Phosphorylation of the Grb2- and phosphatidylinositol 3-kinase p85-binding p36/38 by Syk in Lck-negative T cells.

Science.gov (United States)

von Willebrand, M; Williams, S; Tailor, P; Mustelin, T

1998-06-01

Activation of the mitogen-activated protein kinase (MAPK) pathway by the T-cell antigen receptor (TCR) in T cells involves a positive role for phosphatidylinositol 3-kinase (PI3K) activity. We recently reported that over-expression of the Syk protein tyrosine kinase in the Lck-negative JCaM1 cells enabled the TCR to induce a normal activation of the Erk2 MAPK and enhanced transcription of a reporter gene driven by the nuclear factor of activated T cells and AP-1. Because this system allows us to analyse the targets for Syk in receptor-mediated signalling, we examined the role of PI3K in signalling events between the TCR-regulated Syk and the downstream activation of Erk2. We report that inhibition of PI3K by wortmannin or an inhibitory p85 construct, p85deltaiSH2, reduced the TCR-induced Syk-dependent activation of Erk2, as well as the appearance of phospho-Erk and phospho-Mek. At the same time, expression of Syk resulted in the activation-dependent phosphorylation of three proteins that bound to the src homology 2 (SH2) domains of PI3K p85. The strongest of these bands had an apparent molecular mass of 36-38 kDa on SDS gels, and it was quantitatively removed from the lysates by adsorption to a fusion protein containing the SH2 domain of Grb2. The appearance of this band was Syk dependent, and it was seen only upon triggering of the TCR complex. Thus, p36/38 was phosphorylated by Syk or a Syk-regulated kinase, and this protein may provide a link to the recruitment and activation of PI3K, as well as to the Ras-MAPK pathway, in TCR-triggered T cells.

New superhindered polydentate polyphosphine ligands P(CH2CH2P(t)Bu2)3, PhP(CH2CH2P(t)Bu2)2, P(CH2CH2CH2P(t)Bu2)3, and their ruthenium(II) chloride complexes.

Science.gov (United States)

Gilbert-Wilson, Ryan; Field, Leslie D; Bhadbhade, Mohan M

2012-03-05

The synthesis and characterization of the extremely hindered phosphine ligands, P(CH(2)CH(2)P(t)Bu(2))(3) (P(2)P(3)(tBu), 1), PhP(CH(2)CH(2)P(t)Bu(2))(2) (PhP(2)P(2)(tBu), 2), and P(CH(2)CH(2)CH(2)P(t)Bu(2))(3) (P(3)P(3)(tBu), 3) are reported, along with the synthesis and characterization of ruthenium chloro complexes RuCl(2)(P(2)P(3)(tBu)) (4), RuCl(2)(PhP(2)P(2)(tBu)) (5), and RuCl(2)(P(3)P(3)(tBu)) (6). The bulky P(2)P(3)(tBu) (1) and P(3)P(3)(tBu) (3) ligands are the most sterically encumbered PP(3)-type ligands so far synthesized, and in all cases, only three phosphorus donors are able to bind to the metal center. Complexes RuCl(2)(PhP(2)P(2)(tBu)) (5) and RuCl(2)(P(3)P(3)(tBu)) (6) were characterized by crystallography. Low temperature solution and solid state (31)P{(1)H} NMR were used to demonstrate that the structure of RuCl(2)(P(2)P(3)(tBu)) (4) is probably analogous to that of RuCl(2)(PhP(2)P(2)(tBu)) (5) which had been structurally characterized.

Crystallization and preliminary X-ray crystallographic analysis of Thermotoga maritima CheA P3-P4-P5 domains in complex with CheW

International Nuclear Information System (INIS)

Park, SangYoun; Kim, Keon Young; Kim, Sunmin; Crane, Brian R.

2012-01-01

T. maritima CheA P3-P4-P5 domains were crystallized in complex with CheW. Low-resolution diffraction data were collected to ∼8 Å using synchrotron X-ray radiation. The CheA–CheW complex plays a key role in bacterial chemotaxis signal transduction by initiating phosphotransfer to response regulators via coupling to the chemoreceptors. CheA (P3-P4-P5 domains) and CheW from Thermotoga maritima were overexpressed in Escherichia coli and crystallized as a complex at 298 K using ammonium dihydrogen phosphate as a precipitant. X-ray diffraction data were collected to ∼8 Å resolution at 100 K using synchrotron radiation. The crystal belonged to space group I222 or I2 1 2 1 2 1 , with unit-cell parameters a = 184.2, b = 286.4, c = 327.7 Å. The asymmetric unit may contain six to ten CheA–CheW molecules

The SH3 domain-binding T cell tyrosyl phosphoprotein p120. Demonstration of its identity with the c-cbl protooncogene product and in vivo complexes with Fyn, Grb2, and phosphatidylinositol 3-kinase

NARCIS (Netherlands)

Fukazawa, T.; Reedquist, K. A.; Trub, T.; Soltoff, S.; Panchamoorthy, G.; Druker, B.; Cantley, L.; Shoelson, S. E.; Band, H.

1995-01-01

Previously, we have identified p120 as a Fyn/Lck SH3 and SH2 domain-binding protein that is tyrosine phosphorylated rapidly after T cell receptor triggering. Here, we used direct protein purification, amino acid sequence analysis, reactivity with antibodies, and two-dimensional gel analyses to

WEC3: Wave Energy Converter Code Comparison Project: Preprint

Energy Technology Data Exchange (ETDEWEB)

Combourieu, Adrien; Lawson, Michael; Babarit, Aurelien; Ruehl, Kelley; Roy, Andre; Costello, Ronan; Laporte Weywada, Pauline; Bailey, Helen

2017-01-01

This paper describes the recently launched Wave Energy Converter Code Comparison (WEC3) project and present preliminary results from this effort. The objectives of WEC3 are to verify and validate numerical modelling tools that have been developed specifically to simulate wave energy conversion devices and to inform the upcoming IEA OES Annex VI Ocean Energy Modelling Verification and Validation project. WEC3 is divided into two phases. Phase 1 consists of a code-to-code verification and Phase II entails code-to-experiment validation. WEC3 focuses on mid-fidelity codes that simulate WECs using time-domain multibody dynamics methods to model device motions and hydrodynamic coefficients to model hydrodynamic forces. Consequently, high-fidelity numerical modelling tools, such as Navier-Stokes computational fluid dynamics simulation, and simple frequency domain modelling tools were not included in the WEC3 project.

Activation of PI3K/Akt signaling by n-terminal SH2 domain mutants of the p85α regulatory subunit of PI3K is enhanced by deletion of its c-terminal SH2 domain.

Science.gov (United States)

Hofmann, Bianca T; Jücker, Manfred

2012-10-01

The phosphoinositide 3-kinase (PI3K) is frequently activated in human cancer cells due to gain of function mutations in the catalytic (p110) and the regulatory (p85) subunits. The regulatory subunit consists of an SH3 domain and two SH2 domains. An oncogenic form of p85α named p65 lacking the c-terminal SH2 domain (cSH2) has been cloned from an irradiation-induced murine thymic lymphoma and transgenic mice expressing p65 in T lymphocytes develop a lymphoproliferative disorder. We have recently detected a c-terminal truncated form of p85α named p76α in a human lymphoma cell line lacking most of the cSH2 domain due to a frame shift mutation. Here, we report that the deletion of the cSH2 domain enhances the activating effects of the n-terminal SH2 domain (nSH2) mutants K379E and R340E on the PI3K/Akt pathway and micro tumor formation in a focus assay. Further analysis revealed that this transforming effect is mediated by activation of the catalytic PI3K isoform p110α and downstream signaling through mTOR. Our data further support a mechanistic model in which mutations of the cSH2 domain of p85α can abrogate its negative regulatory function on PI3K activity via the nSH2 domain of p85α. Copyright © 2012 Elsevier Inc. All rights reserved.

Data and code for the exploratory data analysis of the electrical energy demand in the time domain in Greece.

Science.gov (United States)

Tyralis, Hristos; Karakatsanis, Georgios; Tzouka, Katerina; Mamassis, Nikos

2017-08-01

We present data and code for visualizing the electrical energy data and weather-, climate-related and socioeconomic variables in the time domain in Greece. The electrical energy data include hourly demand, weekly-ahead forecasted values of the demand provided by the Greek Independent Power Transmission Operator and pricing values in Greece. We also present the daily temperature in Athens and the Gross Domestic Product of Greece. The code combines the data to a single report, which includes all visualizations with combinations of all variables in multiple time scales. The data and code were used in Tyralis et al. (2017) [1].

Linear dispersion codes in space-frequency domain for SCFDE

DEFF Research Database (Denmark)

Marchetti, Nicola; Cianca, Ernestina; Prasad, Ramjee

2007-01-01

This paper presents a general framework for applying the Linear Dispersion Codes (LDC) in the space and frequency domains to Single Carrier - Frequency Domain Equalization (SCFDE) systems. Space-Frequency (SF)LDC are more suitable than Space-Time (ST)-LDC in high mobility environment. However......, the application of LDC in space-frequency domain in SCFDE systems is not straightforward as in Orthogonal Frequency Division Multiplexing (OFDM), since there is no direct access to the subcarriers at the transmitter. This paper describes how to build the space-time dispersion matrices to be used...

p68 Sam is a substrate of the insulin receptor and associates with the SH2 domains of p85 PI3K.

Science.gov (United States)

Sánchez-Margalet, V; Najib, S

1999-07-23

The 68 kDa Src substrate associated during mitosis is an RNA binding protein with Src homology 2 and 3 domain binding sites. A role for Src associated in mitosis 68 as an adaptor protein in signaling transduction has been proposed in different systems such as T-cell receptors. In the present work, we have sought to assess the possible role of Src associated in mitosis 68 in insulin receptor signaling. We performed in vivo studies in HTC-IR cells and in vitro studies using recombinant Src associated in mitosis 68, purified insulin receptor and fusion proteins containing either the N-terminal or the C-terminal Src homology 2 domain of p85 phosphatidylinositol-3-kinase. We have found that Src associated in mitosis 68 is a substrate of the insulin receptor both in vivo and in vitro. Moreover, tyrosine-phosphorylated Src associated in mitosis 68 was found to associate with p85 phosphatidylinositol-3-kinase in response to insulin, as assessed by co-immunoprecipitation studies. Therefore, Src associated in mitosis 68 may be part of the signaling complexes of insulin receptor along with p85. In vitro studies demonstrate that Src associated in mitosis 68 associates with the Src homology 2 domains of p85 after tyrosine phosphorylation by the activated insulin receptor. Moreover, tyr-phosphorylated Src associated in mitosis 68 binds with a higher affinity to the N-terminal Src homology 2 domain of p85 compared to the C-terminal Src homology 2 domain of p85, suggesting a preferential association of Src associated in mitosis 68 with the N-terminal Src homology 2 domain of p85. This association may be important for the link of the signaling with RNA metabolism.

Characterization of high-power RF structures using time-domain field codes

International Nuclear Information System (INIS)

Shang, C.C.; DeFord, J.F.; Swatloski, T.L.

1992-01-01

We have modeled gyrotron windows and gyrotron amplifier sever structures for TE modes in the 100--150 GHz range and have computed the reflection and transmission characteristics from the field data. Good agreement with frequency domain codes and analytic analysis have been obtained for some simple geometries. We present results for realistic structures with lousy coatings and describe implementation of microwave diagnostics

Time-resolved phosphorous magnetization transfer of the human calf muscle at 3 T and 7 T: A feasibility study

Energy Technology Data Exchange (ETDEWEB)

Valkovič, Ladislav, E-mail: siegfried.trattnig@meduniwien.ac.at [MR Center of Excellence, Department of Radiology, Medical University Vienna, A-1090 Wien, Lazarettgasse 14 (Austria); Institute of Measurement Science, Department of Imaging Methods, Slovak Academy of Sciences, 841 04 Bratislava, Dúbravska cesta 9 (Slovakia); Chmelík, Marek, E-mail: marek.chmelik@meduniwien.ac.at [MR Center of Excellence, Department of Radiology, Medical University Vienna, A-1090 Wien, Lazarettgasse 14 (Austria); Just Kukurova, Ivica, E-mail: ivica.kukurova@meduniwien.ac.at [MR Center of Excellence, Department of Radiology, Medical University Vienna, A-1090 Wien, Lazarettgasse 14 (Austria); Krššák, Martin, E-mail: martin.krssak@meduniwien.ac.at [Department of Internal Medicine III, Medical University Vienna, A-1090 Wien, Lazarettgasse 14 (Austria); Gruber, Stephan, E-mail: stephan@nmr.at [MR Center of Excellence, Department of Radiology, Medical University Vienna, A-1090 Wien, Lazarettgasse 14 (Austria); Frollo, Ivan, E-mail: umerollo@savba.sk [Institute of Measurement Science, Department of Imaging Methods, Slovak Academy of Sciences, 841 04 Bratislava, Dúbravska cesta 9 (Slovakia); Trattnig, Siegfried, E-mail: siegfried.trattnig@meduniwien.ac.at [MR Center of Excellence, Department of Radiology, Medical University Vienna, A-1090 Wien, Lazarettgasse 14 (Austria); Bogner, Wolfgang, E-mail: wolfgang@nmr.at [MR Center of Excellence, Department of Radiology, Medical University Vienna, A-1090 Wien, Lazarettgasse 14 (Austria)

2013-05-15

Phosphorous ({sup 31}P) magnetization transfer (MT) experiments enable the non-invasive investigation of human muscle metabolism in various physiological and pathological conditions. The purpose of our study was to investigate the feasibility of time-resolved MT, and to compare the results of MT experiments at 3 T and 7 T. Six healthy volunteers were examined on a 3 T and a 7 T MR scanner using the same setup and identical measurement protocols. In the calf muscle of all volunteers, four separate MT experiments (each ∼10 min duration) were performed in one session. The forward rate constant of the ATP synthesis reaction (k{sub ATP}) and creatine kinase reaction (k{sub CK}), as well as corresponding metabolic fluxes (F{sub ATP}, F{sub CK}), were estimated. A comparison of these exchange parameters, apparent T{sub 1}s, data quality, quantification precision, and reproducibility was performed. The data quality and reproducibility of the same MT experiments at 7 T was significantly higher (i.e., k{sub ATP} 2.7 times higher and k{sub CK} 3.4 times higher) than at 3 T (p < 0.05). The values for k{sub ATP} (p = 0.35) and k{sub CK} (p = 0.09) at both field strengths were indistinguishable. Even a single MT experiment at 7 T provided better data quality than did a 4 times-longer MT experiment at 3 T. The minimal time-resolution to reliably quantify both F{sub ATP} and F{sub CK} at 7 T was ∼6 min. Our results show that MT experiments at 7 T can be at least 4 times faster than 3 T MT experiments and still provide significantly better quantification. This enables time-resolved MT experiments for the observation of slow metabolic changes in the human calf muscle at 7 T.

Time-resolved phosphorous magnetization transfer of the human calf muscle at 3 T and 7 T: A feasibility study

International Nuclear Information System (INIS)

Valkovič, Ladislav; Chmelík, Marek; Just Kukurova, Ivica; Krššák, Martin; Gruber, Stephan; Frollo, Ivan; Trattnig, Siegfried; Bogner, Wolfgang

2013-01-01

Phosphorous ( 31 P) magnetization transfer (MT) experiments enable the non-invasive investigation of human muscle metabolism in various physiological and pathological conditions. The purpose of our study was to investigate the feasibility of time-resolved MT, and to compare the results of MT experiments at 3 T and 7 T. Six healthy volunteers were examined on a 3 T and a 7 T MR scanner using the same setup and identical measurement protocols. In the calf muscle of all volunteers, four separate MT experiments (each ∼10 min duration) were performed in one session. The forward rate constant of the ATP synthesis reaction (k ATP ) and creatine kinase reaction (k CK ), as well as corresponding metabolic fluxes (F ATP , F CK ), were estimated. A comparison of these exchange parameters, apparent T 1 s, data quality, quantification precision, and reproducibility was performed. The data quality and reproducibility of the same MT experiments at 7 T was significantly higher (i.e., k ATP 2.7 times higher and k CK 3.4 times higher) than at 3 T (p < 0.05). The values for k ATP (p = 0.35) and k CK (p = 0.09) at both field strengths were indistinguishable. Even a single MT experiment at 7 T provided better data quality than did a 4 times-longer MT experiment at 3 T. The minimal time-resolution to reliably quantify both F ATP and F CK at 7 T was ∼6 min. Our results show that MT experiments at 7 T can be at least 4 times faster than 3 T MT experiments and still provide significantly better quantification. This enables time-resolved MT experiments for the observation of slow metabolic changes in the human calf muscle at 7 T

Characterization of high-power RF structures using time-domain field codes

International Nuclear Information System (INIS)

Shang, C.C.; DeFord, J.F.; Swatloski, T.L.

