=2.35) in the given application. PMID:23810849

  8. Optimization of Adaboost Algorithm for Sonar Target Detection in a Multi-Stage ATR System

    NASA Technical Reports Server (NTRS)

    Lin, Tsung Han (Hank)

    2011-01-01

    JPL has developed a multi-stage Automated Target Recognition (ATR) system to locate objects in images. First, input images are preprocessed and sent to a Grayscale Optical Correlator (GOC) filter to identify possible regions-of-interest (ROIs). Second, feature extraction operations are performed using Texton filters and Principal Component Analysis (PCA). Finally, the features are fed to a classifier, to identify ROIs that contain the targets. Previous work used the Feed-forward Back-propagation Neural Network for classification. In this project we investigate a version of Adaboost as a classifier for comparison. The version we used is known as GentleBoost. We used the boosted decision tree as the weak classifier. We have tested our ATR system against real-world sonar images using the Adaboost approach. Results indicate an improvement in performance over a single Neural Network design.

  9. ATR-A1 irradiation experiment on vanadium alloys and low activation steels

    SciTech Connect

    Tasi, H.; Strain, R.V.; Gomes, I.; Hins, A.G.; Smith, D.L.

    1996-04-01

    To study the mechanical properties of vanadium alloys under neutron irradiation at low temperatures, an experiment was designed and constructed for irradiation in the Advanced Test Reactor (ATR). The experiment contained Charpy, tensile, compact tension, TEM, and creep specimens of vanadium alloys. It also contained limited low-activation ferritic steel specimens as part of the collaborative agreement with Monbusho of Japan. The design irradiation temperatures for the vanadium alloy specimens in the experiment are {approx}200 and 300{degrees}C, achieved with passive gap-gap sizing and fill gas blending. To mitigate vanadium-to-chromium transmutation from the thermal neutron flux, the test specimens are contained inside gadolinium flux filters. All specimens are lithium-bonded. The irradiation started in Cycle 108A (December 3, 1995) and is expected to have a duration of three ATR cycles and a peak influence of 4.4 dpa.

  10. The life and death of ATR/sensor fusion and the hope for resurrection

    NASA Astrophysics Data System (ADS)

    Rogers, Steven K.; Sadowski, Charles; Bauer, Kenneth W.; Oxley, Mark E.; Kabrisky, Matthew; Rogers, Adam; Mott, Stephen D.

    2008-04-01

    For over half a century, scientists and engineers have worked diligently to advance computational intelligence. One application of interest is how computational intelligence can bring value to our war fighters. Automatic Target Recognition (ATR) and sensor fusion efforts have fallen far short of the desired capabilities. In this article we review the capabilities requested by war fighters. When compared to our current capabilities, it is easy to conclude current Combat Identification (CID) as a Family of Systems (FoS) does a lousy job. The war fighter needed capable, operationalized ATR and sensor fusion systems ten years ago but it did not happen. The article reviews the war fighter needs and the current state of the art. The article then concludes by looking forward to where we are headed to provide the capabilities required.

  11. Coupling of phonon-polariton modes at dielectric-dielectric interfaces by the ATR technique

    NASA Astrophysics Data System (ADS)

    Cocoletzi, G. H.; Olvera Hernández, J.; Martínez Montes, G.

    1989-08-01

    We report the calculated ATR dispersion relation of the interface phonon-polariton modes in the prism-dielectric-dielectric configuration. Comparison of electromagnetic dispersion relations (EMDR) with the ATR dispersion relations are presented for three different interfaces: I) GaAs/GaP, II) CdF2/CaF2 and III) CaF2/GaP in two propagation windows, using the Otto and Kretschmann geometries for p-polarized light. We have studied the three cases using angle and frequency scans for each window and geometry. The results indicate that it is possible to excite and detect phonon-polariton modes at the dielectric-dielectric interface.

  12. ATR, BRCA1 and gammaH2AX localize to unsynapsed chromosomes at the pachytene stage in human oocytes.

    PubMed

    Garcia-Cruz, R; Roig, I; Robles, P; Scherthan, H; Garcia Caldés, M

    2009-01-01

    Asynapsis of homologous chromosomes at the pachytene stage has been associated with gametogenic failure and infertility, but the cellular mechanisms involved are currently unknown in human meiocytes. In mice, the protein encoded by the breast-cancer susceptibility gene Brca1 has been described to direct kinase ATR (ataxia telangiectasia and Rad3 related) to any unpaired DNA at the pachytene stage, where ATR triggers H2AX phosphorylation, resulting in the silencing of those chromosomes. In this study, the distribution of ATR, BRCA1 and the phosphorylated histone gammaH2AX is assessed by immunofluorescence in human oocytes and it is found that they localize at unpaired chromosomes at the pachytene stage. Evidence is shown to propose that BRCA1, ATR and gammaH2AX in the human may be part of a system such as the one previously described in mouse, which signals unsynapsed chromosomes at pachytene and may lead to their silencing. PMID:19146767

  13. Enhanced ATR algorithm for high resolution multi-band sonar imagery

    NASA Astrophysics Data System (ADS)

    Aridgides, Tom; Fernández, Manuel

    2008-04-01

    An improved automatic target recognition (ATR) processing string has been developed. The overall processing string consists of pre-processing, subimage adaptive clutter filtering (SACF), normalization, detection, data regularization, feature extraction, optimal subset feature selection, feature orthogonalization and classification processing blocks. A new improvement was made to the processing string, data regularization, which entails computing the input data mean, clipping the data to a multiple of its mean and scaling it, prior to feature extraction. The classified objects of 3 distinct strings are fused using the classification confidence values and their expansions as features, and using "summing" or log-likelihood-ratio-test (LLRT) based fusion rules. The utility of the overall processing strings and their fusion was demonstrated with new high-resolution three-frequency band sonar imagery. The ATR processing strings were individually tuned to the corresponding three-frequency band data, making use of the new processing improvement, data regularization, which resulted in a 3:1 reduction in false alarms. Two significant fusion algorithm improvements were made. First, a nonlinear 2nd order (Volterra) feature LLRT fusion algorithm was developed. Second, a repeated application of a subset Volterra feature selection / feature orthogonalization / LLRT fusion block was utilized. It was shown that cascaded Volterra feature LLRT fusion of the ATR processing strings outperforms baseline summing and single-stage Volterra feature LLRT algorithms, yielding significant improvements over the best single ATR processing string results, and providing the capability to correctly call the majority of targets while maintaining a very low false alarm rate.

  14. ATR-FTIR spectroscopy and chemometrics: An interesting tool to discriminate and characterize counterfeit medicines.

    PubMed

    Custers, D; Cauwenbergh, T; Bothy, J L; Courselle, P; De Beer, J O; Apers, S; Deconinck, E

    2015-08-10

    Counterfeit medicines pose a huge threat to public health worldwide. High amounts of counterfeit pharmaceuticals enter the European market and therefore detection of these products is essential. Attenuated Total Reflection Fourier-Transform infrared spectroscopy (ATR-FTIR) might be useful for the screening of counterfeit medicines since it is easy to use and little sample preparation is required. Furthermore, this approach might be helpful to customs to obtain a first evaluation of suspected samples. This study proposes a combination of ATR-FTIR and chemometrics to discriminate and classify counterfeit medicines. A sample set, containing 209 samples in total, was analyzed using ATR-FTIR and the obtained spectra were used as fingerprints in the chemometric data-analysis which included Principal Component Analysis (PCA), k-Nearest Neighbours (k-NN), Classification and Regression Trees (CART) and Soft Independent Modelling of Class Analogy (SIMCA). First it was verified whether the mentioned techniques are capable to distinguish samples containing different active pharmaceutical ingredients (APIs). PCA showed a clear tendency of discrimination based on the API present; k-NN, CART and SIMCA were capable to create suitable prediction models based on the presence of different APIs. However k-NN performs the least while SIMCA performs the best. Secondly, it was tested whether these three models could be expanded to discriminate between genuine and counterfeit samples as well. k-NN was not able to make the desired discrimination and therefore it was not useful. CART performed better but also this model was less suited. SIMCA, on the other hand, resulted in a model with a 100% correct discrimination between genuine and counterfeit drugs. This study shows that chemometric analysis of ATR-FTIR fingerprints is a valuable tool to discriminate genuine from counterfeit samples and to classify counterfeit medicines. PMID:25476739

  15. The Conference Proceedings of the 2003 Air Transport Research Society (ATRS) World Conference, Volume 3

    NASA Technical Reports Server (NTRS)

    Bowen, Brent (Editor); Gudmundsson, Sveinn (Editor); Oum, Tae (Editor)

    2003-01-01

    Volume 3 of the 2003 Air Transport Reserch Society (ATRS) World Conference includes papers on topics relevant to airline operations worldwide. Specific topics include: European Union and civil aviation regimens;simulating decision making in airline operations, passenger points of view on convenient airports; route monopolies and nonlinear pricing; cooperation among airports in Europe; fleet modernizaiton in Brazil;the effects of deregulation on the growth of air transportation in Europe and the United States.

  16. The MRE11 GAR motif regulates DNA double-strand break processing and ATR activation

    PubMed Central

    Yu, Zhenbao; Vogel, Gillian; Coulombe, Yan; Dubeau, Danielle; Spehalski, Elizabeth; Hébert, Josée; Ferguson, David O; Masson, Jean Yves; Richard, Stéphane

    2012-01-01

    The MRE11/RAD50/NBS1 complex is the primary sensor rapidly recruited to DNA double-strand breaks (DSBs). MRE11 is known to be arginine methylated by PRMT1 within its glycine-arginine-rich (GAR) motif. In this study, we report a mouse knock-in allele of Mre11 that substitutes the arginines with lysines in the GAR motif and generates the MRE11RK protein devoid of methylated arginines. The Mre11RK/RK mice were hypersensitive to γ-irradiation (IR) and the cells from these mice displayed cell cycle checkpoint defects and chromosome instability. Moreover, the Mre11RK/RK MEFs exhibited ATR/CHK1 signaling defects and impairment in the recruitment of RPA and RAD51 to the damaged sites. The MRKRN complex formed and localized to the sites of DNA damage and normally activated the ATM pathway in response to IR. The MRKRN complex exhibited exonuclease and DNA-binding defects in vitro responsible for the impaired DNA end resection and ATR activation observed in vivo in response to IR. Our findings provide genetic evidence for the critical role of the MRE11 GAR motif in DSB repair, and demonstrate a mechanistic link between post-translational modifications at the MRE11 GAR motif and DSB processing, as well as the ATR/CHK1 checkpoint signaling. PMID:21826105

  17. Mismatch repair enhances convergent transcription-induced cell death at trinucleotide repeats by activating ATR.

    PubMed

    Chatterjee, Nimrat; Lin, Yunfu; Wilson, John H

    2016-06-01

    Trinucleotide repeat (TNR) expansion beyond a certain threshold results in some 20 incurable neurodegenerative disorders where disease anticipation positively correlates with repeat length. Long TNRs typically display a bias toward further expansion during germinal transmission from parents to offspring, and then are highly unstable in somatic tissues of affected individuals. Understanding mechanisms of TNR instability will provide insights into disease pathogenesis. Previously, we showed that enhanced convergent transcription at long CAG repeat tracks induces TNR instability and cell death via ATR activation. Components of TC-NER (transcription-coupled nucleotide excision repair) and RNaseH enzymes that resolve RNA/DNA hybrids oppose cell death, whereas the MSH2 component of MMR (mismatch repair) enhances cell death. The exact role of the MMR pathway during convergent transcription-induced cell death at CAG repeats is not well understood. In this study, we show that siRNA knockdowns of MMR components-MSH2, MSH3, MLHI, PMS2, and PCNA-reduce DNA toxicity. Furthermore, knockdown of MSH2, MLH1, and PMS2 significantly reduces the frequency of ATR foci formation. These observations suggest that MMR proteins activate DNA toxicity by modulating ATR foci formation during convergent transcription. PMID:27131875

  18. Phenotypic analysis of separation-of-function alleles of MEI-41, Drosophila ATM/ATR.

    PubMed Central

    Laurençon, Anne; Purdy, Amanda; Sekelsky, Jeff; Hawley, R Scott; Su, Tin Tin

    2003-01-01

    ATM/ATR kinases act as signal transducers in eukaryotic DNA damage and replication checkpoints. Mutations in ATM/ATR homologs have pleiotropic effects that range from sterility to increased killing by genotoxins in humans, mice, and Drosophila. Here we report the generation of a null allele of mei-41, Drosophila ATM/ATR homolog, and the use of it to document a semidominant effect on a larval mitotic checkpoint and methyl methanesulfonate (MMS) sensitivity. We also tested the role of mei-41 in a recently characterized checkpoint that delays metaphase/anaphase transition after DNA damage in cellular embryos. We then compare five existing mei-41 alleles to the null with respect to known phenotypes (female sterility, cell cycle checkpoints, and MMS resistance). We find that not all phenotypes are affected equally by each allele, i.e., the functions of MEI-41 in ensuring fertility, cell cycle regulation, and resistance to genotoxins are genetically separable. We propose that MEI-41 acts not in a single rigid signal transduction pathway, but in multiple molecular contexts to carry out its many functions. Sequence analysis identified mutations, which, for most alleles, fall in the poorly characterized region outside the kinase domain; this allowed us to tentatively identify additional functional domains of MEI-41 that could be subjected to future structure-function studies of this key molecule. PMID:12807779

  19. ATR-IR Investigation of Solvent Interactions with Surface-Bound Polymers

    PubMed Central

    2016-01-01

    Solvent interactions with bulk and surface-bound polymer brushes are crucial for functionalities such as controlled friction and thermoresponsive adhesion. To study such interactions, the temperature-induced solvent-quality changes and the effect of surface tethering on the mechanical and tribological properties of poly(dodecyl methacrylate) (P12MA) brushes have been investigated by means of attenuated total reflection infrared spectroscopy (ATR-IR), as well as atomic force microscopy (AFM) and lateral force microscopy (LFM). These results have been compared with temperature-dependent UV–visible spectrophotometry (UV–vis) data for the corresponding bulk polymer solutions. The ATR-IR results clearly show that increasing temperature enhances ethanol uptake in P12MA, which results in film swelling. This is accompanied by a marked increase in both adhesion and friction. We have also shown that a combination of solvents, such as toluene and ethanol, can lead to a temperature-dependent solvent partitioning within the polymer brush. To our knowledge this is the first time preferential solvent uptake in a grafted-from brush has been monitored via in situ ATR-IR. Moreover, we have observed remarkably different behavior for polymer chains in solution compared to the behavior of similar chains bound to a surface. The presented findings on the temperature-dependent solvent interactions of surface-grafted P12MA reveal previously unknown solvation phenomena and open up a range of possible applications in the area of stimuli-responsive materials. PMID:27397856

  20. Cyclohexene Photo-oxidation over Vanadia Catalyst Analyzed by Time Resolved ATR-FT-IR Spectroscopy

    SciTech Connect

    Frei, Heinz; Mul, Guido; Wasylenko, Walter; Hamdy, M. Sameh; Frei, Heinz

    2008-06-04

    Vanadia was incorporated in the 3-dimensional mesoporous material TUD-1 with a loading of 2percent w/w vanadia. The performance in the selective photo-oxidation of liquid cyclohexene was investigated using ATR-FT-IR spectroscopy. Under continuous illumination at 458 nm a significant amount of product, i.e. cyclohexenone, was identified. This demonstrates for the first time that hydroxylated vanadia centers in mesoporous materials can be activated by visible light to induce oxidation reactions. Using the rapid scan method, a strong perturbation of the vanadyl environment could be observed in the selective oxidation process induced by a 458 nm laser pulse of 480 ms duration. This is proposed to be caused by interaction of the catalytic centre with a cyclohexenyl hydroperoxide intermediate. The restoration of the vanadyl environment could be kinetically correlated to the rate of formation of cyclohexenone, and is explained by molecular rearrangement and dissociation of the peroxide to ketone and water. The ketone diffuses away from the active center and ATR infrared probing zone, resulting in a decreasing ketone signal on the tens of seconds time scale after initiation of the photoreaction. This study demonstrates the high potential of time resolved ATR FT-IR spectroscopy for mechanistic studies of liquid phase reactions by monitoring not only intermediates and products, but by correlating the temporal behavior of these species to molecular changes of the vanadyl catalytic site.

  1. Information theoretic bounds of ATR algorithm performance for sidescan sonar target classification

    NASA Astrophysics Data System (ADS)

    Myers, Vincent L.; Pinto, Marc A.

    2005-05-01

    With research on autonomous underwater vehicles for minehunting beginning to focus on cooperative and adaptive behaviours, some effort is being spent on developing automatic target recognition (ATR) algorithms that are able to operate with high reliability under a wide range of scenarios, particularly in areas of high clutter density, and without human supervision. Because of the great diversity of pattern recognition methods and continuously improving sensor technology, there is an acute requirement for objective performance measures that are independent of any particular sensor, algorithm or target definitions. This paper approaches the ATR problem from the point of view of information theory in an attempt to place bounds on the performance of target classification algorithms that are based on the acoustic shadow of proud targets. Performance is bounded by analysing the simplest of shape classification tasks, that of differentiating between a circular and square shadow, thus allowing us to isolate system design criteria and assess their effect on the overall probability of classification. The information that can be used for target recognition in sidescan sonar imagery is examined and common information theory relationships are used to derive properties of the ATR problem. Some common bounds with analytical solutions are also derived.

  2. MELT WIRE SENSORS AVAILABLE TO DETERMINE PEAK TEMPERATURES IN ATR IRRADIATION TESTING

    SciTech Connect

    K. L. Davis; D. Knudson; J. Daw; J. Palmer; J. L. Rempe

    2012-07-01

    In April 2007, the Department of Energy (DOE) designated the Advanced Test Reactor (ATR) a National Scientific User Facility (NSUF) to advance US leadership in nuclear science and technology. By attracting new users from universities, laboratories, and industry, the ATR will support basic and applied nuclear research and development and help address the nation's energy security needs. In support of this new program, the Idaho National Laboratory (INL) has developed in-house capabilities to fabricate, test, and qualify new and enhanced temperature sensors for irradiation testing. Although most efforts emphasize sensors capable of providing real-time data, selected tasks have been completed to enhance sensors provided in irradiation locations where instrumentation leads cannot be included, such as drop-in capsule and Hydraulic Shuttle Irradiation System (HSIS) or 'rabbit' locations. To meet the need for these locations, the INL has developed melt wire temperature sensors for use in ATR irradiation testing. Differential scanning calorimetry and environmental testing of prototypical sensors was used to develop a library of 28 melt wire materials, capable of detecting peak irradiation temperatures ranging from 85 to 1500°C. This paper will discuss the development work and present test results.

  3. Cancer Cells with Alternative Lengthening of Telomeres Do Not Display a General Hypersensitivity to ATR Inhibition.

    PubMed

    Deeg, Katharina I; Chung, Inn; Bauer, Caroline; Rippe, Karsten

    2016-01-01

    Telomere maintenance is a hallmark of cancer as it provides cancer cells with cellular immortality. A significant fraction of tumors uses the alternative lengthening of telomeres (ALT) pathway to elongate their telomeres and to gain an unlimited proliferation potential. Since the ALT pathway is unique to cancer cells, it represents a potentially valuable, currently unexploited target for anti-cancer therapies. Recently, it was proposed that ALT renders cells hypersensitive to ataxia telangiectasia- and RAD3-related (ATR) protein inhibitors (Flynn et al., Science 347, 273). Here, we measured the response of various ALT- or telomerase-positive cell lines to the ATR inhibitor VE-821. In addition, we compared the effect of the inhibitor on cell viability in isogenic cell lines, in which ALT was active or suppressed. In these experiments, a general ATR inhibitor sensitivity of cells with ALT could not be confirmed. We rather propose that the observed variations in sensitivity reflect differences between cell lines that are unrelated to ALT. PMID:27602331

  4. Cancer Cells with Alternative Lengthening of Telomeres Do Not Display a General Hypersensitivity to ATR Inhibition

    PubMed Central

    Deeg, Katharina I.; Chung, Inn; Bauer, Caroline; Rippe, Karsten

    2016-01-01

    Telomere maintenance is a hallmark of cancer as it provides cancer cells with cellular immortality. A significant fraction of tumors uses the alternative lengthening of telomeres (ALT) pathway to elongate their telomeres and to gain an unlimited proliferation potential. Since the ALT pathway is unique to cancer cells, it represents a potentially valuable, currently unexploited target for anti-cancer therapies. Recently, it was proposed that ALT renders cells hypersensitive to ataxia telangiectasia- and RAD3-related (ATR) protein inhibitors (Flynn et al., Science 347, 273). Here, we measured the response of various ALT- or telomerase-positive cell lines to the ATR inhibitor VE-821. In addition, we compared the effect of the inhibitor on cell viability in isogenic cell lines, in which ALT was active or suppressed. In these experiments, a general ATR inhibitor sensitivity of cells with ALT could not be confirmed. We rather propose that the observed variations in sensitivity reflect differences between cell lines that are unrelated to ALT. PMID:27602331