1992-01-01

We have modeled gyrotron windows and gyrotron amplifier sever structures for TE modes in the 100-150 GHz range and have computed the reflection and transmission characteristics from the field data. Good agreement with frequency domain codes and analytic analysis have been obtained for some simple geometries. We present results for realistic structures with lossy coatings and describe implementation of microwave diagnostics. (Author) 5 figs., 7 refs

GRP1 PH Domain, Like AKT1 PH Domain, Possesses a Sentry Glutamate Residue Essential for Specific Targeting to Plasma Membrane PI(3,4,5)P3

Science.gov (United States)

Pilling, Carissa; Landgraf, Kyle E.; Falke, Joseph J.

2011-01-01

During the appearance of the signaling lipid PI(3,4,5)P3, an important subset of pleckstrin homology (PH) domains target signaling proteins to the plasma membrane. To ensure proper pathway regulation, such PI(3,4,5)P3-specific PH domains must exclude the more prevalant, constitutive plasma membrane lipid PI(4,5)P2 and bind the rare PI(3,4,5)P3 target lipid with sufficiently high affinity. Our previous study of the E17K mutant of protein kinase B (AKT1) PH domain, together with evidence from Carpten et al (1), revealed that the native AKT1 E17 residue serves as a sentry glutamate that excludes PI(4,5)P2, thereby playing an essential role in specific PI(3,4,5)P3 targeting (2). The sentry glutamate hypothesis proposes that an analogous sentry glutamate residue is a widespread feature of PI(3,4,5)P3-specific PH domains, and that charge reversal mutation at the sentry glutamate position will yield both increased PI(4,5)P2 affinity and constitutive plasma membrane targeting. To test this hypothesis the present study investigates the E345 residue, a putative sentry glutamate, of General Receptor for Phosphoinositides 1 (GRP1) PH domain. The results show that incorporation of the E345K charge reversal mutation into GRP1 PH domain enhances PI(4,5)P2 affinity 8-fold and yields constitutive plasma membrane targeting in cells, reminiscent of the effects of the E17K mutation in AKT1 PH domain. Hydrolysis of plasma membrane PI(4,5)P2 releases E345K GRP1 PH domain into the cytoplasm and the efficiency of this release increases when target Arf6 binding is disrupted. Overall, the findings provide strong support for the sentry glutamate hypothesis and suggest that the GRP1 E345K mutation will be linked to changes in cell physiology and human pathologies, as demonstrated for AKT1 E17K (1, 3). Analysis of available PH domain structures suggests that a lone glutamate residue (or, in some cases an aspartate) is a common, perhaps ubiquitous, feature of PI(3,4,5)P3-specific binding

Significance of lymphadenectomy with splenectomy in radical surgery for advanced (pT3/pT4) remnant gastric cancer.

Science.gov (United States)

Sugita, Hiroki; Oda, Eri; Hirota, Masahiko; Ishikawa, Shinji; Tomiyasu, Shinjiro; Tanaka, Hiroshi; Arita, Tetsumasa; Yagi, Yasushi; Baba, Hideo

2016-04-01

To date, the optimal surgical strategy for remnant gastric cancer has not been determined. The purpose of this study was to clarify the significance of lymphadenectomy with splenectomy in remnant gastric cancer surgery. This retrospective cohort study was conducted at the Kumamoto Regional Medical Center. The primary endpoint was overall survival after surgery. We retrospectively analyzed the clinicopathologic features, surgical treatments, and long-term prognosis of remnant gastric cancer patients treated with total gastrectomy. A total of 80 patients with gastric cancer in the remnant stomach after distal gastrectomy and who underwent total gastrectomy were enrolled in the study. Splenectomy was performed in 38 patients. Lymph node metastasis in the splenic hilum was not observed in the patients with pT1/pT2 tumors, whereas nodal metastasis at the splenic hilum was detected in 30.4% of the patients with pT3/pT4 tumors. The survival rate of the patients with pT3/pT4 tumors who underwent splenectomy was significantly higher than that of the patients who did not undergo splenectomy, although there was no difference in the patients with pT1/pT2 tumors. Among the patients classified as R0, the survival rate of the patients with pT3/pT4 tumors who underwent splenectomy was significantly higher than that of the patients who did not undergo splenectomy. Lymphadenectomy with splenectomy in radical surgery is beneficial for patients with advanced (pT3/pT4) remnant gastric cancer. Copyright © 2016 Elsevier Inc. All rights reserved.

BOT3P: a mesh generation software package for the transport analysis codes Dort, Tort, Twodant, Threedant and MCNP

International Nuclear Information System (INIS)

Orsi, R.

2003-01-01

Bot3p consists of a set of standard Fortran 77 language programs that gives the users of the deterministic transport codes Dort and Tort some useful diagnostic tools to prepare and check the geometry of their input data files for both Cartesian and cylindrical geometries including graphical display modules. Bot3p produces at the same time the geometrical and material distribution data for the deterministic transport codes Twodant and Threedant and, only in three-dimensional (3D) Cartesian geometry, for the Monte Carlo Transport Code MCNP. This makes it possible to compare directly for the same geometry the effects stemming from the use of different data libraries and solution approaches on transport analysis results. Through the use of Bot3p, radiation transport problems with complex 3D geometrical structures can be modelled easily, as a relatively small amount of engineer-time is required and refinement is achieved by changing few parameters. This tool is useful for solving very large challenging problems. (author)

BOT3P5.2, 3D Mesh Generator and Graphical Display of Geometry for Radiation Transport Codes, Display of Results

International Nuclear Information System (INIS)

Orsi, Roberto; Bidaud, Adrien

2007-01-01

1 - Description of program or function: BOT3P was originally conceived as a set of standard FORTRAN 77 language programs in order to give the users of the DORT and TORT deterministic transport codes some useful diagnostic tools to prepare and check their input data files. Later versions extended the possibility to produce the geometrical, material distribution and fixed neutron source data to other deterministic transport codes such as TWODANT/THREEDANT of the DANTSYS system, PARTISN and, potentially, to any transport code through BOT3P binary output files that can be easily interfaced (see, for example, the Russian two-dimensional (2D) and three-dimensional (3D) discrete ordinates neutron, photon and charged particle transport codes KASKAD-S-2.5 and KATRIN-2.0). As from Version 5.1 BOT3P contained important additions specifically addressed to radiation transport analysis for medical applications. BOT3P-5.2 contains new graphics capabilities. Some of them enable users to select space sub-domains of the total mesh grid in order to improve the zoom simulation of the geometry, both in 2D cuts and in 3D. Moreover the new BOT3P module (PDTM) may improve the interface of BOT3P geometrical models to transport analysis codes. The following programs are included in the BOT3P software package: GGDM, DDM, GGTM, DTM2, DTM3, RVARSCL, COMPARE, MKSRC, CATSM, DTET, and PDTM. The main features of these different programs are described. 2 - Methods: GGDM and GGTM work similarly from the logical point of view. Since the 3D case is more general, the following description refers to GGTM. All the co-ordinate values that characterise the geometrical scheme at the basis of the 3D transport code geometrical and material model are read, sorted and all stored if different from the neighbouring ones more than an input tolerance established by the user. These co-ordinates are always present in the fine-mesh boundary arrays independently of the mesh grid refinement options, because they

p56Lck and p59Fyn Regulate CD28 Binding to Phosphatidylinositol 3-Kinase, Growth Factor Receptor-Bound Protein GRB-2, and T Cell-Specific Protein-Tyrosine Kinase ITK: Implications for T-Cell Costimulation

Science.gov (United States)

Raab, Monika; Cai, Yun-Cai; Bunnell, Stephen C.; Heyeck, Stephanie D.; Berg, Leslie J.; Rudd, Christopher E.

1995-09-01

T-cell activation requires cooperative signals generated by the T-cell antigen receptor ξ-chain complex (TCRξ-CD3) and the costimulatory antigen CD28. CD28 interacts with three intracellular proteins-phosphatidylinositol 3-kinase (PI 3-kinase), T cell-specific protein-tyrosine kinase ITK (formerly TSK or EMT), and the complex between growth factor receptor-bound protein 2 and son of sevenless guanine nucleotide exchange protein (GRB-2-SOS). PI 3-kinase and GRB-2 bind to the CD28 phosphotyrosine-based Tyr-Met-Asn-Met motif by means of intrinsic Src-homology 2 (SH2) domains. The requirement for tyrosine phosphorylation of the Tyr-Met-Asn-Met motif for SH2 domain binding implicates an intervening protein-tyrosine kinase in the recruitment of PI 3-kinase and GRB-2 by CD28. Candidate kinases include p56Lck, p59Fyn, ξ-chain-associated 70-kDa protein (ZAP-70), and ITK. In this study, we demonstrate in coexpression studies that p56Lck and p59Fyn phosphorylate CD28 primarily at Tyr-191 of the Tyr-Met-Asn-Met motif, inducing a 3- to 8-fold increase in p85 (subunit of PI 3-kinase) and GRB-2 SH2 binding to CD28. Phosphatase digestion of CD28 eliminated binding. In contrast to Src kinases, ZAP-70 and ITK failed to induce these events. Further, ITK binding to CD28 was dependent on the presence of p56Lck and is thus likely to act downstream of p56Lck/p59Fyn in a signaling cascade. p56Lck is therefore likely to be a central switch in T-cell activation, with the dual function of regulating CD28-mediated costimulation as well as TCR-CD3-CD4 signaling.

MR spectroscopy of liver in overweight children and adolescents: Investigation of 1H T2 relaxation times at 3 T

International Nuclear Information System (INIS)

Chabanova, Elizaveta; Bille, Dorthe S.; Thisted, Ebbe; Holm, Jens-Christian; Thomsen, Henrik S.

2012-01-01

Objective: The objective was to investigate T 2 relaxation values and to optimize hepatic fat quantification using proton MR spectroscopy ( 1 H MRS) at 3 T in overweight and obese children and adolescents. Subjects: The study included 123 consecutive children and adolescents with a body mass index above the 97th percentile according to age and sex. 1 H MR spectroscopy was performed at 3.0 T using point resolved spectroscopy sequence with series TE. T 2 relaxation values and hepatic fat content corrected for the T 2 relaxation effects were calculated. Results: T 2 values for water ranged from 22 ms to 42 ms (mean value 28 ms) and T 2 values for fat ranged from 36 ms to 99 ms (mean value 64 ms). Poor correlation was observed: (1) between T 2 relaxation times of fat and T 2 relaxation times of water (correlation coefficient r = 0.038, P = 0.79); (2) between T 2 relaxation times of fat and fat content (r = 0.057, P = 0.69); (3) between T 2 relaxation times of water and fat content (r = 0.160, P = 0.26). Correlation between fat peak content and the T 2 corrected fat content decreased with increasing echo time TE: r = 0.97 for TE = 45, r = 0.93 for TE = 75, r = 0.89 for TE = 105, P 1 H MRS at 3 T is an effective technique for measuring hepatic fat content in overweight and obese children and adolescents. It is necessary to measure T 2 relaxation values and to correct the spectra for the T 2 relaxation effects in order to obtain an accurate estimate of the hepatic fat content.

Feasibility of the integration of CRONOS, a 3-D neutronics code, into real-time simulators

International Nuclear Information System (INIS)

Ragusa, J.C.

2001-01-01

In its effort to contribute to nuclear power plant safety, CEA proposes the integration of an engineering grade 3-D neutronics code into a real-time plant analyser. This paper describes the capabilities of the neutronics code CRONOS to achieve a fast running performance. First, we will present current core models in simulators and explain their drawbacks. Secondly, the mean features of CRONOS's spatial-kinetics methods will be reviewed. We will then present an optimum core representation with respect to mesh size, choice of finite elements (FE) basis and execution time, for accurate results as well as the multi 1-D thermal-hydraulics (T/H) model developed to take into account 3-D effects in updating the cross-sections. A Main Steam Line Break (MSLB) End-of-Life (EOL) Hot-Zero-Power (HZP) accident will be used as an example, before we conclude with the perspectives of integrating CRONOS's 3-D core model into real-time simulators. (author)

Feasibility of the integration of CRONOS, a 3-D neutronics code, into real-time simulators

Energy Technology Data Exchange (ETDEWEB)

Ragusa, J.C. [CEA Saclay, Dept. de Mecanique et de Technologie, 91 - Gif-sur-Yvette (France)

2001-07-01

In its effort to contribute to nuclear power plant safety, CEA proposes the integration of an engineering grade 3-D neutronics code into a real-time plant analyser. This paper describes the capabilities of the neutronics code CRONOS to achieve a fast running performance. First, we will present current core models in simulators and explain their drawbacks. Secondly, the mean features of CRONOS's spatial-kinetics methods will be reviewed. We will then present an optimum core representation with respect to mesh size, choice of finite elements (FE) basis and execution time, for accurate results as well as the multi 1-D thermal-hydraulics (T/H) model developed to take into account 3-D effects in updating the cross-sections. A Main Steam Line Break (MSLB) End-of-Life (EOL) Hot-Zero-Power (HZP) accident will be used as an example, before we conclude with the perspectives of integrating CRONOS's 3-D core model into real-time simulators. (author)

Representation of inhomogeneities in the flow and transport codes d{sup 3}f and r{sup 3}t

Energy Technology Data Exchange (ETDEWEB)

Schneider, Anke (ed.)

2013-09-15

The codes d{sup 3}f and r{sup 3}t are well established for modelling density-driven flow and nuclide transport in the far field of repositories for hazardous material in deep geological formations. While originally intended to be applied to the overburden of a salt dome they were adapted to alternative host media such as crystalline rock or mudstone by including fractures into an otherwise porous medium. However, only discrete fractures or fracture networks with a rather limited number of fractures could be dealt with. Networks of smaller fractures - so-called background fractures - can easily consist of hundreds and thousands of significant individual fractures in a model domain and were therefore beyond the scope of d{sup 3}f and r{sup 3}t. One way to circumvent this problem is to replace a discrete fracture network with an equivalent porous medium. While this is a task in itself the codes had also numerically adapted to be to cope with the new methods. This report describes approaches and results of this work. In groundwater flow simulation fractures are usually modelled as lower dimensional objects. But especially in the case of density driven flow situations may occur where the validity of this assumption has to be proved. Here a special approach was developed and implemented that allows an adaptive resolution of the layers. Of central relevance in this respect is the development of local refinement or coarsening criteria, an adaptive discretisation that allows an adaptive transition from low-dimensional to equidimensional modelling of the fractures, and an adaptive multigrid algorithm Furthermore, discretisation methods of higher order for the mixed parabolic-hyperbolic problems were developed. New filtering algebraic multigrid methods as efficient solvers for the large linear equation systems were implemented. The parallelisation was improved by implementation of a parallel communication layer (pcl). For the estimation of parameters for these systems by

Fast resolution of the neutron diffusion equation through public domain Ode codes

Energy Technology Data Exchange (ETDEWEB)

Garcia, V.M.; Vidal, V.; Garayoa, J. [Universidad Politecnica de Valencia, Departamento de Sistemas Informaticos, Valencia (Spain); Verdu, G. [Universidad Politecnica de Valencia, Departamento de Ingenieria Quimica y Nuclear, Valencia (Spain); Gomez, R. [I.E.S. de Tavernes Blanques, Valencia (Spain)

2003-07-01

The time-dependent neutron diffusion equation is a partial differential equation with source terms. The resolution method usually includes discretizing the spatial domain, obtaining a large system of linear, stiff ordinary differential equations (ODEs), whose resolution is computationally very expensive. Some standard techniques use a fixed time step to solve the ODE system. This can result in errors (if the time step is too large) or in long computing times (if the time step is too little). To speed up the resolution method, two well-known public domain codes have been selected: DASPK and FCVODE that are powerful codes for the resolution of large systems of stiff ODEs. These codes can estimate the error after each time step, and, depending on this estimation can decide which is the new time step and, possibly, which is the integration method to be used in the next step. With these mechanisms, it is possible to keep the overall error below the chosen tolerances, and, when the system behaves smoothly, to take large time steps increasing the execution speed. In this paper we address the use of the public domain codes DASPK and FCVODE for the resolution of the time-dependent neutron diffusion equation. The efficiency of these codes depends largely on the preconditioning of the big systems of linear equations that must be solved. Several pre-conditioners have been programmed and tested; it was found that the multigrid method is the best of the pre-conditioners tested. Also, it has been found that DASPK has performed better than FCVODE, being more robust for our problem.We can conclude that the use of specialized codes for solving large systems of ODEs can reduce drastically the computational work needed for the solution; and combining them with appropriate pre-conditioners, the reduction can be still more important. It has other crucial advantages, since it allows the user to specify the allowed error, which cannot be done in fixed step implementations; this, of course

The missing evaluation codes from order domain theory

DEFF Research Database (Denmark)

Andersen, Henning Ejnar; Geil, Olav

The Feng-Rao bound gives a lower bound on the minimum distance of codes defined by means of their parity check matrices. From the Feng-Rao bound it is clear how to improve a large family of codes by leaving out certain rows in their parity check matrices. In this paper we derive a simple lower...... generalized Hamming weight. We interpret our methods into the setting of order domain theory. In this way we fill in an obvious gap in the theory of order domains. The improved codes from the present paper are not in general equal to the Feng-Rao improved codes but the constructions are very much related....