  5. FTIR-ATR spectroscopy applied to quality control of grape-derived spirits.

    PubMed

    Anjos, Ofélia; Santos, António J A; Estevinho, Letícia M; Caldeira, Ilda

    2016-08-15

    The Fourier transform infrared (FTIR) spectroscopic method with attenuated total reflectance (ATR) was used for predicting the alcoholic strength, the methanol, acetaldehyde and fusel alcohols content of grape-derived spirits. FTIR-ATR spectrum in the mid-IR region (4000-400 cm(-1)) was used for the quantitative estimation by applying partial least square (PLS) regression models and the results were correlated with those obtained from reference methods. In the developed method, a cross-validation with 50% of the samples was used for PLS analysis along with a validation test set with 50% of the remaining samples. Good correlation models with a great accuracy were obtained for methanol (r(2)=99.4; RPD=12.8), alcoholic strength (r(2)=97.2; RPD=6.0), acetaldehyde (r(2)=98.2; RPD=7.5) and fusel alcohols (r(2) from 97.4 to 94.1; RPD from 6.2 to 4.1). These results corroborate the hypothesis that FTIR-ATR is a useful technique for the quality control of grape-derived spirits, whose practical application may improve the efficiency and quickness of the current laboratory analysis. PMID:27006210

  6. ATR-IR Investigation of Solvent Interactions with Surface-Bound Polymers.

    PubMed

    Mathis, Christian H; Divandari, Mohammad; Simic, Rok; Naik, Vikrant V; Benetti, Edmondo M; Isa, Lucio; Spencer, Nicholas D

    2016-08-01

    Solvent interactions with bulk and surface-bound polymer brushes are crucial for functionalities such as controlled friction and thermoresponsive adhesion. To study such interactions, the temperature-induced solvent-quality changes and the effect of surface tethering on the mechanical and tribological properties of poly(dodecyl methacrylate) (P12MA) brushes have been investigated by means of attenuated total reflection infrared spectroscopy (ATR-IR), as well as atomic force microscopy (AFM) and lateral force microscopy (LFM). These results have been compared with temperature-dependent UV-visible spectrophotometry (UV-vis) data for the corresponding bulk polymer solutions. The ATR-IR results clearly show that increasing temperature enhances ethanol uptake in P12MA, which results in film swelling. This is accompanied by a marked increase in both adhesion and friction. We have also shown that a combination of solvents, such as toluene and ethanol, can lead to a temperature-dependent solvent partitioning within the polymer brush. To our knowledge this is the first time preferential solvent uptake in a grafted-from brush has been monitored via in situ ATR-IR. Moreover, we have observed remarkably different behavior for polymer chains in solution compared to the behavior of similar chains bound to a surface. The presented findings on the temperature-dependent solvent interactions of surface-grafted P12MA reveal previously unknown solvation phenomena and open up a range of possible applications in the area of stimuli-responsive materials. PMID:27397856

  7. Caenorhabditis elegans ATR checkpoint kinase ATL-1 influences life span through mitochondrial maintenance.

    PubMed

    Suetomi, Kazuhiro; Mereiter, Stefan; Mori, Chihiro; Takanami, Takako; Higashitani, Atsushi

    2013-11-01

    ATR is highly conserved in all eukaryotes and functions as a cell-cycle nuclear checkpoint kinase. In mammals, ATR is essential whose complete absence results in early embryonic lethality and its hypomorphic mutation causes a complex disease known as Seckel syndrome. However, molecular mechanisms that cause a wide variety of symptoms including accelerated aging have remained unclear. Similarly, in the nematode Caenorhabditis elegans, a deletion mutant of ATR ortholog atl-1 appears to develop into normal adults, but their eggs do not hatch and die at early embryogenesis. Here we show that the parental worms of atl-1 defective mutant achieved longevity. Transcription levels of certain superoxide dismutase genes, sod-3 and -5 and enzymatic activity of superoxide dismutases significantly increased in the mutant. Furthermore, lipid peroxidation such as a formation of malondialdehyde was attenuated. Expressions of other genes regulated by DAF-16/FOXO transcription factor were also altered. In contrast, the mutant became hypersensitive to rotenone and ethidium bromide. Compared with the wild type the mitochondrial DNA copy number in the mutant was lesser and its proliferation is more severely inhibited in the presence of rotenone. These results suggest that C. elegans ATL-1 is involved not only in the nuclear checkpoint control but also in the mitochondrial maintenance, and its dysfunction activates mild oxidative stress response, resulting in an alteration of life span. PMID:23434802

  8. Identification and evaluation of a potent novel ATR inhibitor, NU6027, in breast and ovarian cancer cell lines

    PubMed Central

    Peasland, A; Wang, L-Z; Rowling, E; Kyle, S; Chen, T; Hopkins, A; Cliby, W A; Sarkaria, J; Beale, G; Edmondson, R J; Curtin, N J

    2011-01-01

    Background: The ataxia telangiectasia mutated and Rad3-related kinase (ATR) has a key role in the signalling of stalled replication forks and DNA damage to cell cycle checkpoints and DNA repair. It has long been recognised as an important target for cancer therapy but inhibitors have proved elusive. As NU6027, originally developed as a CDK2 inhibitor, potentiated cisplatin in a CDK2-independent manner we postulated that it may inhibit ATR. Methods: Cellular ATR kinase activity was determined by CHK1 phosphorylation in human fibroblasts with inducible dominant-negative ATR-kinase dead expression and human breast cancer MCF7 cells. Cell cycle effects and chemo- and radiopotentiation by NU6027 were determined in MCF7 cells and the role of mismatch repair and p53 was determined in isogenically matched ovarian cancer A2780 cells. Results: NU6027 is a potent inhibitor of cellular ATR activity (IC50=6.7 μ) and enhanced hydroxyurea and cisplatin cytotoxicity in an ATR-dependent manner. NU6027 attenuated G2/M arrest following DNA damage, inhibited RAD51 focus formation and increased the cytotoxicity of the major classes of DNA-damaging anticancer cytotoxic therapy but not the antimitotic, paclitaxel. In A2780 cells sensitisation to cisplatin was greatest in cells with functional p53 and mismatch repair (MMR) and sensitisation to temozolomide was greatest in p53 mutant cells with functional MMR. Importantly, NU6027 was synthetically lethal when DNA single-strand break repair is impaired either through poly(ADP-ribose) polymerase (PARP) inhibition or defects in XRCC1. Conclusion: NU6027 inhibits ATR, impairing G2/M arrest and homologous recombination thus increasing sensitivity to DNA-damaging agents and PARP inhibitors. It provides proof of concept data for clinical development of ATR inhibitors. PMID:21730979

  9. Multi-fuel reformers for fuel cells used in transportation. Phase 1: Multi-fuel reformers

    NASA Astrophysics Data System (ADS)

    1994-05-01

    DOE has established the goal, through the Fuel Cells in Transportation Program, of fostering the rapid development and commercialization of fuel cells as economic competitors for the internal combustion engine. Central to this goal is a safe feasible means of supplying hydrogen of the required purity to the vehicular fuel cell system. Two basic strategies are being considered: (1) on-board fuel processing whereby alternative fuels such as methanol, ethanol or natural gas stored on the vehicle undergo reformation and subsequent processing to produce hydrogen, and (2) on-board storage of pure hydrogen provided by stationary fuel processing plants. This report analyzes fuel processor technologies, types of fuel and fuel cell options for on-board reformation. As the Phase 1 of a multi-phased program to develop a prototype multi-fuel reformer system for a fuel cell powered vehicle, the objective of this program was to evaluate the feasibility of a multi-fuel reformer concept and to select a reforming technology for further development in the Phase 2 program, with the ultimate goal of integration with a DOE-designated fuel cell and vehicle configuration. The basic reformer processes examined in this study included catalytic steam reforming (SR), non-catalytic partial oxidation (POX) and catalytic partial oxidation (also known as Autothermal Reforming, or ATR). Fuels under consideration in this study included methanol, ethanol, and natural gas. A systematic evaluation of reforming technologies, fuels, and transportation fuel cell applications was conducted for the purpose of selecting a suitable multi-fuel processor for further development and demonstration in a transportation application.

  10. A Genome-wide CRISPR Screen Identifies CDC25A as a Determinant of Sensitivity to ATR Inhibitors.

    PubMed

    Ruiz, Sergio; Mayor-Ruiz, Cristina; Lafarga, Vanesa; Murga, Matilde; Vega-Sendino, Maria; Ortega, Sagrario; Fernandez-Capetillo, Oscar

    2016-04-21

    One recurring theme in drug development is to exploit synthetic lethal properties as means to preferentially damage the DNA of cancer cells. We and others have previously developed inhibitors of the ATR kinase, shown to be particularly genotoxic for cells expressing certain oncogenes. In contrast, the mechanisms of resistance to ATR inhibitors remain unexplored. We report here on a genome-wide CRISPR-Cas9 screen that identified CDC25A as a major determinant of sensitivity to ATR inhibition. CDC25A-deficient cells resist high doses of ATR inhibitors, which we show is due to their failure to prematurely enter mitosis in response to the drugs. Forcing mitotic entry with WEE1 inhibitors restores the toxicity of ATR inhibitors in CDC25A-deficient cells. With ATR inhibitors now entering the clinic, our work provides a better understanding of the mechanisms by which these compounds kill cells and reveals genetic interactions that could be used for their rational use. PMID:27067599

  11. ATR-Chk1 signaling inhibition as a therapeutic strategy to enhance cisplatin chemosensitivity in urothelial bladder cancer

    PubMed Central

    Lu, Mei-Chin; Lee, Chia-Lin; Peng, Chieh-Yu; Hsu, Wei-Yu; Dai, Yun-Hao; Chang, Fang-Rong; Zhang, Da-Yong; Wu, Wen-Jeng; Wu, Yang-Chang

    2016-01-01

    DNA damage responses contribute to cisplatin resistance; however, therapeutic strategies to overcome cisplatin resistance have not yet been established. Here, we demonstrate that inhibition of ATR-Chk1 pathway with the potent inhibitor WYC0209 sensitizes bladder cancer cells to cisplatin. In the clinical microarray profile, high ATR expression is associated with poor prognosis in bladder cancer patients who receive chemotherapy. We show that pharmacological and genetic suppressing of ATR sensitized cells to cisplatin. Treatment with WYC0209 or siATR increased levels of cisplatin-DNA adducts, concomitant with decreased levels of p-glycoprotein expression. Additionally, Combinations of cisplatin and WYC0209 show synergistic activity against bladder cancer. Ultimately, WYC0209 enhanced the anti-tumor effects of cisplatin and suppressed p-glycoprotein expression in bladder cancer xenografts. These results indicate that inhibiting ATR-Chk1 activation with WYC0209 suppresses p-glycoprotein expression and increases cisplatin activity in bladder cancer. Our findings collectively suggest that ATR-Chk1 is a target for improving the efficacy of cisplatin in bladder cancer. PMID:26657501

  12. Opportunities for mixed oxide fuel testing in the advanced test reactor to support plutonium disposition

    SciTech Connect

    Terry, W.K.; Ryskamp, J.M.; Sterbentz, J.W.

    1995-08-01

    Numerous technical issues must be resolved before LWR operating licenses can be amended to allow the use of MOX fuel. These issues include the following: (1) MOX fuel fabrication process verification; (2) Whether and how to use burnable poisons to depress MOX fuel initial reactivity, which is higher than that of urania; (3) The effects of WGPu isotopic composition; (4) The feasibility of loading MOX fuel with plutonia content up to 7% by weight; (5) The effects of americium and gallium in WGPu; (6) Fission gas release from MOX fuel pellets made from WGPu; (7) Fuel/cladding gap closure; (8) The effects of power cycling and off-normal events on fuel integrity; (9) Development of radial distributions of burnup and fission products; (10) Power spiking near the interfaces of MOX and urania fuel assemblies; and (11) Fuel performance code validation. The Advanced Test Reactor (ATR) at the Idaho National Engineering Laboratory possesses many advantages for performing tests to resolve most of the issues identified above. We have performed calculations to show that the use of hafnium shrouds can produce spectrum adjustments that will bring the flux spectrum in ATR test loops into a good approximation to the spectrum anticipated in a commercial LWR containing MOX fuel while allowing operation of the test fuel assemblies near their optimum values of linear heat generation rate. The ATR would be a nearly ideal test bed for developing data needed to support applications to license LWRs for operation with MOX fuel made from weapons-grade plutonium. The requirements for planning and implementing a test program in the ATR have been identified. The facilities at Argonne National Laboratory-West can meet all potential needs for pre- and post-irradiation examination that might arise in a MOX fuel qualification program.

  13. A feasibility and optimization study to determine cooling time and burnup of advanced test reactor fuels using a nondestructive technique

    SciTech Connect

    Navarro, Jorge

    2013-12-01

    The goal of this study presented is to determine the best available non-destructive technique necessary to collect validation data as well as to determine burn-up and cooling time of the fuel elements onsite at the Advanced Test Reactor (ATR) canal. This study makes a recommendation of the viability of implementing a permanent fuel scanning system at the ATR canal and leads3 to the full design of a permanent fuel scan system. The study consisted at first in determining if it was possible and which equipment was necessary to collect useful spectra from ATR fuel elements at the canal adjacent to the reactor. Once it was establish that useful spectra can be obtained at the ATR canal the next step was to determine which detector and which configuration was better suited to predict burnup and cooling time of fuel elements non-destructively. Three different detectors of High Purity Germanium (HPGe), Lanthanum Bromide (LaBr3), and High Pressure Xenon (HPXe) in two system configurations of above and below the water pool were used during the study. The data collected and analyzed was used to create burnup and cooling time calibration prediction curves for ATR fuel. The next stage of the study was to determine which of the three detectors tested was better suited for the permanent system. From spectra taken and the calibration curves obtained, it was determined that although the HPGe detector yielded better results, a detector that could better withstand the harsh environment of the ATR canal was needed. The in-situ nature of the measurements required a rugged fuel scanning system, low in maintenance and easy to control system. Based on the ATR canal feasibility measurements and calibration results it was determined that the LaBr3 detector was the best alternative for canal in-situ measurements; however in order to enhance the quality of the spectra collected using this scintillator a deconvolution method was developed. Following the development of the deconvolution method

  14. AGR-2 Data Qualification Report for ATR Cycles 149B, 150A, 150B, 151A, and 151B

    SciTech Connect

    Michael L. Abbott; Binh T. Pham

    2012-06-01

    This report provides the data qualification status of AGR-2 fuel irradiation experimental data from Advanced Test Reactor (ATR) cycles 149B, 150A, 150B, 151A, and 151B), as recorded in the Nuclear Data Management and Analysis System (NDMAS). The AGR-2 data streams addressed include thermocouple temperatures, sweep gas data (flow rate, pressure, and moisture content), and fission product monitoring system (FPMS) data for each of the six capsules in the experiment. A total of 3,307,500 5-minute thermocouple and sweep gas data records were received and processed by NDMAS for this period. There are no AGR-2 data for cycle 150A because the experiment was removed from the reactor. Of these data, 82.2% were determined to be Qualified based on NDMAS accuracy testing and data validity assessment. There were 450,557 Failed temperature records due to thermocouple failures, and 138,528 Failed gas flow records due to gas flow cross-talk and leakage problems that occurred in the capsules after cycle 150A. For FPMS data, NDMAS received and processed preliminary release rate and release-to-birth rate ratio (R/B) data for the first three reactor cycles (cycles 149B, 150B, and 151B). This data consists of 45,983 release rate records and 45,235 R/B records for the 12 radionuclides reported. The qualification status of these FPMS data has been set to In Process until receipt of QA-approved data generator reports. All of the above data have been processed and tested using a SAS®-based enterprise application software system, stored in a secure Structured Query Language database, and made available on the NDMAS Web portal (http://ndmas.inl.gov) for both internal and external VHTR project participants.

  15. Modeling a 5 kWe planar solid oxide fuel cell based system operating on JP-8 fuel and a comparison with tubular cell based system for auxiliary and mobile power applications

    NASA Astrophysics Data System (ADS)

    Tanim, Tanvir; Bayless, David J.; Trembly, Jason P.

    2014-01-01

    A steady state planar solid oxide fuel cell (P-SOFC) based system operating on desulfurized JP-8 fuel was modeled using Aspen Plus simulation software for auxiliary and mobile power applications. An onboard autothermal reformer (ATR) employed to reform the desulfurized JP-8 fuel was coupled with the P-SOFC stack to provide for H2 and CO as fuel, minimizing the cost and complexity associated with hydrogen storage. Characterization of the ATR reformer was conducted by varying the steam to carbon ratio (H2O/C) from 0.1 to 1.0 at different ATR operating temperatures (700-800 °C) while maintaining the P-SOFC stack temperature at 850 °C. A fraction of the anode recycle was used as the steam and heat source for autothermal reforming of the JP-8 fuel, intending to make the system lighter and compact for mobile applications. System modeling revealed a maximum net AC efficiency of 37.1% at 700 °C and 29.2% at 800 °C ATR operating temperatures, respectively. Parametric analyses with respect to fuel utilization factor (Uf) and current density (j) were conducted to determine optimum operating conditions. Finally, the P-SOFC based system was compared with a previously published [1] tubular solid oxide fuel cell based (T-SOFC) system to identify the relative advantages over one another.

  16. Molecular cloning of AtRS4, a seed specific multifunctional RFO synthase/galactosylhydrolase in Arabidopsis thaliana

    PubMed Central

    Gangl, Roman; Behmüller, Robert; Tenhaken, Raimund

    2015-01-01

    Stachyose is among the raffinose family oligosaccharides (RFOs) one of the major water-soluble carbohydrates next to sucrose in seeds of a number of plant species. Especially in leguminous seeds, e.g. chickpea, stachyose is reported as the major component. In contrast to their ambiguous potential as essential source of carbon for germination, RFOs are indigestible for humans and can contribute to diverse abdominal disorders. In the genome of Arabidopsis thaliana, six putative raffinose synthase genes are reported, whereas little is known about these putative raffinose synthases and their biochemical characteristics or their contribution to the RFO physiology in A. thaliana. In this paper, we report on the molecular cloning, functional expression in Escherichia coli and purification of recombinant AtRS4 from A. thaliana and the biochemical characterisation of the putative stachyose synthase (AtSTS, At4g01970) as a raffinose and high affinity stachyose synthase (Km for raffinose 259.2 ± 21.15 μM) as well as stachyose and galactinol specific galactosylhydrolase. A T-DNA insertional mutant in the AtRS4 gene was isolated. Only semi-quantitative PCR from WT siliques showed a specific transcriptional AtRS4 PCR product. Metabolite measurements in seeds of ΔAtRS4 mutant plants revealed a total loss of stachyose in ΔAtRS4 mutant seeds. We conclude that AtRS4 is the only stachyose synthase in the genome of A. thaliana that AtRS4 represents a key regulation mechanism in the RFO physiology of A. thaliana due to its multifunctional enzyme activity and that AtRS4 is possibly the second seed specific raffinose synthase beside AtRS5, which is responsible for Raf accumulation under abiotic stress. PMID:26483807

  17. Molecular cloning of AtRS4, a seed specific multifunctional RFO synthase/galactosylhydrolase in Arabidopsis thaliana.

    PubMed

    Gangl, Roman; Behmüller, Robert; Tenhaken, Raimund

    2015-01-01

    Stachyose is among the raffinose family oligosaccharides (RFOs) one of the major water-soluble carbohydrates next to sucrose in seeds of a number of plant species. Especially in leguminous seeds, e.g. chickpea, stachyose is reported as the major component. In contrast to their ambiguous potential as essential source of carbon for germination, RFOs are indigestible for humans and can contribute to diverse abdominal disorders. In the genome of Arabidopsis thaliana, six putative raffinose synthase genes are reported, whereas little is known about these putative raffinose synthases and their biochemical characteristics or their contribution to the RFO physiology in A. thaliana. In this paper, we report on the molecular cloning, functional expression in Escherichia coli and purification of recombinant AtRS4 from A. thaliana and the biochemical characterisation of the putative stachyose synthase (AtSTS, At4g01970) as a raffinose and high affinity stachyose synthase (Km for raffinose 259.2 ± 21.15 μM) as well as stachyose and galactinol specific galactosylhydrolase. A T-DNA insertional mutant in the AtRS4 gene was isolated. Only semi-quantitative PCR from WT siliques showed a specific transcriptional AtRS4 PCR product. Metabolite measurements in seeds of ΔAtRS4 mutant plants revealed a total loss of stachyose in ΔAtRS4 mutant seeds. We conclude that AtRS4 is the only stachyose synthase in the genome of A. thaliana that AtRS4 represents a key regulation mechanism in the RFO physiology of A. thaliana due to its multifunctional enzyme activity and that AtRS4 is possibly the second seed specific raffinose synthase beside AtRS5, which is responsible for Raf accumulation under abiotic stress. PMID:26483807

  18. ATR- and ATM-Mediated DNA Damage Response Is Dependent on Excision Repair Assembly during G1 but Not in S Phase of Cell Cycle.

    PubMed

    Ray, Alo; Blevins, Chessica; Wani, Gulzar; Wani, Altaf A

    2016-01-01

    Cell cycle checkpoint is mediated by ATR and ATM kinases, as a prompt early response to a variety of DNA insults, and culminates in a highly orchestrated signal transduction cascade. Previously, we defined the regulatory role of nucleotide excision repair (NER) factors, DDB2 and XPC, in checkpoint and ATR/ATM-dependent repair pathway via ATR and ATM phosphorylation and recruitment to ultraviolet radiation (UVR)-induced damage sites. Here, we have dissected the molecular mechanisms of DDB2- and XPC- mediated regulation of ATR and ATM recruitment and activation upon UVR exposures. We show that the ATR and ATM activation and accumulation to UVR-induced damage not only depends on DDB2 and XPC, but also on the NER protein XPA, suggesting that the assembly of an active NER complex is essential for ATR and ATM recruitment. ATR and ATM localization and H2AX phosphorylation at the lesion sites occur as early as ten minutes in asynchronous as well as G1 arrested cells, showing that repair and checkpoint-mediated by ATR and ATM starts early upon UV irradiation. Moreover, our results demonstrated that ATR and ATM recruitment and H2AX phosphorylation are dependent on NER proteins in G1 phase, but not in S phase. We reasoned that in G1 the UVR-induced ssDNA gaps or processed ssDNA, and the bound NER complex promote ATR and ATM recruitment. In S phase, when the UV lesions result in stalled replication forks with long single-stranded DNA, ATR and ATM recruitment to these sites is regulated by different sets of proteins. Taken together, these results provide evidence that UVR-induced ATR and ATM recruitment and activation differ in G1 and S phases due to the existence of distinct types of DNA lesions, which promote assembly of different proteins involved in the process of DNA repair and checkpoint activation. PMID:27442013

  19. ATR- and ATM-Mediated DNA Damage Response Is Dependent on Excision Repair Assembly during G1 but Not in S Phase of Cell Cycle

    PubMed Central

    Ray, Alo; Blevins, Chessica; Wani, Gulzar; Wani, Altaf A.