SH3 domain-mediated recruitment of host cell amphiphysins by alphavirus nsP3 promotes viral RNA replication.

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Maarit Neuvonen

2011-11-01

Full Text Available Among the four non-structural proteins of alphaviruses the function of nsP3 is the least well understood. NsP3 is a component of the viral replication complex, and composed of a conserved aminoterminal macro domain implicated in viral RNA synthesis, and a poorly conserved carboxyterminal region. Despite the lack of overall homology we noted a carboxyterminal proline-rich sequence motif shared by many alphaviral nsP3 proteins, and found it to serve as a preferred target site for the Src-homology 3 (SH3 domains of amphiphysin-1 and -2. Nsp3 proteins of Semliki Forest (SFV, Sindbis (SINV, and Chikungunya viruses all showed avid and SH3-dependent binding to amphiphysins. Upon alphavirus infection the intracellular distribution of amphiphysin was dramatically altered and colocalized with nsP3. Mutations in nsP3 disrupting the amphiphysin SH3 binding motif as well as RNAi-mediated silencing of amphiphysin-2 expression resulted in impaired viral RNA replication in HeLa cells infected with SINV or SFV. Infection of Balb/c mice with SFV carrying an SH3 binding-defective nsP3 was associated with significantly decreased mortality. These data establish SH3 domain-mediated binding of nsP3 with amphiphysin as an important host cell interaction promoting alphavirus replication.

Through analysis of LOFT L2-3 by THYDE-P code

International Nuclear Information System (INIS)

Hirano, Masashi

1981-10-01

A through calculation of Experiment L2-3 of the Loss-of-Fluid Test (LOFT) Facility Power Ascension Series (Experiment Series L2) was performed with the THYDE-P code. The specific objectives of Experiment L2-3 were to determine the thermal-hydraulic behavior of the nuclear core and the thermal-mechanical response of the fuel rod cladding with a maximum linear heat generation rate of 39.4 kW/m. The THYDE-P code is a computer code to analyze both the blowdown and refill-reflood phases of loss-of-coolant accidents (LOCAs) of pressurized water reactors (PWRs) without a change in the methods and the models and is now under verification study and modification. The present calculation was performed by best estimate (BE) options as Sample Calculation Run 40, which is a portion of a series of THYDE-P sample calculations. The calculation was carried out from test initiation until complete submersion of the core volume with subcooled water, i.e. about 60 sec. The trend of the calculated cladding surface temperature was in good agreement with that of the experimental results. (author)

The GRP1 PH domain, like the AKT1 PH domain, possesses a sentry glutamate residue essential for specific targeting to plasma membrane PI(3,4,5)P(3).

Science.gov (United States)

Pilling, Carissa; Landgraf, Kyle E; Falke, Joseph J

2011-11-15

During the appearance of the signaling lipid PI(3,4,5)P(3), an important subset of pleckstrin homology (PH) domains target signaling proteins to the plasma membrane. To ensure proper pathway regulation, such PI(3,4,5)P(3)-specific PH domains must exclude the more prevalant, constitutive plasma membrane lipid PI(4,5)P(2) and bind the rare PI(3,4,5)P(3) target lipid with sufficiently high affinity. Our previous study of the E17K mutant of the protein kinase B (AKT1) PH domain, together with evidence from Carpten et al. [Carpten, J. D., et al. (2007) Nature 448, 439-444], revealed that the native AKT1 E17 residue serves as a sentry glutamate that excludes PI(4,5)P(2), thereby playing an essential role in specific PI(3,4,5)P(3) targeting [Landgraf, K. E., et al. (2008) Biochemistry 47, 12260-12269]. The sentry glutamate hypothesis proposes that an analogous sentry glutamate residue is a widespread feature of PI(3,4,5)P(3)-specific PH domains, and that charge reversal mutation at the sentry glutamate position will yield both increased PI(4,5)P(2) affinity and constitutive plasma membrane targeting. To test this hypothesis, we investigated the E345 residue, a putative sentry glutamate, of the general receptor for phosphoinositides 1 (GRP1) PH domain. The results show that incorporation of the E345K charge reversal mutation into the GRP1 PH domain enhances PI(4,5)P(2) affinity 8-fold and yields constitutive plasma membrane targeting in cells, reminiscent of the effects of the E17K mutation in the AKT1 PH domain. Hydrolysis of plasma membrane PI(4,5)P(2) releases the E345K GRP1 PH domain into the cytoplasm, and the efficiency of this release increases when Arf6 binding is disrupted. Overall, the findings provide strong support for the sentry glutamate hypothesis and suggest that the GRP1 E345K mutation will be linked to changes in cell physiology and human pathologies, as demonstrated for AKT1 E17K [Carpten, J. D., et al. (2007) Nature 448, 439-444; Lindhurst, M. J., et al

Multiplicative Structure and Hecke Rings of Generator Matrices for Codes over Quotient Rings of Euclidean Domains

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Hajime Matsui

2017-12-01

Full Text Available In this study, we consider codes over Euclidean domains modulo their ideals. In the first half of the study, we deal with arbitrary Euclidean domains. We show that the product of generator matrices of codes over the rings mod a and mod b produces generator matrices of all codes over the ring mod a b , i.e., this correspondence is onto. Moreover, we show that if a and b are coprime, then this correspondence is one-to-one, i.e., there exist unique codes over the rings mod a and mod b that produce any given code over the ring mod a b through the product of their generator matrices. In the second half of the study, we focus on the typical Euclidean domains such as the rational integer ring, one-variable polynomial rings, rings of Gaussian and Eisenstein integers, p-adic integer rings and rings of one-variable formal power series. We define the reduced generator matrices of codes over Euclidean domains modulo their ideals and show their uniqueness. Finally, we apply our theory of reduced generator matrices to the Hecke rings of matrices over these Euclidean domains.

Capacity for cooperative binding of thyroid hormone (T3) receptor dimers defines wild type T3 response elements.

Science.gov (United States)

Brent, G A; Williams, G R; Harney, J W; Forman, B M; Samuels, H H; Moore, D D; Larsen, P R

1992-04-01

Thyroid hormone response elements (T3REs) have been identified in a variety of promoters including those directing expression of rat GH (rGH), alpha-myosin heavy chain (rMHC), and malic enzyme (rME). A detailed biochemical and genetic analysis of the rGH element has shown that it consists of three hexamers related to the consensus [(A/G)GGT(C/A)A]. We have extended this analysis to the rMHC and rME elements. Binding of highly purified thyroid hormone receptor (T3R) to T3REs was determined using the gel shift assay, and thyroid hormone (T3) induction was measured in transient tranfections. We show that the wild type version of each of the three elements binds T3R dimers cooperatively. Mutational analysis of the rMHC and rME elements identified domains important for binding T3R dimers and allowed a direct determination of the relationship between T3R binding and function. In each element two hexamers are required for dimer binding, and mutations that interfere with dimer formation significantly reduce T3 induction. Similar to the rGH element, the rMHC T3RE contains three hexameric domains arranged as a direct repeat followed by an inverted copy, although the third domain is weaker than in rGH. All three are required for full function and T3R binding. The rME T3RE is a two-hexamer direct repeat T3RE, which also binds T3R monomer and dimer. Across a series of mutant elements, there was a strong correlation between dimer binding in vitro and function in vivo for rMHC (r = 0.99, P less than 0.01) and rME (r = 0.67, P less than 0.05) T3REs. Our results demonstrate a similar pattern of T3R dimer binding to a diverse array of hexameric sequences and arrangements in three wild type T3REs. Addition of nuclear protein enhanced T3R binding but did not alter the specificity of binding to wild type or mutant elements. Binding of purified T3R to T3REs was highly correlated with function, both with and without the addition of nuclear protein. T3R dimer formation is the common

Electrostatic effects in the folding of the SH3 domain of the c-Src tyrosine kinase: pH-dependence in 3D-domain swapping and amyloid formation.

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Julio Bacarizo

Full Text Available The SH3 domain of the c-Src tyrosine kinase (c-Src-SH3 aggregates to form intertwined dimers and amyloid fibrils at mild acid pHs. In this work, we show that a single mutation of residue Gln128 of this SH3 domain has a significant effect on: (i its thermal stability; and (ii its propensity to form amyloid fibrils. The Gln128Glu mutant forms amyloid fibrils at neutral pH but not at mild acid pH, while Gln128Lys and Gln128Arg mutants do not form these aggregates under any of the conditions assayed. We have also solved the crystallographic structures of the wild-type (WT and Gln128Glu, Gln128Lys and Gln128Arg mutants from crystals obtained at different pHs. At pH 5.0, crystals belong to the hexagonal space group P6₅22 and the asymmetric unit is formed by one chain of the protomer of the c-Src-SH3 domain in an open conformation. At pH 7.0, crystals belong to the orthorhombic space group P2₁2₁2₁, with two molecules at the asymmetric unit showing the characteristic fold of the SH3 domain. Analysis of these crystallographic structures shows that the residue at position 128 is connected to Glu106 at the diverging β-turn through a cluster of water molecules. Changes in this hydrogen-bond network lead to the displacement of the c-Src-SH3 distal loop, resulting also in conformational changes of Leu100 that might be related to the binding of proline rich motifs. Our findings show that electrostatic interactions and solvation of residues close to the folding nucleation site of the c-Src-SH3 domain might play an important role during the folding reaction and the amyloid fibril formation.

Interactions of polyomavirus middle T with the SH2 domains of the pp85 subunit of phosphatidylinositol-3-kinase.

Science.gov (United States)

Yoakim, M; Hou, W; Liu, Y; Carpenter, C L; Kapeller, R; Schaffhausen, B S

1992-01-01

The binding of phosphatidylinositol-3-kinase to the polyomavirus middle T antigen is facilitated by tyrosine phosphorylation of middle T on residue 315. The pp85 subunit of phosphatidylinositol-3-kinase contains two SH2 domains, one in the middle of the molecule and one at the C terminus. When assayed by blotting with phosphorylated middle T, the more N-terminal SH2 domain is responsible for binding to middle T. When assayed in solution with glutathione S transferase fusions, both SH2s are capable of binding phosphorylated middle T. While both SH2 fusions can compete with intact pp85 for binding to middle T, the C-terminal SH2 is the more efficient of the two. Interaction between pp85 or its SH2 domains and middle T can be blocked by a synthetic peptide comprising the tyrosine phosphorylation sequence around middle T residue 315. Despite the fact that middle T can interact with both SH2s, these domains are not equivalent. Only the C-terminal SH2-middle T interaction was blocked by anti-SH2 antibody; the two SH2 fusions also interact with different cellular proteins. Images PMID:1380095

Numerical integration of the Teukolsky equation in the time domain

International Nuclear Information System (INIS)

Pazos-Avalos, Enrique; Lousto, Carlos O.

2005-01-01

We present a fourth-order convergent (2+1)-dimensional, numerical formalism to solve the Teukolsky equation in the time domain. Our approach is first to rewrite the Teukolsky equation as a system of first-order differential equations. In this way we get a system that has the form of an advection equation. This is then used in combination with a series expansion of the solution in powers of time. To obtain a fourth-order scheme we kept terms up to fourth derivative in time and use the advectionlike system of differential equations to substitute the temporal derivatives by spatial derivatives. This scheme is applied to evolve gravitational perturbations in the Schwarzschild and Kerr backgrounds. Our numerical method proved to be stable and fourth-order convergent in r* and θ directions. The correct power-law tail, ∼1/t 2l+3 , for general initial data, and ∼1/t 2l+4 , for time-symmetric data, was found in our runs. We noted that it is crucial to resolve accurately the angular dependence of the mode at late times in order to obtain these values of the exponents in the power-law decay. In other cases, when the decay was too fast and round-off error was reached before a tail was developed, then the quasinormal modes frequencies provided a test to determine the validity of our code

Creating and facilitating change for Person-Centred Coordinated Care (P3C): The development of the Organisational Change Tool (P3C-OCT).

Science.gov (United States)

Horrell, Jane; Lloyd, Helen; Sugavanam, Thavapriya; Close, James; Byng, Richard

2018-04-01

Person Centred Coordinated Care (P3C) is a UK priority for patients, carers, professionals, commissioners and policy makers. Services are developing a range of approaches to deliver this care with a lack of tools to guide implementation. A scoping review and critical examination of current policy, key literature and NHS guidelines, together with stakeholder involvement led to the identification of domains, subdomains and component activities (processes and behaviours) required to deliver P3C. These were validated through codesign with stakeholders via a series of workshops and cognitive interviews. Six core domains of P3C were identified as follows: (i) my goals, (ii) care planning, (iii) transitions, (iv) decision making (v), information and communication and (vi) organizational support activities. These were populated by 29 core subdomains (question items). A number of response codes (components) to each question provide examples of the processes and activities that can be actioned to achieve each core subdomain of P3C. The P3C-OCT provides a coherent approach to monitoring progress and supporting practice development towards P3C. It can be used to generate a shared understanding of the core domains of P3C at a service delivery level, and support reorganization of care for those with complex needs. The tool can reliably detect change over time, as demonstrated in a sample of 40 UK general practices. It is currently being used in four UK evaluations of new models of care and being further developed as a training tool for the delivery of P3C. © 2017 The Authors Health Expectations Published by John Wiley & Sons Ltd.

Requirement of Sequences outside the Conserved Kinase Domain of Fission Yeast Rad3p for Checkpoint Control

Science.gov (United States)

Chapman, Carolyn Riley; Evans, Sarah Tyler; Carr, Antony M.; Enoch, Tamar

1999-01-01

The fission yeast Rad3p checkpoint protein is a member of the phosphatidylinositol 3-kinase-related family of protein kinases, which includes human ATMp. Mutation of the ATM gene is responsible for the disease ataxia-telangiectasia. The kinase domain of Rad3p has previously been shown to be essential for function. Here, we show that although this domain is necessary, it is not sufficient, because the isolated kinase domain does not have kinase activity in vitro and cannot complement a rad3 deletion strain. Using dominant negative alleles of rad3, we have identified two sites N-terminal to the conserved kinase domain that are essential for Rad3p function. One of these sites is the putative leucine zipper, which is conserved in other phosphatidylinositol 3-kinase-related family members. The other is a novel motif, which may also mediate Rad3p protein–protein interactions. PMID:10512862

Interactions of polyomavirus middle T with the SH2 domains of the pp85 subunit of phosphatidylinositol-3-kinase.

OpenAIRE

Yoakim, M; Hou, W; Liu, Y; Carpenter, C L; Kapeller, R; Schaffhausen, B S

1992-01-01

The binding of phosphatidylinositol-3-kinase to the polyomavirus middle T antigen is facilitated by tyrosine phosphorylation of middle T on residue 315. The pp85 subunit of phosphatidylinositol-3-kinase contains two SH2 domains, one in the middle of the molecule and one at the C terminus. When assayed by blotting with phosphorylated middle T, the more N-terminal SH2 domain is responsible for binding to middle T. When assayed in solution with glutathione S transferase fusions, both SH2s are ca...

In vivo measurements of T1 relaxation times of 31P-metabolites in human skeletal muscle

DEFF Research Database (Denmark)

Thomsen, C; Jensen, K E; Henriksen, O

1989-01-01

The T1 relaxation times were estimated for 31P-metabolites in human skeletal muscle. Five healthy volunteers were examined in a 1.5 Tesla wholebody imaging system using an inversion recovery pulse sequence. The calculated T1 relaxation times ranged from 5.517 sec for phosphocreatine to 3.603 sec...

3T deep gray matter T2 hypointensity correlates with disability over time in stable relapsing-remitting multiple sclerosis: a 3-year pilot study.

Science.gov (United States)

Zhang, Y; Metz, L M; Yong, V W; Mitchell, J R

2010-10-15

Abnormally decreased deep gray matter (GM) signal intensity on T2-weighted MRI (T2 hypointensity) is associated with brain atrophy and disability progression in patients with multiple sclerosis (MS) and is believed to represent excessive iron deposition. We investigated the time course of deep GM T2 hypointensity and its relationship with disability at 3T in 8 stable relapsing-remitting (RR) MS patients treated with minocycline over 3years. MRI and disability measurements were compared at baseline, 6, 12, 24, and 36months. Grand mean deep GM T2 hypointensity was negatively correlated with EDSS over time (r=-0.94, P=0.02). This correlation was strongest in the head of caudate (r=-0.95, P=0.01) and putamen (r=-0.89, P=0.04). Additionally, baseline grand mean deep GM T2 hypointensity appears to predict third year EDSS (r=-0.72, P=0.04). These results suggest that iron associated deep GM injury correlates with patient disability in stable RRMS. Measurements of deep GM T2 hypointensity at high field MRI may prove to be useful in monitoring individuals with MS. Further studies are required to confirm these results in a large sample and to determine if T2 hypointensity changes in clinically active MS patients. Copyright 2010 Elsevier B.V. All rights reserved.

Post test analysis of TEPSS tests -P2-, -P3-, -P5- and -P7- using the system code RELAP5/MOD 3.2

International Nuclear Information System (INIS)

Luebbesmeyer, D.