    2016-01-01

    Cell cycle checkpoint is mediated by ATR and ATM kinases, as a prompt early response to a variety of DNA insults, and culminates in a highly orchestrated signal transduction cascade. Previously, we defined the regulatory role of nucleotide excision repair (NER) factors, DDB2 and XPC, in checkpoint and ATR/ATM-dependent repair pathway via ATR and ATM phosphorylation and recruitment to ultraviolet radiation (UVR)-induced damage sites. Here, we have dissected the molecular mechanisms of DDB2- and XPC- mediated regulation of ATR and ATM recruitment and activation upon UVR exposures. We show that the ATR and ATM activation and accumulation to UVR-induced damage not only depends on DDB2 and XPC, but also on the NER protein XPA, suggesting that the assembly of an active NER complex is essential for ATR and ATM recruitment. ATR and ATM localization and H2AX phosphorylation at the lesion sites occur as early as ten minutes in asynchronous as well as G1 arrested cells, showing that repair and checkpoint-mediated by ATR and ATM starts early upon UV irradiation. Moreover, our results demonstrated that ATR and ATM recruitment and H2AX phosphorylation are dependent on NER proteins in G1 phase, but not in S phase. We reasoned that in G1 the UVR-induced ssDNA gaps or processed ssDNA, and the bound NER complex promote ATR and ATM recruitment. In S phase, when the UV lesions result in stalled replication forks with long single-stranded DNA, ATR and ATM recruitment to these sites is regulated by different sets of proteins. Taken together, these results provide evidence that UVR-induced ATR and ATM recruitment and activation differ in G1 and S phases due to the existence of distinct types of DNA lesions, which promote assembly of different proteins involved in the process of DNA repair and checkpoint activation. PMID:27442013

  20. Root discrimination of closely related crop and weed species using FT MIR-ATR spectroscopy

    PubMed Central

    Meinen, Catharina; Rauber, Rolf

    2015-01-01

    Root discrimination of species is a pre-condition for studying belowground competition processes between crop and weed species. In this experiment, we tested Fourier transform mid-infrared (FT MIR)-attenuated total reflection (ATR) spectroscopy to discriminate roots of closely related crop and weed species grown in the greenhouse: maize/barnyard grass, barley/wild oat, wheat/blackgrass (Poaceae), and sugar beet/common lambsquarters (Chenopodiaceae). Fresh (moist) and dried root segments as well as ground roots were analyzed by FT MIR-ATR spectroscopy. Root absorption spectra showed species specific peak distribution and peak height. A clear separation according to species was not possible with fresh root segments. Dried root segments (including root basis, middle section, and root tip) of maize/barnyard grass and sugar beet/common lambsquarters formed completely separated species clusters. Wheat and blackgrass separated in species specific clusters when root tips were removed from cluster analysis. A clear separation of dried root segments according to species was not possible in the case of barley and wild oat. Cluster analyses of ground roots revealed a 100% separation of all tested crop and weed species combinations. Spectra grouped in Poaceae and Chenopodiaceae clusters. Within the Poaceae cluster, C3 and C4 species differed significantly in heterogeneity. Thus, root spectra reflected the degree of kinship. To quantify species proportion in root mixtures, a two- and a three-species model for species quantification in root mixtures of maize, barnyard grass, and wild oat was calculated. The models showed low standard errors of prediction (RMSEP) and high residual predictive deviation values in an external test set validation. Hence, FT MIR-ATR spectroscopy seems to be a promising tool for root research even between closely related plant species. PMID:26483799

  1. Radiosensitization of Human Leukemic HL-60 Cells by ATR Kinase Inhibitor (VE-821): Phosphoproteomic Analysis

    PubMed Central

    Šalovská, Barbora; Fabrik, Ivo; Ďurišová, Kamila; Link, Marek; Vávrová, Jiřina; Řezáčová, Martina; Tichý, Aleš

    2014-01-01

    DNA damaging agents such as ionizing radiation or chemotherapy are frequently used in oncology. DNA damage response (DDR)—triggered by radiation-induced double strand breaks—is orchestrated mainly by three Phosphatidylinositol 3-kinase-related kinases (PIKKs): Ataxia teleangiectasia mutated (ATM), DNA-dependent protein kinase (DNA-PK) and ATM and Rad3-related kinase (ATR). Their activation promotes cell-cycle arrest and facilitates DNA damage repair, resulting in radioresistance. Recently developed specific ATR inhibitor, VE-821 (3-amino-6-(4-(methylsulfonyl)phenyl)-N-phenylpyrazine-2-carboxamide), has been reported to have a significant radio- and chemo-sensitizing effect delimited to cancer cells (largely p53-deficient) without affecting normal cells. In this study, we employed SILAC-based quantitative phosphoproteomics to describe the mechanism of the radiosensitizing effect of VE-821 in human promyelocytic leukemic cells HL-60 (p53-negative). Hydrophilic interaction liquid chromatography (HILIC)-prefractionation with TiO2-enrichment and nano-liquid chromatography—tandem mass spectrometry (LC-MS/MS) analysis revealed 9834 phosphorylation sites. Proteins with differentially up-/down-regulated phosphorylation were mostly localized in the nucleus and were involved in cellular processes such as DDR, all phases of the cell cycle, and cell division. Moreover, sequence motif analysis revealed significant changes in the activities of kinases involved in these processes. Taken together, our data indicates that ATR kinase has multiple roles in response to DNA damage throughout the cell cycle and that its inhibitor VE-821 is a potent radiosensitizing agent for p53-negative HL-60 cells. PMID:25003641

  2. Cleaning-in-place of immunoaffinity resins monitored by in situ ATR-FTIR spectroscopy.

    PubMed

    Boulet-Audet, Maxime; Byrne, Bernadette; Kazarian, Sergei G

    2015-09-01

    In the next 10 years, the pharmaceutical industry anticipates that revenue from biotherapeutics will overtake those generated from small drug molecules. Despite effectively treating a range of chronic and life-threatening diseases, the high cost of biotherapeutics limits their use. For biotherapeutic monoclonal antibodies (mAbs), an important production cost is the affinity resin used for protein capture. Cleaning-in-place (CIP) protocols aim to optimise the lifespan of the resin by slowing binding capacity decay. Binding assays can determine resin capacity from the mobile phase, but do not reveal the underlying causes of Protein A ligand degradation. The focus needs to be on the stationary phase to examine the effect of CIP on the resin. To directly determine both the local Protein A ligand concentration and conformation on two Protein A resins, we developed a method based on attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy. ATR-FTIR spectroscopic imaging revealed that applying a carefully controlled load to agarose beads produces an even and reproducible contact with the internal reflection element. This allowed detection and quantification of the binding capacity of the stationary phase. ATR-FTIR spectroscopy also showed that Protein A proteolysis does not seem to occur under typical CIP conditions (below 1 M NaOH). However, our data revealed that concentrations of NaOH above 0.1 M cause significant changes in Protein A conformation. The addition of >0.4 M trehalose during CIP significantly reduced NaOH-induced ligand unfolding observed for one of the two Protein A resins tested. Such insights could help to optimise CIP protocols in order to extend resin lifetime and reduce mAb production costs. PMID:26159572

  3. ATR-FTIR spectroscopy: a chemometric approach for studying the lipid organisation of the stratum corneum.

    PubMed

    Laugel, C; Yagoubi, N; Baillet, A

    2005-05-01

    The barrier function of skin resides in the lipid components of the stratum corneum, particularly their spatial organisation. FTIR spectroscopy has already been used as a relevant tool to study this lipid organisation: IR vibration band shifts have been attributed to the variations in lipid organisation induced by temperature. Our study included a stratum corneum model, composed of the three main lipids: palmitic acid as an example of fatty acids, cholesterol and ceramide III as an example of ceramide. Different films with various ratios of these lipids were studied. In our analytical strategy, the interest of using a chemometric analysis of global data obtained from ATR-FTIR spectra to highlight the main interactions involved in the molecular organisation of lipids has been demonstrated. Two kinds of interaction between the three main lipids have been shown: a non polar interaction between the long hydrocarbon chains and a polar interaction as the hydrogen bonding between polar functional groups. By varying the lipid ratio, we have shown first that the relative importance of each interaction was modified, second, that the induced modification of organisation can be detected by chemometric analysis of the ATR-FTIR spectra. The role of each kind of lipid in the organisation has been discussed. In conclusion, associating the ATR-FTIR with chemometric treatment is a promising tool: firstly, to understand the consequence of lipid relative compositions on the structural organisation of the stratum corneum, secondly, to show the relationship between lipid organisation and percutaneous penetration data. Indeed, this methodology will be transposed to in vivo studies with IR measurements through a probe. PMID:15854625

  4. Competitive sorption of carbonate and arsenic to hematite: combined ATR-FTIR and batch experiments.

    PubMed

    Brechbühl, Yves; Christl, Iso; Elzinga, Evert J; Kretzschmar, Ruben

    2012-07-01

    The competitive sorption of carbonate and arsenic to hematite was investigated in closed-system batch experiments. The experimental conditions covered a pH range of 3-7, arsenate concentrations of 3-300 μM, and arsenite concentrations of 3-200 μM. Dissolved carbonate concentrations were varied by fixing the CO(2) partial pressure at 0.39 (atmospheric), 10, or 100 hPa. Sorption data were modeled with a one-site three plane model considering carbonate and arsenate surface complexes derived from ATR-FTIR spectroscopy analyses. Macroscopic sorption data revealed that in the pH range 3-7, carbonate was a weak competitor for both arsenite and arsenate. The competitive effect of carbonate increased with increasing CO(2) partial pressure and decreasing arsenic concentrations. For arsenate, sorption was reduced by carbonate only at slightly acidic to neutral pH values, whereas arsenite sorption was decreased across the entire pH range. ATR-FTIR spectra indicated the predominant formation of bidentate binuclear inner-sphere surface complexes for both sorbed arsenate and sorbed carbonate. Surface complexation modeling based on the dominant arsenate and carbonate surface complexes indicated by ATR-FTIR and assuming inner-sphere complexation of arsenite successfully described the macroscopic sorption data. Our results imply that in natural arsenic-contaminated systems where iron oxide minerals are important sorbents, dissolved carbonate may increase aqueous arsenite concentrations, but will affect dissolved arsenate concentrations only at neutral to alkaline pH and at very high CO(2) partial pressures. PMID:22494686

  5. Unified generalized Bayesian accrual of evidence for robust ATR: new results

    NASA Astrophysics Data System (ADS)

    Hoffman, John R.; Mahler, Ronald P. S.; Prasanth, Ravi; Huff, Melvyn; Ravichandran, Ravi B.; Mehra, Raman K.; Musick, Stanton

    2001-08-01

    We describe ongoing work in applying Finite Set Statistics (FISST) techniques to a Synthetic Aperture Radar (SAR) Automatic Target Recognition (ATR) problem. It summarizes recent results in an ongoing project in which we are applying FISST filtering approaches to the problem of identifying ground targets from Synthetic Aperture Radar. The signatures for these targets are ambiguous because of extended operating conditions, that is the images have uncharacterizeable noise introduced in the form of mud, dents, etc. We propose a number of mechanisms for compensating for this noise.

  6. Characterisation Of Polysacharides And Lipids From Selected Green Algae Species By FTIR-ATR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Bartošová, Alica; Blinová, Lenka; Gerulová, Kristína

    2015-06-01

    Fourier transform infrared (FTIR) spectroscopy was used in this study to identify and determine spectral features of Chromochloris zofingiensis (Dönz) Fucíková et L.A. Lewis (SAG 211-14, Gottingen, Germany), Acutodesmus obliguus (Turpin) Hegewald (SAG 276-1, Gottingen, Germany) and Chlorella sorokiniana (K. Brandt) Pröschold et Darienko (SAG 211-40c, Gottingen, Germany). Polysaccharides and lipids from these three algae species were determined using Fourier Transformed Infrared Spectroscopy (FTIR) with ATR accessory with diamante crystal in spectral range from 400 - 4000 cm-1 and resolution 4.

  7. Identification of herbarium whole-leaf samples of Epilobium species by ATR-IR spectroscopy.

    PubMed

    Strgulc Krajsek, Simona; Buh, Primoz; Zega, Anamarija; Kreft, Samo

    2008-02-01

    A simple, high-accuracy FT-IR method based on attenuated total reflection (ATR) was developed for the rapid determination of leaf samples of Epilobium species. The method is superior to other analytical techniques, since there is no need of laborious sample preparation such as grinding or extraction and solvent removal. A total of 70 herbarium specimens, belonging to all 13 Epilobium and to 2 Chamerion species growing in Slovenia, were analyzed. With the 100 most-informative wavenumbers in the range 700-1800 cm(-1), we obtained over 90% accuracy of species identification, with discriminant multivariate statistical analysis on the measurements made on whole dried leaves. PMID:18293444

  8. Registration of heavy metal ions and pesticides with ATR planar waveguide enzyme sensors

    NASA Astrophysics Data System (ADS)

    Nabok, Alexei; Haron, Saharudin; Ray, Asim

    2004-11-01

    The proposed novel type of enzyme optical sensors is based on a combination of SiO2/Si3N4/SiO2 planar waveguide ATR (attenuated total reflection) transducer, fabricated by standard silicon planar technology, with the composite polyelectrolyte self-assembled coating containing both organic chromophores and enzyme molecules. Such devices were deployed to monitor typical industrial and agricultural water pollutants, such as heavy metal ions and pesticides, acting as inhibitors of enzyme reactions. The sensitivity of registration of these pollutants in the range of 1 ppb was achieved. The use of different enzymes in the sensitive membrane provides a background for pattern recognition of the above pollutants.

  9. Rapid monitoring of grapevine reserves using ATR-FT-IR and chemometrics.

    PubMed

    Schmidtke, Leigh M; Smith, Jason P; Müller, Markus C; Holzapfel, Bruno P

    2012-06-30

    Predictions of grapevine yield and the management of sugar accumulation and secondary metabolite production during berry ripening may be improved by monitoring nitrogen and starch reserves in the perennial parts of the vine. The standard method for determining nitrogen concentration in plant tissue is by combustion analysis, while enzymatic hydrolysis followed by glucose quantification is commonly used for starch. Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FT-IR) combined with chemometric modelling offers a rapid means for the determination of a range of analytes in powdered or ground samples. ATR-FT-IR offers significant advantages over combustion or enzymatic analysis of samples due to the simplicity of instrument operation, reproducibility and speed of data collection. In the present investigation, 1880 root and wood samples were collected from Shiraz, Semillon and Riesling vineyards in Australia and Germany. Nitrogen and starch concentrations were determined using standard analytical methods, and ATR-FT-IR spectra collected for each sample using a Bruker Alpha instrument. Samples were randomly assigned to either calibration or test data sets representing two thirds and one third of the samples respectively. Signal preprocessing included extended multiplicative scatter correction for water and carbon dioxide vapour, standard normal variate scaling with second derivative and variable selection prior to regression. Excellent predictive models for percent dry weight (DW) of nitrogen (range: 0.10-2.65% DW, median: 0.45% DW) and starch (range: 0.25-42.82% DW, median: 7.77% DW) using partial least squares (PLS) or support vector machine (SVM) analysis for linear and nonlinear regression respectively, were constructed and cross validated with low root mean square errors of prediction (RMSEP). Calibrations employing SVM-regression provided the optimum predictive models for nitrogen (R(2)=0.98 and RMSEP=0.07% DW) compared to PLS regression

  10. Structure-Activity Relations In Enzymes: An Application Of IR-ATR Modulation Spectroscopy

    NASA Astrophysics Data System (ADS)

    Fringeli, Urs P.; Ahlstrom, Peter; Vincenz, Claudius; Fringeli, Marianna

    1985-12-01

    Relations between structure and specific activity in immobilized acetylcholinesterase (ACNE) have been studied by means of pH- and Ca++-modulation technique combined with attenuated total reflection (ATR) infrared (IR) spectroscopy and enzyme activity measurement. Periodic modulation of pH and Ca++-concentration enabled a periodic on-off switching of about 40% of the total enzyme activity. It was found that about 0.5 to 1% of the amino acids were involved in this process. These 15 to 30 amino acids assumed antiparallel pleated sheet structure in the inhibited state and random and/or helical structure in the activated state.

  11. Pharmacological targeting the ATR-CHK1-WEE1 axis involves balancing cell growth stimulation and apoptosis.

    PubMed

    Mak, Joyce P Y; Man, Wing Yu; Ma, Hoi Tang; Poon, Randy Y C

    2014-11-15

    The ATR-CHK1-WEE1 kinase cascade's functions in the DNA damage checkpoints are well established. Moreover, its roles in the unperturbed cell cycle are also increasingly being recognized. In this connection, a number of small-molecule inhibitors of ATR, CHK1, and WEE1 are being evaluated in clinical trials. Understanding precisely how cells respond to different concentrations of inhibitors is therefore of paramount importance and has broad clinical implications. Here we present evidence that in the absence of DNA damage, pharmacological inactivation of ATR was less effective in inducing mitotic catastrophe than inhibition of WEE1 and CHK1. Small-molecule inhibitors of CHK1 (AZD7762) or WEE1 (MK-1775) induced mitotic catastrophe, as characterized by dephosphorylation of CDK1(Tyr15), phosphorylation of histone H39(Ser10), and apoptosis. Unexpectedly, partial inhibition of WEE1 and CHK1 had the opposite effect of accelerating the cell cycle without inducing apoptosis, thereby increasing the overall cell proliferation. This was also corroborated by the finding that cell proliferation was enhanced by kinase-inactive versions of WEE1. We demonstrated that these potential limitations of the inhibitors could be overcome by targeting more than one components of the ATR-CHK1-WEE1 simultaneously. These observations reveal insights into the complex responses to pharmacological inactivation of the ATR-CHK1-WEE1 axis. PMID:25301733

  12. Distinct but Concerted Roles of ATR, DNA-PK, and Chk1 in Countering Replication Stress during S Phase.

    PubMed

    Buisson, Rémi; Boisvert, Jessica L; Benes, Cyril H; Zou, Lee

    2015-09-17

    The ATR-Chk1 pathway is critical for DNA damage responses and cell-cycle progression. Chk1 inhibition is more deleterious to cycling cells than ATR inhibition, raising questions about ATR and Chk1 functions in the absence of extrinsic replication stress. Here we show that a key role of ATR in S phase is to coordinate RRM2 accumulation and origin firing. ATR inhibitor (ATRi) induces massive ssDNA accumulation and replication catastrophe in a fraction of early S-phase cells. In other S-phase cells, however, ATRi induces moderate ssDNA and triggers a DNA-PK and Chk1-mediated backup pathway to suppress origin firing. The backup pathway creates a threshold such that ATRi selectively kills cells under high replication stress, whereas Chk1 inhibitor induces cell death at a lower threshold. The levels of ATRi-induced ssDNA correlate with ATRi sensitivity in a panel of cell lines, suggesting that ATRi-induced ssDNA could be predictive of ATRi sensitivity in cancer cells. PMID:26365377

  13. Targeting ATR in vivo using the novel inhibitor VE-822 results in selective sensitization of pancreatic tumors to radiation

    PubMed Central

    Fokas, E; Prevo, R; Pollard, J R; Reaper, P M; Charlton, P A; Cornelissen, B; Vallis, K A; Hammond, E M; Olcina, M M; Gillies McKenna, W; Muschel, R J; Brunner, T B

    2012-01-01

    Combined radiochemotherapy is the currently used therapy for locally advanced pancreatic ductal adenocarcinoma (PDAC), but normal tissue toxicity limits its application. Here we test the hypothesis that inhibition of ATR (ATM-Rad3-related) could increase the sensitivity of the cancer cells to radiation or chemotherapy without affecting normal cells. We tested VE-822, an ATR inhibitor, for in vitro and in vivo radiosensitization. Chk1 phosphorylation was used to indicate ATR activity, γH2AX and 53BP1 foci as evidence of DNA damage and Rad51 foci for homologous recombination activity. Sensitivity to radiation (XRT) and gemcitabine was measured with clonogenic assays in vitro and tumor growth delay in vivo. Murine intestinal damage was evaluated after abdominal XRT. VE-822 inhibited ATR in vitro and in vivo. VE-822 decreased maintenance of cell-cycle checkpoints, increased persistent DNA damage and decreased homologous recombination in irradiated cancer cells. VE-822 decreased survival of pancreatic cancer cells but not normal cells in response to XRT or gemcitabine. VE-822 markedly prolonged growth delay of pancreatic cancer xenografts after XRT and gemcitabine-based chemoradiation without augmenting normal cell or tissue toxicity. These findings support ATR inhibition as a promising new approach to improve the therapeutic ration of radiochemotherapy for patients with PDAC. PMID:23222511

  14. Targeting ATR in vivo using the novel inhibitor VE-822 results in selective sensitization of pancreatic tumors to radiation.