2000-01-01

For the PANDA-Test-Facility (TEPSS configuration) post-test calculations and analyses have been performed for experiment -P2- (Early Start), -P3- (PCC start up), -P5- (Symmetric case, Two PCCs only) and -P7- (Severe Accident). Post test calculations have been performed with the system code RELAP5/Mod 3.2 using two different nodalization of the PANDA facility namely a basis nodalization and a much reduced one. The general trend of the calculations can be summarised: RELAP5/Mod3.2 calculated the general trends of the experiments sufficiently accurate; Using the reduced nodalization the results seem to be slightly more accurate than for the basic nodalization; On the other hand, calculations based on the reduced nodalization are not significantly faster than those with basic nodalization; The mass error is in the order of 200 to 900 kg. (author)

Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains

Energy Technology Data Exchange (ETDEWEB)

Xu, Qingping; Mengin-Lecreulx, Dominique; Liu, Xueqian W.; Patin, Delphine; Farr, Carol L.; Grant, Joanna C.; Chiu, Hsiu-Ju; Jaroszewski, Lukasz; Knuth, Mark W.; Godzik, Adam; Lesley, Scott A.; Elsliger, Marc-André; Deacon, Ashley M.; Wilson, Ian A.

2015-09-15

<p>Bacterial SH3 (SH3b) domains are commonly fused with papain-like Nlp/P60 cell wall hydrolase domains. To understand how the modular architecture of SH3b and NlpC/P60 affects the activity of the catalytic domain, three putative NlpC/P60 cell wall hydrolases were biochemically and structurally characterized. These enzymes all have γ-d-Glu-A₂pm (A₂pm is diaminopimelic acid) cysteine amidase (ordl-endopeptidase) activities but with different substrate specificities. One enzyme is a cell wall lysin that cleaves peptidoglycan (PG), while the other two are cell wall recycling enzymes that only cleave stem peptides with an N-terminall-Ala. Their crystal structures revealed a highly conserved structure consisting of two SH3b domains and a C-terminal NlpC/P60 catalytic domain, despite very low sequence identity. Interestingly, loops from the first SH3b domain dock into the ends of the active site groove of the catalytic domain, remodel the substrate binding site, and modulate substrate specificity. Two amino acid differences at the domain interface alter the substrate binding specificity in favor of stem peptides in recycling enzymes, whereas the SH3b domain may extend the peptidoglycan binding surface in the cell wall lysins. Remarkably, the cell wall lysin can be converted into a recycling enzyme with a single mutation.p> <p>IMPORTANCEPeptidoglycan is a meshlike polymer that envelops the bacterial plasma membrane and bestows structural integrity. Cell wall lysins and recycling enzymes are part of a set of lytic enzymes that target covalent bonds connecting the amino acid and amino sugar building blocks of the PG network. These hydrolases are involved in processes such as cell growth and division, autolysis, invasion, and PG turnover and recycling. To avoid cleavage of unintended substrates, these enzymes have very selective substrate specificities. Our biochemical and structural

The connection domain in reverse transcriptase facilitates the in vivo annealing of tRNALys3 to HIV-1 genomic RNA

Directory of Open Access Journals (Sweden)

Niu Meijuan

2004-10-01

Full Text Available Abstract The primer tRNA for reverse transcription in HIV-1, tRNALys3, is selectively packaged into the virus during its assembly, and annealed to the viral genomic RNA. The ribonucleoprotein complex that is involved in the packaging and annealing of tRNALys into HIV-1 consists of Gag, GagPol, tRNALys, lysyl-tRNA synthetase (LysRS, and viral genomic RNA. Gag targets tRNALys for viral packaging through Gag's interaction with LysRS, a tRNALys-binding protein, while reverse transcriptase (RT sequences within GagPol (the thumb domain bind to tRNALys. The further annealing of tRNALys3 to viral RNA requires nucleocapsid (NC sequences in Gag, but not the NC sequences GagPol. In this report, we further show that while the RT connection domain in GagPol is not required for tRNALys3 packaging into the virus, it is required for tRNALys3 annealing to the viral RNA genome.

Calculation of the energy of particles emitted by the reactions {sup 3}{sub 1}T (d,n) {sup 4}{sub 2}He, D (d,n) {sup 3}{sub 2}He and D (d,p) T; Calcul de l'energie des particules emises par les reactions {sup 3}{sub 1}T (d,n) {sup 4}{sub 2}He, D (d,n) {sup 3}{sub 2}He et D (d,p) T

Energy Technology Data Exchange (ETDEWEB)

Oria, M; Sorriaux, A [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1965-07-01

With a view to ease the work of research workers using 150 kV electrostatic accelerators, we have calculated the energy and the emission angle of particles emitted during the reactions {sub 1}{sup 3}T(d,n){sub 2}{sup 4}He, {sub 1}{sup 2}D(d,n){sub 2}{sup 3}He and {sub 1}{sup 2}D(d,p){sub 1}{sup 3}T. The results are classified in tables and arranged according to the acceleration energy of the deuterons. Since the energies considered are relatively low we have limited our study to the non-relativistic domain; this simplification results in a maximum energy variation with respect to the real energy values of 1 per cent. We give also two curves representing the variations in the total cross-sections for the reactions T (d,n){sub 2}{sup 4}He and D (d,n){sub 2}{sup 3}He. (authors) [French] De facon a faciliter la tache des experimentateurs utilisant des accelerateurs electrostatiques de 150 kV, nous avons calcule l'energie et l'angle d'emission des particules emises lors des reactions {sub 1}{sup 3}T(d,n){sub 2}{sup 4}He, {sub 1}{sup 2}D(d,n){sub 2}{sup 3}He and {sub 1}{sup 2}D(d,p){sub 1}{sup 3}T. Les resultats ont ete classes dans des tableaux, et ordonnes en fonction de l'energie d'acceleration des deuterons. Les energies considerees etant relativement peu elevees, nous avons limite notre etude au domaine non relativiste, cette simplification n'entraine qu'une variation maximale de 1 pour cent sur les valeurs reelles des energies. Nous avons joint a ce calcul deux courbes representant la variation des sections efficaces totales des reactions T (d,n){sub 2}{sup 4}He et D (d,n){sub 2}{sup 3}He. (auteurs)

Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain

International Nuclear Information System (INIS)

Parent, Kristin N.; Tang, Jinghua; Cardone, Giovanni; Gilcrease, Eddie B.; Janssen, Mandy E.; Olson, Norman H.; Casjens, Sherwood R.; Baker, Timothy S.

2014-01-01

CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions of the CUS-3 virion. Its coat protein structure adopts the “HK97-fold” shared by other tailed phages and is quite similar to that in phages P22 and Sf6 despite only weak amino acid sequence similarity. In addition, these coat proteins share a unique extra external domain (“I-domain”), suggesting that the group of P22-like phages has evolved over a very long time period without acquiring a new coat protein gene from another phage group. On the other hand, the morphology of the CUS-3 tailspike differs significantly from that of P22 or Sf6, but is similar to the tailspike of phage K1F, a member of the extremely distantly related T7 group of phages. We conclude that CUS-3 obtained its tailspike gene from a distantly related phage quite recently. - Highlights: • Asymmetric and symmetric three-dimensional reconstructions of phage CUS-3 are presented. • CUS-3 major capsid protein has a conserved I-domain, which is found in all three categories of “P22-like phage”. • CUS-3 has very different tailspike receptor binding domain from those of P22 and Sf6. • The CUS-3 tailspike likely was acquired by horizontal gene transfer

Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain

Energy Technology Data Exchange (ETDEWEB)

Parent, Kristin N., E-mail: kparent@msu.edu [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378 (United States); Tang, Jinghua; Cardone, Giovanni [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378 (United States); Gilcrease, Eddie B. [University of Utah School of Medicine, Division of Microbiology and Immunology, Department of Pathology, Salt Lake City, UT 84112 (United States); Janssen, Mandy E.; Olson, Norman H. [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378 (United States); Casjens, Sherwood R., E-mail: sherwood.casjens@path.utah.edu [University of Utah School of Medicine, Division of Microbiology and Immunology, Department of Pathology, Salt Lake City, UT 84112 (United States); Baker, Timothy S., E-mail: tsb@ucsd.edu [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378 (United States); University of California, San Diego, Division of Biological Sciences, La Jolla, CA, 92093 (United States)

2014-09-15

CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions of the CUS-3 virion. Its coat protein structure adopts the “HK97-fold” shared by other tailed phages and is quite similar to that in phages P22 and Sf6 despite only weak amino acid sequence similarity. In addition, these coat proteins share a unique extra external domain (“I-domain”), suggesting that the group of P22-like phages has evolved over a very long time period without acquiring a new coat protein gene from another phage group. On the other hand, the morphology of the CUS-3 tailspike differs significantly from that of P22 or Sf6, but is similar to the tailspike of phage K1F, a member of the extremely distantly related T7 group of phages. We conclude that CUS-3 obtained its tailspike gene from a distantly related phage quite recently. - Highlights: • Asymmetric and symmetric three-dimensional reconstructions of phage CUS-3 are presented. • CUS-3 major capsid protein has a conserved I-domain, which is found in all three categories of “P22-like phage”. • CUS-3 has very different tailspike receptor binding domain from those of P22 and Sf6. • The CUS-3 tailspike likely was acquired by horizontal gene transfer.

Gene-Auto: Automatic Software Code Generation for Real-Time Embedded Systems

Science.gov (United States)

Rugina, A.-E.; Thomas, D.; Olive, X.; Veran, G.

2008-08-01

This paper gives an overview of the Gene-Auto ITEA European project, which aims at building a qualified C code generator from mathematical models under Matlab-Simulink and Scilab-Scicos. The project is driven by major European industry partners, active in the real-time embedded systems domains. The Gene- Auto code generator will significantly improve the current development processes in such domains by shortening the time to market and by guaranteeing the quality of the generated code through the use of formal methods. The first version of the Gene-Auto code generator has already been released and has gone thought a validation phase on real-life case studies defined by each project partner. The validation results are taken into account in the implementation of the second version of the code generator. The partners aim at introducing the Gene-Auto results into industrial development by 2010.

Methodology for time-domain estimation of storm time geoelectric fields using the 3-D magnetotelluric response tensors

Science.gov (United States)

Kelbert, Anna; Balch, Christopher C.; Pulkkinen, Antti; Egbert, Gary D.; Love, Jeffrey J.; Rigler, E. Joshua; Fujii, Ikuko

2017-07-01

Geoelectric fields at the Earth's surface caused by magnetic storms constitute a hazard to the operation of electric power grids and related infrastructure. The ability to estimate these geoelectric fields in close to real time and provide local predictions would better equip the industry to mitigate negative impacts on their operations. Here we report progress toward this goal: development of robust algorithms that convolve a magnetic storm time series with a frequency domain impedance for a realistic three-dimensional (3-D) Earth, to estimate the local, storm time geoelectric field. Both frequency domain and time domain approaches are presented and validated against storm time geoelectric field data measured in Japan. The methods are then compared in the context of a real-time application.

SH2 domains of the p85 alpha subunit of phosphatidylinositol 3-kinase regulate binding to growth factor receptors.

Science.gov (United States)

McGlade, C J; Ellis, C; Reedijk, M; Anderson, D; Mbamalu, G; Reith, A D; Panayotou, G; End, P; Bernstein, A; Kazlauskas, A

1992-01-01

The binding of cytoplasmic signaling proteins such as phospholipase C-gamma 1 and Ras GTPase-activating protein to autophosphorylated growth factor receptors is directed by their noncatalytic Src homology region 2 (SH2) domains. The p85 alpha regulatory subunit of phosphatidylinositol (PI) 3-kinase, which associates with several receptor protein-tyrosine kinases, also contains two SH2 domains. Both p85 alpha SH2 domains, when expressed individually as fusion proteins in bacteria, bound stably to the activated beta receptor for platelet-derived growth factor (PDGF). Complex formation required PDGF stimulation and was dependent on receptor tyrosine kinase activity. The bacterial p85 alpha SH2 domains recognized activated beta PDGF receptor which had been immobilized on a filter, indicating that SH2 domains contact autophosphorylated receptors directly. Several receptor tyrosine kinases within the PDGF receptor subfamily, including the colony-stimulating factor 1 receptor and the Steel factor receptor (Kit), also associate with PI 3-kinase in vivo. Bacterially expressed SH2 domains derived from the p85 alpha subunit of PI 3-kinase bound in vitro to the activated colony-stimulating factor 1 receptor and to Kit. We infer that the SH2 domains of p85 alpha bind to high-affinity sites on these receptors, whose creation is dependent on receptor autophosphorylation. The SH2 domains of p85 are therefore primarily responsible for the binding of PI 3-kinase to activated growth factor receptors. Images PMID:1372092

Acoustic, finite-difference, time-domain technique development

International Nuclear Information System (INIS)

Kunz, K.

1994-01-01

A close analog exists between the behavior of sound waves in an ideal gas and the radiated waves of electromagnetics. This analog has been exploited to obtain an acoustic, finite-difference, time-domain (AFDTD) technique capable of treating small signal vibrations in elastic media, such as air, water, and metal, with the important feature of bending motion included in the behavior of the metal. This bending motion is particularly important when the metal is formed into sheets or plates. Bending motion does not have an analog in electromagnetics, but can be readily appended to the acoustic treatment since it appears as a single additional term in the force equation for plate motion, which is otherwise analogous to the electromagnetic wave equation. The AFDTD technique has been implemented in a code architecture that duplicates the electromagnetic, finite-difference, time-domain technique code. The main difference in the implementation is the form of the first-order coupled differential equations obtained from the wave equation. The gradient of pressure and divergence of velocity appear in these equations in the place of curls of the electric and magnetic fields. Other small changes exist as well, but the codes are essentially interchangeable. The pre- and post-processing for model construction and response-data evaluation of the electromagnetic code, in the form of the TSAR code at Lawrence Livermore National Laboratory, can be used for the acoustic version. A variety of applications is possible, pending validation of the bending phenomenon. The applications include acoustic-radiation-pattern predictions for a submerged object; mine detection analysis; structural noise analysis for cars; acoustic barrier analysis; and symphonic hall/auditorium predictions and speaker enclosure modeling

Layered and Laterally Constrained 2D Inversion of Time Domain Induced Polarization Data

DEFF Research Database (Denmark)

Fiandaca, Gianluca; Ramm, James; Auken, Esben

description of the transmitter waveform and of the receiver transfer function allowing for a quantitative interpretation of the parameters. The code has been optimized for parallel computation and the inversion time is comparable to codes inverting just for direct current resistivity. The new inversion......In a sedimentary environment, quasi-layered models often represent the actual geology more accurately than smooth minimum-structure models. We have developed a new layered and laterally constrained inversion algorithm for time domain induced polarization data. The algorithm is based on the time...... transform of a complex resistivity forward response and the inversion extracts the spectral information of the time domain measures in terms of the Cole-Cole parameters. The developed forward code and inversion algorithm use the full time decay of the induced polarization response, together with an accurate...

Time domain simulation of Gd3+-Gd3+ distance measurements by EPR

Science.gov (United States)

Manukovsky, Nurit; Feintuch, Akiva; Kuprov, Ilya; Goldfarb, Daniella

2017-07-01

Gd3+-based spin labels are useful as an alternative to nitroxides for intramolecular distance measurements at high fields in biological systems. However, double electron-electron resonance (DEER) measurements using model Gd3+ complexes featured a low modulation depth and an unexpected broadening of the distance distribution for short Gd3+-Gd3+ distances, when analysed using the software designed for S = 1/2 pairs. It appears that these effects result from the different spectroscopic characteristics of Gd3+—the high spin, the zero field splitting (ZFS), and the flip-flop terms in the dipolar Hamiltonian that are often ignored for spin-1/2 systems. An understanding of the factors affecting the modulation frequency and amplitude is essential for the correct analysis of Gd3+-Gd3+ DEER data and for the educated choice of experimental settings, such as Gd3+ spin label type and the pulse parameters. This work uses time-domain simulations of Gd3+-Gd3+ DEER by explicit density matrix propagation to elucidate the factors shaping Gd3+ DEER traces. The simulations show that mixing between the |+½, -½> and |-½, +½> states of the two spins, caused by the flip-flop term in the dipolar Hamiltonian, leads to dampening of the dipolar modulation. This effect may be mitigated by a large ZFS or by pulse frequency settings allowing for a decreased contribution of the central transition and the one adjacent to it. The simulations reproduce both the experimental line shapes of the Fourier-transforms of the DEER time domain traces and the trends in the behaviour of the modulation depth, thus enabling a more systematic design and analysis of Gd3+ DEER experiments.

Learning dictionaries of sparse codes of 3D movements of body joints for real-time human activity understanding.