    PubMed

    Fokas, E; Prevo, R; Pollard, J R; Reaper, P M; Charlton, P A; Cornelissen, B; Vallis, K A; Hammond, E M; Olcina, M M; Gillies McKenna, W; Muschel, R J; Brunner, T B

    2012-01-01

    Combined radiochemotherapy is the currently used therapy for locally advanced pancreatic ductal adenocarcinoma (PDAC), but normal tissue toxicity limits its application. Here we test the hypothesis that inhibition of ATR (ATM-Rad3-related) could increase the sensitivity of the cancer cells to radiation or chemotherapy without affecting normal cells. We tested VE-822, an ATR inhibitor, for in vitro and in vivo radiosensitization. Chk1 phosphorylation was used to indicate ATR activity, γH2AX and 53BP1 foci as evidence of DNA damage and Rad51 foci for homologous recombination activity. Sensitivity to radiation (XRT) and gemcitabine was measured with clonogenic assays in vitro and tumor growth delay in vivo. Murine intestinal damage was evaluated after abdominal XRT. VE-822 inhibited ATR in vitro and in vivo. VE-822 decreased maintenance of cell-cycle checkpoints, increased persistent DNA damage and decreased homologous recombination in irradiated cancer cells. VE-822 decreased survival of pancreatic cancer cells but not normal cells in response to XRT or gemcitabine. VE-822 markedly prolonged growth delay of pancreatic cancer xenografts after XRT and gemcitabine-based chemoradiation without augmenting normal cell or tissue toxicity. These findings support ATR inhibition as a promising new approach to improve the therapeutic ration of radiochemotherapy for patients with PDAC. PMID:23222511

  15. Fuel flexible fuel injector

    SciTech Connect

    Tuthill, Richard S; Davis, Dustin W; Dai, Zhongtao

    2015-02-03

    A disclosed fuel injector provides mixing of fuel with airflow by surrounding a swirled fuel flow with first and second swirled airflows that ensures mixing prior to or upon entering the combustion chamber. Fuel tubes produce a central fuel flow along with a central airflow through a plurality of openings to generate the high velocity fuel/air mixture along the axis of the fuel injector in addition to the swirled fuel/air mixture.

  16. Fuel plate and fusion insulator irradiation test program

    SciTech Connect

    Miller, L.G.; Beeston, J.M.

    1980-11-01

    As the prices of fuel fabricating, shipping, and reprocessing continue to rise at rapid rates, research people look for alternate methods to keep their reactor fuel costs within limited funds. Extending fuel element lifetimes without jeopardizing reactor safety can reduce fuel costs by up to a factor of two. But to gain this factor, some fuel plate tests must be performed to the higher burnup to verify burnup fuel plate performance. In this proposed test, fuel plates will be constructed to a maximum fuel loading which can be produced on a commercial basis, contain a maximum boron content as used in ATR to reduce initial reactor reactivity, and will be loaded with UAl/sub 2/ to obtain higher uranium content and better operating performance over UAl/sub 3/.

  17. Investigation on the adsorption characteristics of sodium benzoate and taurine on gold nanoparticle film by ATR-FTIR spectroscopy

    NASA Astrophysics Data System (ADS)

    Kumar, Naveen; Thomas, S.; Tokas, R. B.; Kshirsagar, R. J.

    2014-01-01

    Fourier transform infrared (FTIR) spectroscopic studies of sodium benzoate and taurine adsorbed on gold nanoparticle (AuNp) film on silanised glass slides have been studied by attenuated total reflection technique (ATR). The surface morphology of the AuNp films has been measured by Atomic Force Microscopy. The ATR spectra of sodium benzoate and taurine deposited on AuNp film are compared with ATR spectra of their powdered bulk samples. A new red-shifted band appeared along with the symmetric and asymmetric stretches of carboxylate group of sodium benzoate leading to a broadening of the above peaks. Similar behavior is also seen in the case of symmetric and asymmetric stretches of sulphonate group of taurine. The results indicate presence of both chemisorbed and physisorbed layers of both sodium benzoate and taurine on the AuNp film with bottom layer chemically bound to AuNp through carboxylate and sulphonate groups respectively.

  18. New automated terrain and feature extraction approach for the Predator UAV TESAR ATR system

    NASA Astrophysics Data System (ADS)

    Rosario, Dalton S.

    1999-08-01

    This paper describes a technique recently developed for target detection and false alarm reduction for the Predator unmanned aerial vehicle (UAV) tactical endurance synthetic aperture radar (TESAR) automatic target recognition (ATR) system. The approach does not attempt to label various objects in the SAR image (i.e., buildings, trees, roads); instead, it finds target-like characteristics in the image and compares their statistical/spatial relationship to larger structures in the scene. To do this, the approach merges the output of multiple CFAR (constant false alarm ratio) surfaces through a sequence of mathematical morphology tests. The output is further tested by a 'smart' clustering procedure, which performs an object- size test. With the use of these CFAR surfaces, a methodical sequence of morphological tests will find and retain large structures in the scene and eliminate cues that fall within these structures. The presence of supporting shadow downrange from the sensor is also used to eliminate objects with heights not typical to those of targets. Finally, a fast procedure performs a size test on elongated streaks. This procedure allows long objects to be smartly clustered as a single object while ensuring target proximity scenarios have no performance degradation. Application of this false alarm mitigator/detector to the Predator's SAR ATR algorithm suite produced a stunning reduction of one order of magnitude in the number of cues yielded by its baseline detector. This performance was consistent in scenes having natural and/or cultural clutter.

  19. Mebendazole crystal forms in tablet formulations. An ATR-FTIR/chemometrics approach to polymorph assignment.

    PubMed

    Calvo, Natalia L; Kaufman, Teodoro S; Maggio, Rubén M

    2016-04-15

    Structural polymorphism of active pharmaceutical ingredients (API) is a relevant concern for the modern pharmaceutical industry, since different polymorphic forms may display dissimilar properties, critically affecting the performance of the corresponding drug products. Mebendazole (MEB) is a widely used broad spectrum anthelmintic drug of the benzimidazole class, which exhibits structural polymorphism (Forms A-C). Form C, which displays the best pharmaceutical profile, is the recommended one for clinical use. The polymorphs of MEB were prepared and characterized by spectroscopic, calorimetric and microscopic means. The polymorphs were employed to develop a suitable chemometrics-assisted sample display model based on the first two principal components of their ATR-FTIR spectra in the 4000-600 cm(-1) region. The model was internally and externally validated employing the leave-one-out procedure and an external validation set, respectively. Its suitability for revealing the polymorphic identity of MEB in tablets was successfully assessed analyzing commercial tablets under different physical forms (whole, powdered, dried, sieved and aged). It was concluded that the ATR-FTIR/PCA (principal component analysis) association is a fast, efficient and non-destructive technique for assigning the solid-state forms of MEB in its drug products, with minimum sample pre-treatment. PMID:26874854

  20. Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopic analysis of regenerated bone

    NASA Astrophysics Data System (ADS)

    Benetti, Carolina; Kazarain, Sergei G.; Alves, Marco A. V.; Blay, Alberto; Correa, Luciana; Zezell, Denise M.

    2014-03-01

    The cutting of bone is routinely required in medical procedures, especially in dental applications. In such cases, bone regeneration and new bone quality can determine the success of the treatment. This study investigated the main spectral differences of undamaged and healed bone using the ATR-FTIR spectroscopy technique. Three rabbits were submitted to a surgical procedure; a small piece of bone (3x3 mm2) was removed from both sides of their jaws using a high speed drill. After 15 days, the rabbits were euthanized and the jaws were removed. A bone slice was cut from each side of the jaw containing regions of undamaged and newly formed bone, resulting in six samples which were polished for spectroscopic comparison. The samples were analyzed by FTIR spectroscopy using a diamond ATR accessory. Spectral characteristics were compared and particular attention was paid to the proportion of phosphate to amide I bands and the width of the phosphate band. The results show that the ratio of phosphate to amide I is smaller in new bone tissue than in the undamaged bone, indicating a higher organic content in the newly formed bone. The analysis of the width of the phosphate band suggests a crystallinity difference between both tissues, since the width was higher in the new bone than in the natural bone. These results suggest that the differences observed in bone aging processes by FTIR spectroscopic can be applied to the study of healing processes.

  1. Characterization of Printing Inks Using DART-Q-TOF-MS and Attenuated Total Reflectance (ATR) FTIR.

    PubMed

    Williamson, Rhett; Raeva, Anna; Almirall, Jose R

    2016-05-01

    The rise in improved and widely accessible printing technology has resulted in an interest to develop rapid and minimally destructive chemical analytical techniques that can characterize printing inks for forensic document analysis. Chemical characterization of printing inks allows for both discrimination of inks originating from different sources and the association of inks originating from the same source. Direct analysis in real-time mass spectrometry (DART-MS) and attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) were used in tandem to analyze four different classes of printing inks: inkjets, toners, offset, and intaglio. A total of 319 samples or ~ 80 samples from each class were analyzed directly on a paper substrate using the two methods. DART-MS was found to characterize the semi-volatile polymeric vehicle components, while ATR-FTIR provided chemical information associated with the bulk components of these inks. Complimentary data results in improved discrimination when both techniques are used in succession resulting in >96% discrimination for all toners, 95% for all inkjets, >92% for all offset, and >54% for all intaglio inks. PMID:27122410

  2. Modulation of ATR-mediated DNA damage checkpoint response by cryptochrome 1

    PubMed Central

    Kang, Tae-Hong; Leem, Sun-Hee

    2014-01-01

    Mammalian cryptochromes (Crys) are essential circadian clock factors implicated in diverse clock-independent physiological functions, including DNA damage responses. Here we show that Cry1 modulates the ATR-mediated DNA damage checkpoint (DDC) response by interacting with Timeless (Tim) in a time-of-day-dependent manner. The DDC capacity in response to UV irradiation showed a circadian rhythm. Interestingly, clock-deficient Cry1 and Cry2 double knockout (CryDKO) cells retained substantial DDC capacity compared with clock-proficient wild-type cells, although the Cry1-modulated oscillation of the DDC capacity was abolished in CryDKO cells. We found temporal interaction of Cry1 and Tim in the nucleus. When Cry1 was expressed in the nucleus, it was critical for circadian ATR activity. We regenerated rhythmic DDC responses by ectopically expressing Cry1 in CryDKO cells. In addition, we also investigated the DDC capacity in the liver of mice that were intraperitoneally injected with cisplatin at different circadian times (CT). When mice were injected at CT20, about 2-fold higher expression of phosphorylated minichromosome maintenance protein 2 (p-MCM2) was detected compared with mice injected at CT08, which consequently affected the removal rate of cisplatin-DNA adducts from genomic DNA. Taken together, our data demonstrate the intimate interaction between the circadian clock and the DDC system during genotoxic stress in clock-ticking cells. PMID:24489120

  3. Kinetics of phosphate adsorption on goethite: comparing batch adsorption and ATR-IR measurements.

    PubMed

    Luengo, Carina; Brigante, Maximiliano; Antelo, Juan; Avena, Marcelo

    2006-08-15

    The adsorption kinetics of phosphate on goethite has been studied by batch adsorption experiments and by in situ ATR-IR spectroscopy at different pH, initial phosphate concentrations and stirring rates. Batch adsorption results are very similar to those reported by several authors, and show a rather fast initial adsorption taking place in a few minutes followed by a slower process taking place in days or weeks. The adsorption kinetics could be also monitored by integrating the phosphate signals obtained in ATR-IR experiments, and a very good agreement between both techniques was found. At pH 4.5 two surface complexes, the bidentate nonprotonated (FeO)(2)PO(2) and the bidentate protonated (FeO)(2)(OH)PO complexes, are formed at the surface. There are small changes in the relative concentrations of these species as the reaction proceeds, and they seem to evolve in time rather independently. At pH 7.5 and 9 the dominating surface species is (FeO)(2)PO(2), which is accompanied by an extra unidentified species at low concentration. They also seem to evolve independently as the reaction proceeds. The results are consistent with a mechanism that involve a fast adsorption followed by a slow diffusion into pores, and are not consistent with surface precipitation of iron phosphate. PMID:16643942

  4. In vivo interstitial glucose characterization and monitoring in the skin by ATR-FTIR spectroscopy

    NASA Astrophysics Data System (ADS)

    Skrebova Eikje, Natalja

    2011-03-01

    Successful development of real-time non-invasive glucose monitoring would represent a major advancement not only in the treatment and management of patients with diabetes mellitus and carbohydrate metabolism disorders, but also for understanding in those biochemical, metabolic and (patho-)physiological processes of glucose at the molecular level in vivo. Here, ATR-FTIR spectroscopy technique has been challenged not only for in vivo measurement of interstitial glucose levels, but also for their non-invasive molecular qualitative and quantitative comparative characterization in the skin tissue. The results, based on calculated mean values of determined 5 glucose-specific peaks in the glucose-related 1000-1160 cm-1 region, showed intra- and inter-subject differences in interstitial glucose activity levels with their changes at different times and doses of OGTT, while raising questions about the relationships between interstitial and blood glucose levels. In conclusion, the introduction of ATR-FTIR spectroscopy technique has opened up an access to the interstitial fluid space in the skin tissue for interstitial glucose characterization and monitoring in vivo. Though interstitial versus blood glucose monitoring has different characteristics, it can be argued that accurate and precise measurements of interstitial glucose levels may be more important clinically.

  5. Focusing, imaging, and ATR for the Gotcha 2008 wide angle SAR collection

    NASA Astrophysics Data System (ADS)

    Gianelli, Christopher D.; Xu, Luzhou

    2013-05-01

    The following work discusses IAA's approach to tackling the wide angle, circular spotlight, synthetic aperture radar (SAR) problem from the 2008 Gotcha wide angle SAR data set, which is publicly released, with unlimited distribution. This data set comes with a MATLAB image formation routine and attendant graphical user inter- face (GUI). We begin by introducing a simple approach to focusing the collected phase history data that utilizes point targets (quadrahedral targets) present in the scene. Two SAR imaging algorithms are then presented, namely, the data-independent backprojection (BP) algorithm and the data-adaptive sparse learning via itera- tive minimization (SLIM) algorithm. These imaging approaches are compared using the 2008 Gotcha wide angle SAR data to perform both a clutter discrimination experiment, as well as an automatic target recognition (ATR) experiment. The ATR system is composed of a target pose and target center estimation preprocessing system, and includes a novel target feature for the final classification stage. Empirical results obtained by applying the focusing approach and imaging algorithms to the 2008 Gotcha wide angle SAR data set are presented and described. The results presented highlight the benefit of applying the SLIM algorithm over its data-independent counterpart, as well as the utility of the novel target feature.

  6. Rapid detection of melamine adulteration in dairy milk by SB-ATR-Fourier transform infrared spectroscopy.

    PubMed

    Jawaid, Sana; Talpur, Farah N; Sherazi, S T H; Nizamani, Shafi M; Khaskheli, Abid A

    2013-12-01

    Melamine is a nitrogenous chemical substance used principally as a starting material for the manufacture of synthetic resins. Due to its very high proportion of nitrogen melamine has been added illegitimately to foods and feeds to increase the measured protein content, which determines the value of the product. These issues prompted private as well as governmental laboratories to develop methods for the analysis of melamine in a wide variety of food products and ingredients. Owing to this fact present study is aimed to use single bounce attenuated total reflectance (SB-ATR) Fourier transform infrared spectroscopy (FTIR) method as an effective rapid tool for the detection and quantification of melamine in milk (liquid and powder). Partial least-squares (PLS) models were established for correlating spectral data to melamine concentration with R(2)>0.99, and RMSEC 0.370. Linear calibration curves were obtained over the calibration range of 25-0.0625%. The LOD and LOQ of the method was 0.00025% (2.5 ppm) and 0.0015% (15 ppm) respectively. Proposed SB-ATR-FTIR method requires little or no sample preparation with an assay time of 1-2 min. PMID:23871060

  7. Control of HIPK2 stability by ubiquitin ligase Siah-1 and checkpoint kinases ATM and ATR.

    PubMed

    Winter, Melanie; Sombroek, Dirk; Dauth, Ilka; Moehlenbrink, Jutta; Scheuermann, Karin; Crone, Johanna; Hofmann, Thomas G

    2008-07-01

    The tumour suppressor HIPK2 is an important regulator of cell death induced by DNA damage, but how its activity is regulated remains largely unclear. Here we demonstrate that HIPK2 is an unstable protein that colocalizes and interacts with the E3 ubiquitin ligase Siah-1 in unstressed cells. Siah-1 knockdown increases HIPK2 stability and steady-state levels, whereas Siah-1 expression facilitates HIPK2 polyubiquitination, degradation and thereby inactivation. During recovery from sublethal DNA damage, HIPK2, which is stabilized on DNA damage, is degraded through a Siah-1-dependent, p53-controlled pathway. Downregulation of Siah-1 inhibits HIPK2 degradation and recovery from damage, driving the cells into apoptosis. We have also demonstrated that DNA damage triggers disruption of the HIPK2-Siah-1 complex, resulting in HIPK2 stabilization and activation. Disruption of the HIPK2-Siah-1 complex is mediated by the ATM/ATR pathway and involves ATM/ATR-dependent phosphorylation of Siah-1 at Ser 19. Our results provide a molecular framework for HIPK2 regulation in unstressed and damaged cells. PMID:18536714

  8. ATR-FTIR microscopy in mapping mode for the study of verdigris and its secondary products

    NASA Astrophysics Data System (ADS)

    Prati, S.; Bonacini, I.; Sciutto, G.; Genty-Vincent, A.; Cotte, M.; Eveno, M.; Menu, M.; Mazzeo, R.

    2016-01-01

    To study degradation processes occurring on painting materials, the use of high-resolution micro-analytical techniques is highly requested since it provides a detailed identification and localisation of both the original and deteriorated ingredients. Among the various pigments recently studied, the characterisation of verdigris has received a major interest. This pigment has not a unique chemical formula, but its composition depends on the recipe employed for its manufacturing. Moreover, verdigris paints are not stable and are subject to a colour change from blue-green to green, which occurs in the first few months after the application. In this paper, we focused our attention on the use of ATR-FTIR mapping as a useful method to identify verdigris secondary products and pathways. Several mock-ups and real samples have been analysed, and the correlation among the detected compounds and their spatial location, obtained by the application of ATR-FTIR microscopy in mapping mode, allowed formulating some hypotheses on the degradation pattern of verdigris, which may feed the discussion on the transformation and stability of this pigment. From an analytical point of view, we showed how FTIR mapping approaches may be extremely useful both for the identification of compounds in complex matrix in which single spectra may limit the exhaustive characterisations due to bands overlapping and for the study of degradation pathways by taking into consideration the relative distribution of degradation products.

  9. TPP1 Blocks an ATR-Mediated Resection Mechanism at Telomeres.

    PubMed

    Kibe, Tatsuya; Zimmermann, Michal; de Lange, Titia

    2016-01-21

    The regulation of 5' end resection at DSBs and telomeres prevents genome instability. DSB resection is positively and negatively regulated by ATM signaling through CtIP/MRN and 53BP1-bound Rif1, respectively. Similarly, telomeres lacking TRF2 undergo ATM-controlled CtIP-dependent hyper-resection when the repression by 53BP1/Rif1 is alleviated. However, telomere resection in the absence of 53BP1/Rif1 is more extensive upon complete removal of shelterin, indicating additional protection against resection by shelterin. Here we show that TPP1 and POT1a/b in shelterin block a resection pathway distinct from that repressed by TRF2. This second pathway is regulated by ATR signaling, involves Exo1 and BLM, and is inhibited by 53BP1/Rif1. Thus, mammalian cells have two distinct 5' end-resection pathways that are regulated by DNA damage signaling, in part through Rif1-mediated inhibition. The data show that telomeres are protected from hyper-resection through the repression of the ATM and ATR kinases by TRF2 and TPP1-bound POT1a/b, respectively. PMID:26778124

  10. 53BP1 deficiency combined with telomere dysfunction activates ATR-dependent DNA damage response.

    PubMed

    Martínez, Paula; Flores, Juana M; Blasco, Maria A

    2012-04-16

    TRF1 protects mammalian telomeres from fusion and fragility. Depletion of TRF1 leads to telomere fusions as well as accumulation of γ-H2AX foci and activation of both the ataxia telangiectasia mutated (ATM)- and the ataxia telangiectasia and Rad3 related (ATR)-mediated deoxyribonucleic acid (DNA) damage response (DDR) pathways. 53BP1, which is also present at dysfunctional telomeres, is a target of ATM that accumulates at DNA double-strand breaks and favors nonhomologous end-joining (NHEJ) repair over ATM-dependent resection and homology-directed repair (homologous recombination [HR]). To address the role of 53BP1 at dysfunctional telomeres, we generated mice lacking TRF1 and 53BP1. 53BP1 deficiency significantly rescued telomere fusions in mouse embryonic fibroblasts (MEFs) lacking TRF1, but they showed evidence of a switch from the NHEJ- to HR-mediated repair of uncapped telomeres. Concomitantly, double-mutant MEFs showed evidence of hyperactivation of the ATR-dependent DDR. In intact mice, combined 53BP1/TRF1 deficiency in stratified epithelia resulted in earlier onset of DNA damage and increased CHK1 phosphorylation during embryonic development, leading to aggravation of skin phenotypes. PMID:22508511