Science.gov (United States)

Qi, Jin; Yang, Zhiyong

2014-01-01

Real-time human activity recognition is essential for human-robot interactions for assisted healthy independent living. Most previous work in this area is performed on traditional two-dimensional (2D) videos and both global and local methods have been used. Since 2D videos are sensitive to changes of lighting condition, view angle, and scale, researchers begun to explore applications of 3D information in human activity understanding in recently years. Unfortunately, features that work well on 2D videos usually don't perform well on 3D videos and there is no consensus on what 3D features should be used. Here we propose a model of human activity recognition based on 3D movements of body joints. Our method has three steps, learning dictionaries of sparse codes of 3D movements of joints, sparse coding, and classification. In the first step, space-time volumes of 3D movements of body joints are obtained via dense sampling and independent component analysis is then performed to construct a dictionary of sparse codes for each activity. In the second step, the space-time volumes are projected to the dictionaries and a set of sparse histograms of the projection coefficients are constructed as feature representations of the activities. Finally, the sparse histograms are used as inputs to a support vector machine to recognize human activities. We tested this model on three databases of human activities and found that it outperforms the state-of-the-art algorithms. Thus, this model can be used for real-time human activity recognition in many applications.

Learning dictionaries of sparse codes of 3D movements of body joints for real-time human activity understanding.

Directory of Open Access Journals (Sweden)

Jin Qi

Full Text Available Real-time human activity recognition is essential for human-robot interactions for assisted healthy independent living. Most previous work in this area is performed on traditional two-dimensional (2D videos and both global and local methods have been used. Since 2D videos are sensitive to changes of lighting condition, view angle, and scale, researchers begun to explore applications of 3D information in human activity understanding in recently years. Unfortunately, features that work well on 2D videos usually don't perform well on 3D videos and there is no consensus on what 3D features should be used. Here we propose a model of human activity recognition based on 3D movements of body joints. Our method has three steps, learning dictionaries of sparse codes of 3D movements of joints, sparse coding, and classification. In the first step, space-time volumes of 3D movements of body joints are obtained via dense sampling and independent component analysis is then performed to construct a dictionary of sparse codes for each activity. In the second step, the space-time volumes are projected to the dictionaries and a set of sparse histograms of the projection coefficients are constructed as feature representations of the activities. Finally, the sparse histograms are used as inputs to a support vector machine to recognize human activities. We tested this model on three databases of human activities and found that it outperforms the state-of-the-art algorithms. Thus, this model can be used for real-time human activity recognition in many applications.

Spectral phase encoding of ultra-short optical pulse in time domain for OCDMA application.

Science.gov (United States)

Wang, Xu; Wada, Naoya

2007-06-11

We propose a novel reconfigurable time domain spectral phase encoding (SPE) scheme for coherent optical code-division-multiple-access application. In the proposed scheme, the ultra-short optical pulse is stretched by dispersive device and the SPE is done in time domain using high speed phase modulator. The time domain SPE scheme is robust to wavelength drift of the light source and is very flexible and compatible with the fiber optical system. Proof-of-principle experiments of encoding with 16-chip, 20 GHz/chip binary-phase-shift-keying codes and 1.25 Gbps data transmission have been successfully demonstrated together with an arrayed-wave-guide decoder.

Time Domain Induced Polarization

DEFF Research Database (Denmark)

Fiandaca, Gianluca; Auken, Esben; Christiansen, Anders Vest

2012-01-01

Time-domain-induced polarization has significantly broadened its field of reference during the last decade, from mineral exploration to environmental geophysics, e.g., for clay and peat identification and landfill characterization. Though, insufficient modeling tools have hitherto limited the use...... of time-domaininduced polarization for wider purposes. For these reasons, a new forward code and inversion algorithm have been developed using the full-time decay of the induced polarization response, together with an accurate description of the transmitter waveform and of the receiver transfer function......, to reconstruct the distribution of the Cole-Cole parameters of the earth. The accurate modeling of the transmitter waveform had a strong influence on the forward response, and we showed that the difference between a solution using a step response and a solution using the accurate modeling often is above 100...

Central Decoding for Multiple Description Codes based on Domain Partitioning

Directory of Open Access Journals (Sweden)

M. Spiertz

2006-01-01

Full Text Available Multiple Description Codes (MDC can be used to trade redundancy against packet loss resistance for transmitting data over lossy diversity networks. In this work we focus on MD transform coding based on domain partitioning. Compared to Vaishampayan’s quantizer based MDC, domain based MD coding is a simple approach for generating different descriptions, by using different quantizers for each description. Commonly, only the highest rate quantizer is used for reconstruction. In this paper we investigate the benefit of using the lower rate quantizers to enhance the reconstruction quality at decoder side. The comparison is done on artificial source data and on image data. 

Pinning, rotation, and metastability of BiFeO3 cycloidal domains in a magnetic field

Science.gov (United States)

Fishman, Randy S.

2018-01-01

Earlier models for the room-temperature multiferroic BiFeO3 implicitly assumed that a very strong anisotropy restricts the domain wave vectors q to the threefold-symmetric axis normal to the static polarization P . However, recent measurements demonstrate that the domain wave vectors q rotate within the hexagonal plane normal to P away from the magnetic field orientation m . We show that the previously neglected threefold anisotropy K3 restricts the wave vectors to lie along the threefold axis in zero field. Taking m to lie along a threefold axis, the domain with q parallel to m remains metastable below Bc 1≈7 T. Due to the pinning of domains by nonmagnetic impurities, the wave vectors of the other two domains start to rotate away from m above 5.6 T, when the component of the torque τ =M ×B along P exceeds a threshold value τpin. Since τ =0 when m ⊥q , the wave vectors of those domains never become completely perpendicular to the magnetic field. Our results explain recent measurements of the critical field as a function of field orientation, small-angle neutron scattering measurements of the wave vectors, as well as spectroscopic measurements with m along a threefold axis. The model developed in this paper also explains how the three multiferroic domains of BiFeO3 for a fixed P can be manipulated by a magnetic field.

Time-dependent anisotropic external sources in transient 3-D transport code TORT-TD

International Nuclear Information System (INIS)

Seubert, A.; Pautz, A.; Becker, M.; Dagan, R.

2009-01-01

This paper describes the implementation of a time-dependent distributed external source in TORT-TD by explicitly considering the external source in the ''fixed-source'' term of the implicitly time-discretised 3-D discrete ordinates transport equation. Anisotropy of the external source is represented by a spherical harmonics series expansion similar to the angular fluxes. The YALINA-Thermal subcritical assembly serves as a test case. The configuration with 280 fuel rods has been analysed with TORT-TD using cross sections in 18 energy groups and P1 scattering order generated by the KAPROS code system. Good agreement is achieved concerning the multiplication factor. The response of the system to an artificial time-dependent source consisting of two square-wave pulses demonstrates the time-dependent external source capability of TORT-TD. The result is physically plausible as judged from validation calculations. (orig.)

V.S.O.P. (99/05) computer code system

International Nuclear Information System (INIS)

Ruetten, H.J.; Haas, K.A.; Brockmann, H.; Scherer, W.

2005-11-01

V.S.O.P. is a computer code system for the comprehensive numerical simulation of the physics of thermal reactors. It implies the setup of the reactor and of the fuel element, processing of cross sections, neutron spectrum evaluation, neutron diffusion calculation in two or three dimensions, fuel burnup, fuel shuffling, reactor control, thermal hydraulics and fuel cycle costs. The thermal hydraulics part (steady state and time-dependent) is restricted to HTRs and to two spatial dimensions. The code can simulate the reactor operation from the initial core towards the equilibrium core. V.S.O.P.(99 / 05) represents the further development of V.S.O.P. (99). Compared to its precursor, the code system has been improved in many details. Major improvements and extensions have been included concerning the neutron spectrum calculation, the 3-d neutron diffusion options, and the thermal hydraulic section with respect to 'multi-pass'-fuelled pebblebed cores. This latest code version was developed and tested under the WINDOWS-XP - operating system. The storage requirement for the executables and the basic libraries associated with the code amounts to about 15 MB. Another 5 MB are required - if desired - for storage of the source code (∼65000 Fortran statements). (orig.)

V.S.O.P. (99/05) computer code system

Energy Technology Data Exchange (ETDEWEB)

Ruetten, H.J.; Haas, K.A.; Brockmann, H.; Scherer, W.

2005-11-01

V.S.O.P. is a computer code system for the comprehensive numerical simulation of the physics of thermal reactors. It implies the setup of the reactor and of the fuel element, processing of cross sections, neutron spectrum evaluation, neutron diffusion calculation in two or three dimensions, fuel burnup, fuel shuffling, reactor control, thermal hydraulics and fuel cycle costs. The thermal hydraulics part (steady state and time-dependent) is restricted to HTRs and to two spatial dimensions. The code can simulate the reactor operation from the initial core towards the equilibrium core. V.S.O.P.(99 / 05) represents the further development of V.S.O.P. (99). Compared to its precursor, the code system has been improved in many details. Major improvements and extensions have been included concerning the neutron spectrum calculation, the 3-d neutron diffusion options, and the thermal hydraulic section with respect to 'multi-pass'-fuelled pebblebed cores. This latest code version was developed and tested under the WINDOWS-XP - operating system. The storage requirement for the executables and the basic libraries associated with the code amounts to about 15 MB. Another 5 MB are required - if desired - for storage of the source code ({approx}65000 Fortran statements). (orig.)

Triiodothyronine increases mRNA and protein leptin levels in short time in 3T3-L1 adipocytes by PI3K pathway activation.

Directory of Open Access Journals (Sweden)

Miriane de Oliveira

Full Text Available The present study aimed to examine the effects of thyroid hormone (TH, more precisely triiodothyronine (T3, on the modulation of leptin mRNA expression and the involvement of the phosphatidyl inositol 3 kinase (PI3K signaling pathway in adipocytes, 3T3-L1, cell culture. We examined the involvement of this pathway in mediating TH effects by treating 3T3-L1 adipocytes with physiological (P=10nM or supraphysiological (SI=100 nM T3 dose during one hour (short time, in the absence or the presence of PI3K inhibitor (LY294002. The absence of any treatment was considered the control group (C. RT-qPCR was used for mRNA expression analyzes. For data analyzes ANOVA complemented with Tukey's test was used at 5% significance. T3 increased leptin mRNA expression in P (2.26 ± 0.36, p 0.001. These results demonstrate that the activation of the PI3K signaling pathway has a role in TH-mediated direct and indirect leptin gene expression in 3T3-L1 adipocytes.

Review of the SCDAP/RELAP5/MOD3.1 code structure and core T/H model before core damage

International Nuclear Information System (INIS)

Kim, See Darl; Kim, Dong Ha

1998-04-01

The SCDAP/RELAP5 code has been developed for best estimate transient simulation of light water reactor coolant systems during a severe accident. The code is being developed at the INEL under the primary sponsorship of the Office of Nuclear Regulatory Research of the U.S. NRC. As The current time, the SCDAP/RELAP5/MOD3.1 code is the result of merging the RELAP5/MOD3 and SCDAP models. The code models the coupled behavior of the reactor coolant system, core, fission product released during a severe accident transient as well as large and small break loss of coolant accidents, operational transients such as anticipated transient without SCRAM, loss of offsite power, loss of feedwater, and loss of flow. Major purpose of the report is to provide information about the characteristics of SCDAP/RELAP5/MOD3.1 core T/H models for an integrated severe accident computer code being developed under the mid/long-term project. This report analyzes the overall code structure which consists of the input processor, transient controller, and plot file handler. The basic governing equations to simulate the thermohydraulics of the primary system are also described. As the focus is currently concentrated in the core, core nodalization parameters of the intact geometry and the phenomenological subroutines for the damaged core are summarized for the future usage. In addition, the numerical approach for the heat conduction model is investigated along with heat convection model. These studies could provide a foundation for input preparation and model improvement. (author). 6 refs., 3 tabs., 4 figs

Computing the Feng-Rao distances for codes from order domains

DEFF Research Database (Denmark)

Ruano Benito, Diego

2007-01-01

We compute the Feng–Rao distance of a code coming from an order domain with a simplicial value semigroup. The main tool is the Apéry set of a semigroup that can be computed using a Gröbner basis.......We compute the Feng–Rao distance of a code coming from an order domain with a simplicial value semigroup. The main tool is the Apéry set of a semigroup that can be computed using a Gröbner basis....

Finite-difference time-domain analysis of time-resolved terahertz spectroscopy experiments

DEFF Research Database (Denmark)

Larsen, Casper; Cooke, David G.; Jepsen, Peter Uhd

2011-01-01

In this paper we report on the numerical analysis of a time-resolved terahertz (THz) spectroscopy experiment using a modified finite-difference time-domain method. Using this method, we show that ultrafast carrier dynamics can be extracted with a time resolution smaller than the duration of the T...

Construction of pEgr.p-TNFα and its expression in NIH3T3 cells induced by ionizing irradiation

International Nuclear Information System (INIS)

Wu Congmei; Li Xiuyi; Liu Shuzheng

2001-01-01

Objective: To isolate and amplify Egr-1 promoter, construct pEgr.p-TNFα and study its response to different doses of ionizing radiation. Methods: Egr-1 promote was isolated from genomic DNA by PCR to construct pEgr.p-TNFα expression plasmid. Plasmids were transfected into NIH3T3 cells with liposome and the expression level of TNFα was detected by ELISA after irradiation with different doses of X-ray. Results: The sequence of Egr-1 promoter obtained was essentially same as reported. Egr-1 promoter and TNF α cDNA were inserted into expression vector correctly. Eight hours after irradiation with different doses of X-rays, the expression level of TNFα was higher than that of nonirradiated group (P< 0.05-0.001). Conclusion: Egr-1 promoter obtained can be activated by ionizing irradiation and regulate the expression of downstream gene. Low dose irradiation is for the first time found to be able to induce the expression of the downstream gene. the observation may be of potential significance in tumor therapy

Joint time-frequency domain proportional fair scheduler with HARQ for 3GPP LTE systems

OpenAIRE

Beh, KC; Doufexi, A; Armour, SMD

2008-01-01

This paper explores the potential gain of joint diversity in both frequency domain and time domain which can be exploited to achieve spectral efficiency gains whilst simultaneously facilitating QoS/ fairness in an OFDMA system particularly in 3GPP Long Term Evolution (LTE)). The performance of several joint time-frequency schedulers is investigated. Simulation results show that joint time frequency schedulers achieve significantly superior performance compared to a more conventional time doma...

OECD/NRC BWR Turbine Trip Benchmark: Simulation by POLCA-T Code

International Nuclear Information System (INIS)

Panayotov, Dobromir

2004-01-01

Westinghouse transient code POLCA-T brings together the system thermal-hydraulics plant models and three-dimensional (3-D) neutron kinetics core models. Participation in the OECD/NRC BWR Turbine Trip (TT) Benchmark is a part of our efforts toward the code's validation. The paper describes the objectives for TT analyses and gives a brief overview of the developed plant system input deck and 3-D core model.The results of exercise 1, system model without netronics, are presented. Sensitivity studies performed cover the maximal time step, turbine stop valve position and mass flow, feedwater temperature, and steam bypass mass flow. Results of exercise 2, 3-D core neutronic and thermal-hydraulic model with boundary conditions, are also presented. Sensitivity studies include the core inlet temperature, cladding properties, and direct heating to core coolant and bypass.The entire plant model was validated in the framework of the benchmark's phase 3. Sensitivity studies include the effect of SCRAM initialization and carry-under. The results obtained - transient fission power and its initial axial distribution and steam dome, core exit, lower and upper plenum, main steam line, and turbine inlet pressures - showed good agreement with measured data. Thus, the POLCA-T code capabilities for correct simulation of pressurizing transients with very fast power were proved

3D scene reconstruction based on multi-view distributed video coding in the Zernike domain for mobile applications

Science.gov (United States)

Palma, V.; Carli, M.; Neri, A.

2011-02-01

In this paper a Multi-view Distributed Video Coding scheme for mobile applications is presented. Specifically a new fusion technique between temporal and spatial side information in Zernike Moments domain is proposed. Distributed video coding introduces a flexible architecture that enables the design of very low complex video encoders compared to its traditional counterparts. The main goal of our work is to generate at the decoder the side information that optimally blends temporal and interview data. Multi-view distributed coding performance strongly depends on the side information quality built at the decoder. At this aim for improving its quality a spatial view compensation/prediction in Zernike moments domain is applied. Spatial and temporal motion activity have been fused together to obtain the overall side-information. The proposed method has been evaluated by rate-distortion performances for different inter-view and temporal estimation quality conditions.

Incidental pT2-T3 gallbladder cancer after a cholecystectomy: outcome of staging at 3 months prior to a radical resection

Science.gov (United States)

Ausania, Fabio; Tsirlis, Theodoris; White, Steven A; French, Jeremy J; Jaques, Bryon C; Charnley, Richard M; Manas, Derek M

2013-01-01

Introduction Patients with incidental pT2-T3 gallbladder cancer (IGC) after a cholecystectomy may benefit from a radical re-resection although their optimal treatment strategy is not well defined. In this Unit, such patients undergo delayed staging at 3 months after a cholecystectomy to assess the evidence of a residual tumour, extra hepatic spread and the biological behaviour of the tumour. The aim of this study was to evaluate the outcome of patients who had delayed staging at 3 months after a cholecystectomy. Methods From July 2003 to July 2011, 56 patients with T2-T3 gallbladder cancer were referred to this Unit of which 49 were diagnosed incidentally on histology after a cholecystectomy. All 49 patients underwent delayed pre-operative staging using multi-detector computed tomography (MDCT) followed selectively by laparoscopy at 3 months after a cholecystectomy. Data were collected from a prospectively held database. The peri-operative and long-term outcomes of patients were analysed. SPSS software was used for statistical analysis. Results There were 38 pT2 and 11 pT3 tumours. After delayed staging, 24/49 (49%) patients underwent a radical resection, 24/49 (49%) were found to be inoperable on pre-operative assessment and 1/49 (2%) patient underwent an exploratory laparotomy and were found to be unresectable. The overall median survival from referral was 20.7 months (54.8 months for the group who had a radical re-resection versus 9.7 months for the group who had unresectable disease, P < 0.001). These results compare favourably with the reported outcome of fast-track management for incidental pT2-T3 gallbladder cancer from other major series in the literature. Conclusion Delayed staging in patients with incidental T2-T3 gallbladder cancer after a cholecystectomy is a useful strategy to select patients who will benefit from a resection and avoid unnecessary major surgery. PMID:23458168

Generalized Sudan's List Decoding for Order Domain Codes

DEFF Research Database (Denmark)

Geil, Hans Olav; Matsumoto, Ryutaroh

2007-01-01

We generalize Sudan's list decoding algorithm without multiplicity to evaluation codes coming from arbitrary order domains. The number of correctable errors by the proposed method is larger than the original list decoding without multiplicity....

Parametric time-frequency domain spatial audio

CERN Document Server

Delikaris-Manias, Symeon; Politis, Archontis

2018-01-01

This book provides readers with the principles and best practices in spatial audio signal processing. It describes how sound fields and their perceptual attributes are captured and analyzed within the time-frequency domain, how essential representation parameters are coded, and how such signals are efficiently reproduced for practical applications. The book is split into four parts starting with an overview of the fundamentals. It then goes on to explain the reproduction of spatial sound before offering an examination of signal-dependent spatial filtering. The book finishes with coverage of both current and future applications and the direction that spatial audio research is heading in. Parametric Time-frequency Domain Spatial Audio focuses on applications in entertainment audio, including music, home cinema, and gaming--covering the capturing and reproduction of spatial sound as well as its generation, transduction, representation, transmission, and perception. This book will teach readers the tools needed...

Efficient Dual Domain Decoding of Linear Block Codes Using Genetic Algorithms

Directory of Open Access Journals (Sweden)

Ahmed Azouaoui

2012-01-01

Full Text Available A computationally efficient algorithm for decoding block codes is developed using a genetic algorithm (GA. The proposed algorithm uses the dual code in contrast to the existing genetic decoders in the literature that use the code itself. Hence, this new approach reduces the complexity of decoding the codes of high rates. We simulated our algorithm in various transmission channels. The performance of this algorithm is investigated and compared with competitor decoding algorithms including Maini and Shakeel ones. The results show that the proposed algorithm gives large gains over the Chase-2 decoding algorithm and reach the performance of the OSD-3 for some quadratic residue (QR codes. Further, we define a new crossover operator that exploits the domain specific information and compare it with uniform and two point crossover. The complexity of this algorithm is also discussed and compared to other algorithms.

A 3D spectral anelastic hydrodynamic code for shearing, stratified flows

Science.gov (United States)

Barranco, Joseph A.; Marcus, Philip S.

2006-11-01

We have developed a three-dimensional (3D) spectral hydrodynamic code to study vortex dynamics in rotating, shearing, stratified systems (e.g., the atmosphere of gas giant planets, protoplanetary disks around newly forming protostars). The time-independent background state is stably stratified in the vertical direction and has a unidirectional linear shear flow aligned with one horizontal axis. Superposed on this background state is an unsteady, subsonic flow that is evolved with the Euler equations subject to the anelastic approximation to filter acoustic phenomena. A Fourier Fourier basis in a set of quasi-Lagrangian coordinates that advect with the background shear is used for spectral expansions in the two horizontal directions. For the vertical direction, two different sets of basis functions have been implemented: (1) Chebyshev polynomials on a truncated, finite domain, and (2) rational Chebyshev functions on an infinite domain. Use of this latter set is equivalent to transforming the infinite domain to a finite one with a cotangent mapping, and using cosine and sine expansions in the mapped coordinate. The nonlinear advection terms are time-integrated explicitly, the pressure/enthalpy terms are integrated semi-implicitly, and the Coriolis force and buoyancy terms are treated semi-analytically. We show that internal gravity waves can be damped by adding new terms to the Euler equations. The code exhibits excellent parallel performance with the message passing interface (MPI). As a demonstration of the code, we simulate the merger of two 3D vortices in the midplane of a protoplanetary disk.

Comparison of computer codes (CE-THERM, FRAP-T5, GT3-FLECHT, and TRUMP-FLECHT) with data from the NRU-LOCA thermal hydraulic tests

International Nuclear Information System (INIS)

Mohr, C.L.; Rausch, W.N.; Hesson, G.M.

1981-07-01

The LOCA Simulation Program in the NRU reactor is the first set of experiments to provide data on the behavior of full-length, nuclear-heated PWR fuel bundles during the heatup, reflood, and quench phases of a loss-of-coolant accident (LOCA). This paper compares the temperature time histories of 4 experimental test cases with 4 computer codes: CE-THERM, FRAP-T5, GT3-FLECHT, and TRUMP-FLECHT. The preliminary comparisons between prediction and experiment show that the state-of-the art fuel codes have large uncertainties and are not necessarily conservative in predicting peak temperatures, turn around times, and bundle quench times

Musculoskeletal MRI at 3.0 T and 7.0 T: A comparison of relaxation times and image contrast

International Nuclear Information System (INIS)

Jordan, Caroline D.; Saranathan, Manojkumar; Bangerter, Neal K.; Hargreaves, Brian A.; Gold, Garry E.

2013-01-01

Objective: The purpose of this study was to measure and compare the relaxation times of musculoskeletal tissues at 3.0 T and 7.0 T, and to use these measurements to select appropriate parameters for musculoskeletal protocols at 7.0 T. Materials and methods: We measured the T 1 and T 2 relaxation times of cartilage, muscle, synovial fluid, bone marrow and subcutaneous fat at both 3.0 T and 7.0 T in the knees of five healthy volunteers. The T 1 relaxation times were measured using a spin-echo inversion recovery sequence with six inversion times. The T 2 relaxation times were measured using a spin-echo sequence with seven echo times. The accuracy of both the T 1 and T 2 measurement techniques was verified in phantoms at both magnetic field strengths. We used the measured relaxation times to help design 7.0 T musculoskeletal protocols that preserve the favorable contrast characteristics of our 3.0 T protocols, while achieving significantly higher resolution at higher SNR efficiency. Results: The T 1 relaxation times in all tissues at 7.0 T were consistently higher than those measured at 3.0 T, while the T 2 relaxation times at 7.0 T were consistently lower than those measured at 3.0 T. The measured relaxation times were used to help develop high resolution 7.0 T protocols that had similar fluid-to-cartilage contrast to that of the standard clinical 3.0 T protocols for the following sequences: proton-density-weighted fast spin-echo (FSE), T 2 -weighted FSE, and 3D-FSE-Cube. Conclusion: The T 1 and T 2 changes were within the expected ranges. Parameters for musculoskeletal protocols at 7.0 T can be optimized based on these values, yielding improved resolution in musculoskeletal imaging with similar contrast to that of standard 3.0 T clinical protocols

Domain Decomposition strategy for pin-wise full-core Monte Carlo depletion calculation with the reactor Monte Carlo Code

Energy Technology Data Exchange (ETDEWEB)

Liang, Jingang; Wang, Kan; Qiu, Yishu [Dept. of Engineering Physics, LiuQing Building, Tsinghua University, Beijing (China); Chai, Xiao Ming; Qiang, Sheng Long [Science and Technology on Reactor System Design Technology Laboratory, Nuclear Power Institute of China, Chengdu (China)

2016-06-15

Because of prohibitive data storage requirements in large-scale simulations, the memory problem is an obstacle for Monte Carlo (MC) codes in accomplishing pin-wise three-dimensional (3D) full-core calculations, particularly for whole-core depletion analyses. Various kinds of data are evaluated and quantificational total memory requirements are analyzed based on the Reactor Monte Carlo (RMC) code, showing that tally data, material data, and isotope densities in depletion are three major parts of memory storage. The domain decomposition method is investigated as a means of saving memory, by dividing spatial geometry into domains that are simulated separately by parallel processors. For the validity of particle tracking during transport simulations, particles need to be communicated between domains. In consideration of efficiency, an asynchronous particle communication algorithm is designed and implemented. Furthermore, we couple the domain decomposition method with MC burnup process, under a strategy of utilizing consistent domain partition in both transport and depletion modules. A numerical test of 3D full-core burnup calculations is carried out, indicating that the RMC code, with the domain decomposition method, is capable of pin-wise full-core burnup calculations with millions of depletion regions.

Performance of asynchronous fiber-optic code division multiple access system based on three-dimensional wavelength/time/space codes and its link analysis.

Science.gov (United States)

Singh, Jaswinder

2010-03-10

A novel family of three-dimensional (3-D) wavelength/time/space codes for asynchronous optical code-division-multiple-access (CDMA) systems with "zero" off-peak autocorrelation and "unity" cross correlation is reported. Antipodal signaling and differential detection is employed in the system. A maximum of [(W x T+1) x W] codes are generated for unity cross correlation, where W and T are the number of wavelengths and time chips used in the code and are prime. The conditions for violation of the cross-correlation constraint are discussed. The expressions for number of generated codes are determined for various code dimensions. It is found that the maximum number of codes are generated for S systems. The codes have a code-set-size to code-size ratio greater than W/S. For instance, with a code size of 2065 (59 x 7 x 5), a total of 12,213 users can be supported, and 130 simultaneous users at a bit-error rate (BER) of 10(-9). An arrayed-waveguide-grating-based reconfigurable encoder/decoder design for 2-D implementation for the 3-D codes is presented so that the need for multiple star couplers and fiber ribbons is eliminated. The hardware requirements of the coders used for various modulation/detection schemes are given. The effect of insertion loss in the coders is shown to be significantly reduced with loss compensation by using an amplifier after encoding. An optical CDMA system for four users is simulated and the results presented show the improvement in performance with the use of loss compensation.

Finite difference time domain solution of electromagnetic scattering on the hypercube

International Nuclear Information System (INIS)

Calalo, R.H.; Lyons, J.R.; Imbriale, W.A.

1988-01-01

Electromagnetic fields interacting with a dielectric or conducting structure produce scattered electromagnetic fields. To model the fields produced by complicated, volumetric structures, the finite difference time domain (FDTD) method employs an iterative solution to Maxwell's time dependent curl equations. Implementations of the FDTD method intensively use memory and perform numerous calculations per time step iteration. The authors have implemented an FDTD code on the California Institute of Technology/Jet Propulsion Laboratory Mark III Hypercube. This code allows to solve problems requiring as many as 2,048,000 unit cells on a 32 node Hypercube. For smaller problems, the code produces solutions in a fraction of the time to solve the same problems on sequential computers

The simplified P3 approach on a trigonal geometry in the nodal reactor code DYN3D

International Nuclear Information System (INIS)

Duerigen, S.; Fridman, E.

2011-01-01

DYN3D is a three-dimensional nodal diffusion code for steady-state and transient analyses of Light-Water Reactors with square and hexagonal fuel assembly geometries. Currently, several versions of the DYN3D code are available including a multi-group diffusion and a simplified P 3 (SP 3 ) neutron transport option. In this work, the multi-group SP 3 method based on trigonal-z geometry was developed. The method is applicable to the analysis of reactor cores with hexagonal fuel assemblies and allows flexible mesh refinement, which is of particular importance for WWER-type Pressurized Water Reactors as well as for innovative reactor concepts including block type High-Temperature Reactors and Sodium Fast Reactors. In this paper, the theoretical background for the trigonal SP 3 methodology is outlined and the results of a preliminary verification analysis are presented by means of a simplified WWER-440 core test example. The accordant cross sections and reference solutions were produced by the Monte Carlo code SERPENT. The DYN3D results are in good agreement with the reference solutions. The average deviation in the nodal power distribution is about 1%. (Authors)

FoxP3 mRNA splice forms in synovial CD4+ T cells in rheumatoid arthritis and psoriatic arthritis

DEFF Research Database (Denmark)

Ryder, L Rebekka; Bartels, Else Marie; Woetmann, Anders

2012-01-01

Our aim was to elucidate the relative amount of the different splice forms of FoxP3 mRNA in CD4+ T cells in peripheral blood (PB) compared to synovial fluid (SF) in RA and PsA patients. FoxP3 mRNA was measured using a quantitative real-time PCR method. CD4+ T cells were isolated from 17 paired...... samples of PB and SF from RA and PsA patients, and PB from 10 controls. FoxP3fl and FoxP3Δ2 mRNA was significantly increased (6.7 and 2.1-fold, respectively) in PB CD4+ T cells from RA patients compared to controls. FoxP3fl and Δ2 mRNA in SF CD4+ T cells was increased compared to controls in sero......-negative RA and PsA, but not in sero-positive RA patients, who had a high FoxP3 expression in both PB and SF. The FoxP3Δ2Δ7 mRNA was barely detectable in patient samples, and not at all in healthy individuals. We provide evidence of an increased expression of FoxP3 splice forms in synovial CD4+ T cells from...

P - aminobenzoic - 3,5 - T acid

International Nuclear Information System (INIS)

Mihaila, V.; Corol, Delia

1999-01-01

The p-aminobenzoic acid (PABA) is used in the treatment of rheumatoid arthritis and dermatological diseases. The tritium labelling of PABA leads to the elucidation of essential biomedical aspects concerning the collagen behavior. The process of tritium introduction into the PABA molecule consists of two steps: 1. Bromination of PABA with elemental bromine in 3 and 5 positions; 2. Replacement of bromine with tritium by a substitution catalytic reaction.. PABA - 3,5 - T is purified by thin layer preparative chromatography and is characterized radiochemically by radioactivity measurements carried out by liquid scintillators. The chemical concentration is determined by UV spectrophotometry. The quenching is estimated using a calibration curve of the pure product. The specific activities (about 50-60 Ci/mM) allow very sensitive biomedical studies to be performed. (authors)

Application of multi-thread computing and domain decomposition to the 3-D neutronics Fem code Cronos

International Nuclear Information System (INIS)

Ragusa, J.C.

2003-01-01

The purpose of this paper is to present the parallelization of the flux solver and the isotopic depletion module of the code, either using Message Passing Interface (MPI) or OpenMP. Thread parallelism using OpenMP was used to parallelize the mixed dual FEM (finite element method) flux solver MINOS. Investigations regarding the opportunity of mixing parallelism paradigms will be discussed. The isotopic depletion module was parallelized using domain decomposition and MPI. An attempt at using OpenMP was unsuccessful and will be explained. This paper is organized as follows: the first section recalls the different types of parallelism. The mixed dual flux solver and its parallelization are then presented. In the third section, we describe the isotopic depletion solver and its parallelization; and finally conclude with some future perspectives. Parallel applications are mandatory for fine mesh 3-dimensional transport and simplified transport multigroup calculations. The MINOS solver of the FEM neutronics code CRONOS2 was parallelized using the directive based standard OpenMP. An efficiency of 80% (resp. 60%) was achieved with 2 (resp. 4) threads. Parallelization of the isotopic depletion solver was obtained using domain decomposition principles and MPI. Efficiencies greater than 90% were reached. These parallel implementations were tested on a shared memory symmetric multiprocessor (SMP) cluster machine. The OpenMP implementation in the solver MINOS is only the first step towards fully using the SMPs cluster potential with a mixed mode parallelism. Mixed mode parallelism can be achieved by combining message passing interface between clusters with OpenMP implicit parallelism within a cluster

Application of multi-thread computing and domain decomposition to the 3-D neutronics Fem code Cronos

Energy Technology Data Exchange (ETDEWEB)

Ragusa, J.C. [CEA Saclay, Direction de l' Energie Nucleaire, Service d' Etudes des Reacteurs et de Modelisations Avancees (DEN/SERMA), 91 - Gif sur Yvette (France)

2003-07-01

The purpose of this paper is to present the parallelization of the flux solver and the isotopic depletion module of the code, either using Message Passing Interface (MPI) or OpenMP. Thread parallelism using OpenMP was used to parallelize the mixed dual FEM (finite element method) flux solver MINOS. Investigations regarding the opportunity of mixing parallelism paradigms will be discussed. The isotopic depletion module was parallelized using domain decomposition and MPI. An attempt at using OpenMP was unsuccessful and will be explained. This paper is organized as follows: the first section recalls the different types of parallelism. The mixed dual flux solver and its parallelization are then presented. In the third section, we describe the isotopic depletion solver and its parallelization; and finally conclude with some future perspectives. Parallel applications are mandatory for fine mesh 3-dimensional transport and simplified transport multigroup calculations. The MINOS solver of the FEM neutronics code CRONOS2 was parallelized using the directive based standard OpenMP. An efficiency of 80% (resp. 60%) was achieved with 2 (resp. 4) threads. Parallelization of the isotopic depletion solver was obtained using domain decomposition principles and MPI. Efficiencies greater than 90% were reached. These parallel implementations were tested on a shared memory symmetric multiprocessor (SMP) cluster machine. The OpenMP implementation in the solver MINOS is only the first step towards fully using the SMPs cluster potential with a mixed mode parallelism. Mixed mode parallelism can be achieved by combining message passing interface between clusters with OpenMP implicit parallelism within a cluster.

Cardiac cine MRI: Comparison of 1.5 T, non-enhanced 3.0 T and blood pool enhanced 3.0 T imaging

International Nuclear Information System (INIS)

Gerretsen, S.C.; Versluis, B.; Bekkers, S.C.A.M.; Leiner, T.

2008-01-01

Introduction: Cardiac cine imaging using balanced steady state free precession sequences (bSSFP) suffers from artefacts at 3.0 T. We compared bSSFP cardiac cine imaging at 1.5 T with gradient echo imaging at 3.0 T with and without a blood pool contrast agent. Materials and methods: Eleven patients referred for cardiac cine imaging underwent imaging at 1.5 T and 3.0 T. At 3.0 T images were acquired before and after administration of 0.03 mmol/kg gadofosveset. Blood pool signal-to-noise ratio (SNR), temporal variations in SNR, ejection fraction and myocardial mass were compared. Subjective image quality was scored on a four-point scale. Results: Blood pool SNR increased with more than 75% at 3.0 T compared to 1.5 T (p < 0.001); after contrast administration at 3.0 T SNR increased with 139% (p < 0.001). However, variations in blood pool SNR at 3.0 T were nearly three times as high versus those at 1.5 T in the absence of contrast medium (p < 0.001); after contrast administration this was reduced to approximately a factor 1.4 (p = 0.21). Saturation artefacts led to significant overestimation of ejection fraction in the absence of contrast administration (1.5 T: 44.7 ± 3.1 vs. 3.0 T: 50.7 ± 4.2 [p = 0.04] vs. 3.0 T post contrast: 43.4 ± 2.9 [p = 0.55]). Subjective image quality was highest for 1.5 T (2.8 ± 0.3), and lowest for non-enhanced 3.0 T (1.7 ± 0.6; p = 0.006). Conclusions: GRE cardiac cine imaging at 3.0 T after injection of the blood pool agent gadofosveset leads to improved objective and subjective cardiac cine image quality at 3.0 T and to the same conclusions regarding cardiac ejection fraction compared to bSSFP imaging at 1.5 T

Domain walls and the C P anomaly in softly broken supersymmetric QCD

Science.gov (United States)

Draper, Patrick

2018-04-01

In ordinary QCD with light, degenerate, fundamental flavors, C P symmetry is spontaneously broken at θ =π , and domain wall solutions connecting the vacua can be constructed in chiral perturbation theory. In some cases the breaking of C P saturates a 't Hooft anomaly, and anomaly inflow requires nontrivial massless excitations on the domain walls. Analogously, C P can be spontaneously broken in supersymmetric QCD (SQCD) with light flavors and small soft breaking parameters. We study C P breaking and domain walls in softly broken SQCD with Nfcomputed at leading order in the soft breaking parameters, producing a phase diagram for the stable wall trajectory. We also comment on domain walls in the similar case of QCD with an adjoint and fundamental flavors, and on the impact of adding an axion in this theory.

3D Structure and Interaction of p24β and p24δ Golgi Dynamics Domains: Implication for p24 Complex Formation and Cargo Transport.

Science.gov (United States)

Nagae, Masamichi; Hirata, Tetsuya; Morita-Matsumoto, Kana; Theiler, Romina; Fujita, Morihisa; Kinoshita, Taroh; Yamaguchi, Yoshiki

2016-10-09

The p24 family consists of four subfamilies (p24α, p24β, p24γ, and p24δ), and the proteins are thought to form hetero-oligomeric complexes for efficient transport of cargo proteins from the endoplasmic reticulum to the Golgi apparatus. The proteins possess a conserved luminal Golgi dynamics (GOLD) domain, whose functions are largely unknown. Here, we present structural and biochemical studies of p24β1 and p24δ1 GOLD domains. Use of GOLD domain-deleted mutants revealed that the GOLD domain of p24δ1 is required for proper p24 hetero-oligomeric complex formation and efficient transport of GPI-anchored proteins. The p24β1 and p24δ1 GOLD domains share a common β-sandwich fold with a characteristic intrasheet disulfide bond. The GOLD domain of p24δ1 crystallized as dimers, allowing the analysis of a homophilic interaction site. Surface plasmon resonance and solution NMR analyses revealed that p24β1 and p24δ1 GOLD domains interact weakly (K d = ~10 -4 M). Bi-protein titration provided interaction site maps. We propose that the heterophilic interaction of p24 GOLD domains contributes to the formation of the p24 hetero-oligomeric complex and to efficient cargo transport. Copyright © 2016 Elsevier Ltd. All rights reserved.

T P Yadav

Indian Academy of Sciences (India)

Home; Journals; Bulletin of Materials Science. T P Yadav. Articles written in Bulletin of Materials Science. Volume 31 Issue 3 June 2008 pp 313-318. Investigation on carbon nanomaterials: Coaxial CNT-cylinders and CNT-polymer composite · Kalpana Awasthi T P Yadav P R Mishra S Awasthi O N Srivastava · More Details ...

Numerical simulation of electromagnetic waves in Schwarzschild space-time by finite difference time domain method and Green function method

Science.gov (United States)

Jia, Shouqing; La, Dongsheng; Ma, Xuelian

2018-04-01

The finite difference time domain (FDTD) algorithm and Green function algorithm are implemented into the numerical simulation of electromagnetic waves in Schwarzschild space-time. FDTD method in curved space-time is developed by filling the flat space-time with an equivalent medium. Green function in curved space-time is obtained by solving transport equations. Simulation results validate both the FDTD code and Green function code. The methods developed in this paper offer a tool to solve electromagnetic scattering problems.

Musculoskeletal MRI at 3.0 T and 7.0 T: a comparison of relaxation times and image contrast.

Science.gov (United States)

Jordan, Caroline D; Saranathan, Manojkumar; Bangerter, Neal K; Hargreaves, Brian A; Gold, Garry E

2013-05-01

The purpose of this study was to measure and compare the relaxation times of musculoskeletal tissues at 3.0 T and 7.0 T, and to use these measurements to select appropriate parameters for musculoskeletal protocols at 7.0 T. We measured the T₁ and T₂ relaxation times of cartilage, muscle, synovial fluid, bone marrow and subcutaneous fat at both 3.0 T and 7.0 T in the knees of five healthy volunteers. The T₁ relaxation times were measured using a spin-echo inversion recovery sequence with six inversion times. The T₂ relaxation times were measured using a spin-echo sequence with seven echo times. The accuracy of both the T₁ and T₂ measurement techniques was verified in phantoms at both magnetic field strengths. We used the measured relaxation times to help design 7.0 T musculoskeletal protocols that preserve the favorable contrast characteristics of our 3.0 T protocols, while achieving significantly higher resolution at higher SNR efficiency. The T₁ relaxation times in all tissues at 7.0 T were consistently higher than those measured at 3.0 T, while the T₂ relaxation times at 7.0 T were consistently lower than those measured at 3.0 T. The measured relaxation times were used to help develop high resolution 7.0 T protocols that had similar fluid-to-cartilage contrast to that of the standard clinical 3.0 T protocols for the following sequences: proton-density-weighted fast spin-echo (FSE), T₂-weighted FSE, and 3D-FSE-Cube. The T₁ and T₂ changes were within the expected ranges. Parameters for musculoskeletal protocols at 7.0 T can be optimized based on these values, yielding improved resolution in musculoskeletal imaging with similar contrast to that of standard 3.0 T clinical protocols. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

FoxP3+ regulatory T cells are distinct from leukemia cells in HTLV-1-associated adult T-cell leukemia.

Science.gov (United States)

Toulza, Frederic; Nosaka, Kisato; Takiguchi, Masafumi; Pagliuca, Tony; Mitsuya, Hiroaki; Tanaka, Yuetsu; Taylor, Graham P; Bangham, Charles R M

2009-11-15

Human T-lymphotropic virus type 1 (HTLV-1) is the causative agent of adult T-cell leukemia/lymphoma (ATLL). It has been postulated that ATLL cells might act as regulatory T cells (T(regs)) which, in common with ATLL cells, express both CD25 and FoxP3, and so contribute to the severe immune suppression typical of ATLL. We report here that the frequency of CD25(+) cells varied independently of the frequency of FoxP3(+) cells in both a cross-sectional study and in a longitudinal study of 2 patients with chronic ATLL. Furthermore, the capacity of ATLL cells to suppress proliferation of heterologous CD4(+)CD25(-) cells correlated with the frequency of CD4(+) FoxP3(+) cells but was independent of CD25 expression. Finally, the frequency of CD4(+)FoxP3(+) cells was inversely correlated with the lytic activity of HTLV-1-specific CTLs in patients with ATLL. We conclude that ATLL is not a tumor of FoxP3(+) regulatory T cells, and that a population of FoxP3(+) cells distinct from ATLL cells has regulatory functions and may impair the cell-mediated immune response to HTLV-1 in patients with ATLL.

Gene fusions AHRR-NCOA2, NCOA2-ETV4, ETV4-AHRR, P4HA2-TBCK, and TBCK-P4HA2 resulting from the translocations t(5;8;17)(p15;q13;q21) and t(4;5)(q24;q31) in a soft tissue angiofibroma.

Science.gov (United States)

Panagopoulos, Ioannis; Gorunova, Ludmila; Viset, Trond; Heim, Sverre

2016-11-01

We present an angiofibroma of soft tissue with the karyotype 46,XY,t(4;5)(q24;q31),t(5;8;17)(p15;q13;q21)[8]/46,XY,t(1;14)(p31;q32)[2]/46,XY[3]. RNA‑sequencing showed that the t(4;5)(q24;q31) resulted in recombination of the genes TBCK on 4q24 and P4HA2 on 5q31.1 with generation of an in‑frame TBCK‑P4HA2 and the reciprocal but out‑of‑frame P4HA2‑TBCK fusion transcripts. The putative TBCK‑P4HA2 protein would contain the kinase, the rhodanese‑like domain, and the Tre‑2/Bub2/Cdc16 (TBC) domains of TBCK together with the P4HA2 protein which is a component of the prolyl 4‑hydroxylase. The t(5;8;17)(p15;q13;q21) three‑way chromosomal translocation targeted AHRR (on 5p15), NCOA2 (on 8q13), and ETV4 (on 17q21) generating the in‑frame fusions AHRR‑NCOA2 and NCOA2‑ETV4 as well as an out‑of‑frame ETV4‑AHRR transcript. In the AHRR‑NCOA2 protein, the C‑terminal part of AHRR is replaced by the C‑terminal part of NCOA2 which contains two activation domains. The NCOA2‑ETV4 protein would contain the helix‑loop‑helix, PAS_9 and PAS_11, CITED domains, the SRC‑1 domain of NCOA2 and the ETS DNA‑binding domain of ETV4. No fusion gene corresponding to t(1;14)(p31;q32) was found. Our findings indicate that, in spite of the recurrence of AHRR‑NCOA2 in angiofibroma of soft tissue, additional genetic events (or fusion genes) might be required for the development of this tumor.

Time-Domain Simulation of RF Couplers

International Nuclear Information System (INIS)

Smithe, David; Carlsson, Johan; Austin, Travis

2009-01-01

We have developed a finite-difference time-domain (FDTD) fluid-like approach to integrated plasma-and-coupler simulation [1], and show how it can be used to model LH and ICRF couplers in the MST and larger tokamaks.[2] This approach permits very accurate 3-D representation of coupler geometry, and easily includes non-axi-symmetry in vessel wall, magnetic equilibrium, and plasma density. The plasma is integrated with the FDTD Maxwell solver in an implicit solve that steps over electron time-scales, and permits tenuous plasma in the coupler itself, without any need to distinguish or interface between different regions of vacuum and/or plasma. The FDTD algorithm is also generalized to incorporate a time-domain sheath potential [3] on metal structures within the simulation, to look for situations where the sheath potential might generate local sputtering opportunities. Benchmarking of the time-domain sheath algorithm has been reported in the references. Finally, the time-domain software [4] permits the use of particles, either as field diagnostic (test particles) or to self-consistently compute plasma current from the applied RF power.

OSSMETER D3.2 – Report on Source Code Activity Metrics

NARCIS (Netherlands)

J.J. Vinju (Jurgen); A. Shahi (Ashim)

2014-01-01

htmlabstractThis deliverable is part of WP3: Source Code Quality and Activity Analysis. It provides descriptions and initial prototypes of the tools that are needed for source code activity analysis. It builds upon the Deliverable 3.1 where infra-structure and a domain analysis have been

Rascal: A domain specific language for source code analysis and manipulation

NARCIS (Netherlands)

P. Klint (Paul); T. van der Storm (Tijs); J.J. Vinju (Jurgen); A. Walenstein; S. Schuppe

2009-01-01

htmlabstractMany automated software engineering tools require tight integration of techniques for source code analysis and manipulation. State-of-the-art tools exist for both, but the domains have remained notoriously separate because different computational paradigms fit each domain best. This

RASCAL : a domain specific language for source code analysis and manipulationa

NARCIS (Netherlands)

Klint, P.; Storm, van der T.; Vinju, J.J.

2009-01-01

Many automated software engineering tools require tight integration of techniques for source code analysis and manipulation. State-of-the-art tools exist for both, but the domains have remained notoriously separate because different computational paradigms fit each domain best. This impedance

Investigation of T-cell immunoglobulin- and mucin-domain-containing molecule-3 (TIM-3) polymorphisms in essential thrombocythaemia (ET).

Science.gov (United States)

Han, Fuyan; Wang, Guanghai; Li, Yuantang; Tian, Wenjun; Dong, Zhenfang; Cheng, Shiqing; Liu, Yiqing; Qu, Teng; Wang, Xiaoying; Wang, Yong; Zhang, Bingchang; Ju, Ying

2017-07-01

T-cell immunoglobulin- and mucin-domain-containing molecule-3 (TIM-3) is preferentially expressed on terminally differentiated Th1 cells and inhibits their IFN-γ production. It has been reported that chronic inflammation may be an important driving force for myeloproliferative neoplasms (MPNs). Therefore, we hypothesized that as an important inflammation regulator, TIM-3 may be involved in essential thrombocythaemia (ET). The goal of this study was to investigate whether the -1516G > T, -574G > T and +4259T > G single-nucleotide polymorphisms (SNPs) within the TIM-3 gene contribute to the genetic susceptibility of individuals to ET. Genotyping of the TIM-3 -1516G > T, -574G > T and + 4259T > G SNPs was performed in 175 patients with ET and in 151 controls via a polymerase chain reaction-restriction fragment length polymorphism assay. We also investigated the relationships between the genotypes of each SNP and the risk factors of ET such as routine blood indexes, age and JAK2 V617F mutation. The genotype and allele frequencies of the -1516G > T SNP (p = 0.016 and 0.019, respectively), the -574G > T SNP (p = 0.035 and 0.038, respectively) and the +4259T > G SNP (p = 0.036 and 0.038, respectively) of the ET patients and the controls were significantly different. A haplotype analysis found that the GGT and TGT haplotypes had significantly different distributions between ET and controls (p = 0.041 and 0.041, respectively). However, no significant differences were detected between the genotypes of all SNPs and routine blood indexes, age and JAK2V617F mutation. The -1516G > T, -574G > T and +4259T > G SNPs within TIM-3 gene might play an important role as a genetic risk factor in the pathogenesis of ET.

THYDE-P2 code: RCS (reactor-coolant system) analysis code

International Nuclear Information System (INIS)

Asahi, Yoshiro; Hirano, Masashi; Sato, Kazuo

1986-12-01

THYDE-P2, being characterized by the new thermal-hydraulic network model, is applicable to analysis of RCS behaviors in response to various disturbances including LB (large break)-LOCA(loss-of-coolant accident). In LB-LOCA analysis, THYDE-P2 is capable of through calculation from its initiation to complete reflooding of the core without an artificial change in the methods and models. The first half of the report is the description of the methods and models for use in the THYDE-P2 code, i.e., (1) the thermal-hydraulic network model, (2) the various RCS components models, (3) the heat sources in fuel, (4) the heat transfer correlations, (5) the mechanical behavior of clad and fuel, and (6) the steady state adjustment. The second half of the report is the user's mannual for the THYDE-P2 code (version SV04L08A) containing items; (1) the program control (2) the input requirements, (3) the execution of THYDE-P2 job, (4) the output specifications and (5) the sample problem to demonstrate capability of the thermal-hydraulic network model, among other things. (author)

Turbo coding, turbo equalisation and space-time coding for transmission over fading channels

CERN Document Server

Hanzo, L; Yeap, B

2002-01-01

Against the backdrop of the emerging 3G wireless personal communications standards and broadband access network standard proposals, this volume covers a range of coding and transmission aspects for transmission over fading wireless channels. It presents the most important classic channel coding issues and also the exciting advances of the last decade, such as turbo coding, turbo equalisation and space-time coding. It endeavours to be the first book with explicit emphasis on channel coding for transmission over wireless channels. Divided into 4 parts: Part 1 - explains the necessary background for novices. It aims to be both an easy reading text book and a deep research monograph. Part 2 - provides detailed coverage of turbo conventional and turbo block coding considering the known decoding algorithms and their performance over Gaussian as well as narrowband and wideband fading channels. Part 3 - comprehensively discusses both space-time block and space-time trellis coding for the first time in literature. Par...

Time-dependent anisotropic distributed source capability in transient 3-d transport code tort-TD

International Nuclear Information System (INIS)

Seubert, A.; Pautz, A.; Becker, M.; Dagan, R.

2009-01-01

The transient 3-D discrete ordinates transport code TORT-TD has been extended to account for time-dependent anisotropic distributed external sources. The extension aims at the simulation of the pulsed neutron source in the YALINA-Thermal subcritical assembly. Since feedback effects are not relevant in this zero-power configuration, this offers a unique opportunity to validate the time-dependent neutron kinetics of TORT-TD with experimental data. The extensions made in TORT-TD to incorporate a time-dependent anisotropic external source are described. The steady state of the YALINA-Thermal assembly and its response to an artificial square-wave source pulse sequence have been analysed with TORT-TD using pin-wise homogenised cross sections in 18 prompt energy groups with P 1 scattering order and 8 delayed neutron groups. The results demonstrate the applicability of TORT-TD to subcritical problems with a time-dependent external source. (authors)

Hybrid diffusion-P3 equation in N-layered turbid media: steady-state domain.

Science.gov (United States)

Shi, Zhenzhi; Zhao, Huijuan; Xu, Kexin

2011-10-01

This paper discusses light propagation in N-layered turbid media. The hybrid diffusion-P3 equation is solved for an N-layered finite or infinite turbid medium in the steady-state domain for one point source using the extrapolated boundary condition. The Fourier transform formalism is applied to derive the analytical solutions of the fluence rate in Fourier space. Two inverse Fourier transform methods are developed to calculate the fluence rate in real space. In addition, the solutions of the hybrid diffusion-P3 equation are compared to the solutions of the diffusion equation and the Monte Carlo simulation. For the case of small absorption coefficients, the solutions of the N-layered diffusion equation and hybrid diffusion-P3 equation are almost equivalent and are in agreement with the Monte Carlo simulation. For the case of large absorption coefficients, the model of the hybrid diffusion-P3 equation is more precise than that of the diffusion equation. In conclusion, the model of the hybrid diffusion-P3 equation can replace the diffusion equation for modeling light propagation in the N-layered turbid media for a wide range of absorption coefficients.

Patterns of Failure After Radical Cystectomy for pT3-4 Bladder Cancer: Implications for Adjuvant Radiation Therapy

Energy Technology Data Exchange (ETDEWEB)

Reddy, Abhinav V. [Department of Radiation and Cellular Oncology, University of Chicago Pritzker School of Medicine, Chicago, Illinois (United States); Pariser, Joseph J.; Pearce, Shane M. [Section of Urology, Department of Surgery, University of Chicago Pritzker School of Medicine, Chicago, Illinois (United States); Weichselbaum, Ralph R. [Department of Radiation and Cellular Oncology, University of Chicago Pritzker School of Medicine, Chicago, Illinois (United States); Smith, Norm D.; Steinberg, Gary D. [Section of Urology, Department of Surgery, University of Chicago Pritzker School of Medicine, Chicago, Illinois (United States); Liauw, Stanley L., E-mail: sliauw@radonc.uchicago.edu [Department of Radiation and Cellular Oncology, University of Chicago Pritzker School of Medicine, Chicago, Illinois (United States)

2016-04-01

Purpose: In patients with muscle-invasive bladder cancer, local-regional failure (LF) has been reported to occur in up to 20% of patients following radical cystectomy. The goals of this study were to describe patterns of LF, as well as assess factors associated with LF in a cohort of patients with pT3-4 bladder cancer. This information may have implications towards the use of adjuvant radiation therapy. Methods and Materials: Patients with pathologic T3-4 N0-1 bladder cancer were examined from an institutional radical cystectomy database. Preoperative demographics and pathologic characteristics were examined. Outcomes included overall survival and LF. Local-regional failures were defined using follow-up imaging reports and scans, and the locations of LF were characterized. Variables were tested by univariate and multivariate analysis for association with LF and overall survival. Results: A total of 334 patients had pT3-4 and N0-1 disease after radical cystectomy and bilateral pelvic lymph node dissection. Of these, 46% received perioperative chemotherapy. The median age was 71 years old, and median follow-up was 11 months. On univariate analysis, margin status, pT stage, and pN stage, were all associated with LF (P<.05), however, on multivariate analysis, only pT and pN stages were significantly associated with LF (P<.05). Three strata of risk were defined, including low-risk patients with pT3N0 disease, intermediate-risk patients with pT3N1 or pT4N0 disease, and high-risk patients with pT4N1 disease, who had a 2-year incidence of LF of 12%, 33%, and 72%, respectively. The most common sites of pelvic relapse included the external and internal iliac lymph nodes (LNs) and obturator LN regions. Notably, 34% of patients with LF had local-regional only disease at the time of recurrence. Conclusions: Patients with pT4 or N1 disease have a 2-year risk of LF that exceeds 30%. These patients may be the most likely to benefit from local adjuvant therapies.

Expression and Purification of Functional Ligand-binding Domains of T1R3 Taste Receptors

Energy Technology Data Exchange (ETDEWEB)

Nie,Y.; Hobbs, J.; Vigues, S.; Olson, W.; Conn, G.; Munger, S.

2006-01-01

Chemosensory receptors, including odor, taste, and vomeronasal receptors, comprise the largest group of G protein-coupled receptors (GPCRs) in the mammalian genome. However, little is known about the molecular determinants that are critical for the detection and discrimination of ligands by most of these receptors. This dearth of understanding is due in part to difficulties in preparing functional receptors suitable for biochemical and biophysical analyses. Here we describe in detail two strategies for the expression and purification of the ligand-binding domain of T1R taste receptors, which are constituents of the sweet and umami taste receptors. These class C GPCRs contain a large extracellular N-terminal domain (NTD) that is the site of interaction with most ligands and that is amenable to expression as a separate polypeptide in heterologous cells. The NTD of mouse T1R3 was expressed as two distinct fusion proteins in Escherichia coli and purified by column chromatography. Spectroscopic analysis of the purified NTD proteins shows them to be properly folded and capable of binding ligands. This methodology should not only facilitate the characterization of T1R ligand interactions but may also be useful for dissecting the function of other class C GPCRs such as the large family of orphan V2R vomeronasal receptors.

Epitaxial Growth of Hetero-Ln-MOF Hierarchical Single Crystals for Domain- and Orientation-Controlled Multicolor Luminescence 3D Coding Capability.

Science.gov (United States)

Pan, Mei; Zhu, Yi-Xuan; Wu, Kai; Chen, Ling; Hou, Ya-Jun; Yin, Shao-Yun; Wang, Hai-Ping; Fan, Ya-Nan; Su, Cheng-Yong

2017-11-13

Core-shell or striped heteroatomic lanthanide metal-organic framework hierarchical single crystals were obtained by liquid-phase anisotropic epitaxial growth, maintaining identical periodic organization while simultaneously exhibiting spatially segregated structure. Different types of domain and orientation-controlled multicolor photophysical models are presented, which show either visually distinguishable or visible/near infrared (NIR) emissive colors. This provides a new bottom-up strategy toward the design of hierarchical molecular systems, offering high-throughput and multiplexed luminescence color tunability and readability. The unique capability of combining spectroscopic coding with 3D (three-dimensional) microscale spatial coding is established, providing potential applications in anti-counterfeiting, color barcoding, and other types of integrated and miniaturized optoelectronic materials and devices. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Epitaxial growth of hetero-Ln-MOF hierarchical single crystals for domain- and orientation-controlled multicolor luminescence 3D coding capability

International Nuclear Information System (INIS)

Pan, Mei; Zhu, Yi-Xuan; Wu, Kai; Chen, Ling; Hou, Ya-Jun; Yin, Shao-Yun; Wang, Hai-Ping; Fan, Ya-Nan; Su, Cheng-Yong

2017-01-01

Core-shell or striped heteroatomic lanthanide metal-organic framework hierarchical single crystals were obtained by liquid-phase anisotropic epitaxial growth, maintaining identical periodic organization while simultaneously exhibiting spatially segregated structure. Different types of domain and orientation-controlled multicolor photophysical models are presented, which show either visually distinguishable or visible/near infrared (NIR) emissive colors. This provides a new bottom-up strategy toward the design of hierarchical molecular systems, offering high-throughput and multiplexed luminescence color tunability and readability. The unique capability of combining spectroscopic coding with 3D (three-dimensional) microscale spatial coding is established, providing potential applications in anti-counterfeiting, color barcoding, and other types of integrated and miniaturized optoelectronic materials and devices. (copyright 2017 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

Epitaxial growth of hetero-Ln-MOF hierarchical single crystals for domain- and orientation-controlled multicolor luminescence 3D coding capability

Energy Technology Data Exchange (ETDEWEB)

Pan, Mei; Zhu, Yi-Xuan; Wu, Kai; Chen, Ling; Hou, Ya-Jun; Yin, Shao-Yun; Wang, Hai-Ping; Fan, Ya-Nan [MOE Laboratory of Bioinorganic and Synthetic Chemistry, Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou (China); Su, Cheng-Yong [MOE Laboratory of Bioinorganic and Synthetic Chemistry, Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou (China); State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou (China)

2017-11-13

Core-shell or striped heteroatomic lanthanide metal-organic framework hierarchical single crystals were obtained by liquid-phase anisotropic epitaxial growth, maintaining identical periodic organization while simultaneously exhibiting spatially segregated structure. Different types of domain and orientation-controlled multicolor photophysical models are presented, which show either visually distinguishable or visible/near infrared (NIR) emissive colors. This provides a new bottom-up strategy toward the design of hierarchical molecular systems, offering high-throughput and multiplexed luminescence color tunability and readability. The unique capability of combining spectroscopic coding with 3D (three-dimensional) microscale spatial coding is established, providing potential applications in anti-counterfeiting, color barcoding, and other types of integrated and miniaturized optoelectronic materials and devices. (copyright 2017 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

Expression, purification, crystallization and preliminary phasing of the heteromerization domain of the tRNA-export and aminoacylation cofactor Arc1p from yeast

International Nuclear Information System (INIS)

Simader, Hannes; Suck, Dietrich

2006-01-01

The heteromerization domain of an aminoacyl-tRNA synthetase cofactor from yeast was crystallized, complete selenomethionine MAD data were collected to 2.8 Å resolution and preliminary phasing reveals the presence of 20 monomers in the asymmetric unit. Eukaryotic aminoacyl-tRNA synthetases (aaRSs) must be integrated into an efficient tRNA-export and shuttling machinery. This is reflected by the presence of additional protein–protein interaction domains and a correspondingly higher degree of complex formation in eukaryotic aaRSs. However, the structural basis of interaction between eukaryotic aaRSs and associated protein cofactors has remained elusive. The N-terminal heteromerization domain of the tRNA aminoacylation and export cofactor Arc1p has been cloned from yeast, expressed and purified. Crystals have been obtained belonging to space group C2, with unit-cell parameters a = 222.32, b = 89.46, c = 126.79 Å, β = 99.39°. Calculated Matthews coefficients are compatible with the presence of 10–25 monomers in the asymmetric unit. A complete multiple-wavelength anomalous dispersion data set has been collected from a selenomethionine-substituted crystal at 2.8 Å resolution. Preliminary phasing reveals the presence of 20 monomers organized in five tetramers per asymmetric unit

Methodology for Time-Domain Estimation of Storm-Time Electric Fields Using the 3D Earth Impedance

Science.gov (United States)

Kelbert, A.; Balch, C. C.; Pulkkinen, A. A.; Egbert, G. D.; Love, J. J.; Rigler, E. J.; Fujii, I.

2016-12-01

Magnetic storms can induce geoelectric fields in the Earth's electrically conducting interior, interfering with the operations of electric-power grid industry. The ability to estimate these electric fields at Earth's surface in close to real-time and to provide local short-term predictions would improve the ability of the industry to protect their operations. At any given time, the electric field at the Earth's surface is a function of the time-variant magnetic activity (driven by the solar wind), and the local electrical conductivity structure of the Earth's crust and mantle. For this reason, implementation of an operational electric field estimation service requires an interdisciplinary, collaborative effort between space science, real-time space weather operations, and solid Earth geophysics. We highlight in this talk an ongoing collaboration between USGS, NOAA, NASA, Oregon State University, and the Japan Meteorological Agency, to develop algorithms that can be used for scenario analyses and which might be implemented in a real-time, operational setting. We discuss the development of a time domain algorithm that employs discrete time domain representation of the impedance tensor for a realistic 3D Earth, known as the discrete time impulse response (DTIR), convolved with the local magnetic field time series, to estimate the local electric field disturbances. The algorithm is validated against measured storm-time electric field data collected in the United States and Japan. We also discuss our plans for operational real-time electric field estimation using 3D Earth impedances.

Time-of-flight positron emission tomography (T.O.F. P.E.T.)

International Nuclear Information System (INIS)

Allemand, R.

1984-10-01

A new important step has been made in the performances of the time-of-flight positron imaging for the two last years. It has been proved that a high spatial resolution can be obtained with the T.O.F. technique. It has also been shown that the overall sensitivity (taking into account the sensitivity gain and BaF2 detection characteristics) is quite close to the one of conventional methods. On the other hand, the basic advantages related to the high counting rate capability, the random coincidences rejection etc... of course remain. It is probably safe to assume that significant improvements can be expected if new technological efforts are invested. Unfortunately, P.E.T. is a complex and expensive tool which has been only used up to now in the research groups (about 50 centers in the world). The justification of new technical developments will be quite clear when this modality will be considered in the assessment of diseases and in clinical diagnostic applications

High-Fidelity RF Gun Simulations with the Parallel 3D Finite Element Particle-In-Cell Code Pic3P

Energy Technology Data Exchange (ETDEWEB)

Candel, A; Kabel, A.; Lee, L.; Li, Z.; Limborg, C.; Ng, C.; Schussman, G.; Ko, K.; /SLAC

2009-06-19

SLAC's Advanced Computations Department (ACD) has developed the first parallel Finite Element 3D Particle-In-Cell (PIC) code, Pic3P, for simulations of RF guns and other space-charge dominated beam-cavity interactions. Pic3P solves the complete set of Maxwell-Lorentz equations and thus includes space charge, retardation and wakefield effects from first principles. Pic3P uses higher-order Finite Elementmethods on unstructured conformal meshes. A novel scheme for causal adaptive refinement and dynamic load balancing enable unprecedented simulation accuracy, aiding the design and operation of the next generation of accelerator facilities. Application to the Linac Coherent Light Source (LCLS) RF gun is presented.

Inhomogeneous nucleation and domain wall motion with Barkhausen avalanches in epitaxial PbZr0.4Ti0.6O3 thin films

International Nuclear Information System (INIS)

Yang, Sang Mo; Kim, Hun Ho; Kim, Tae Heon; Kim, Ik Joo; Yoon, Jong Gul

2012-01-01

We investigated the ferroelectric (FE) domain nucleation and domain wall motion in epitaxial PbZr 0.4 Ti 0.6 O 3 capacitors by using modified piezoresponse force microscopy with the domain-tracing method. From time-dependent FE domain evolution images, we observed that defect-mediated inhomogeneous nucleation occurred with a stochastic nature. In addition, we found that the number of nuclei N(t) was linearly proportional to log t, where t is the accumulated time of the applied pulse fields. The time-dependence of N(t) suggests a distribution of energy barriers for nucleation, which may determine the stochastic nature of domain nucleation. We also observed that the domain grew with consecutive Barkhausen avalanches and that the growth direction became anisotropic when the domain radius was larger than a critical radius of about 100 nm.

tRNA gene diversity in the three domains of life

Directory of Open Access Journals (Sweden)

Kosuke eFujishima

2014-05-01

Full Text Available Transfer RNA (tRNA is widely known for its key role in decoding mRNA into protein. Despite their necessity and relatively short nucleotide sequences, a large diversity of gene structures and RNA secondary structures of pre-tRNAs and mature tRNAs have recently been discovered in the three domains of life. Growing evidences of disrupted tRNA genes in the genomes of Archaea reveals unique gene structures such as, intron-containing tRNA, split tRNA, and permuted tRNA. Coding sequence for these tRNAs are either separated with introns, fragmented, or permuted at the genome level. Although evolutionary scenario behind the tRNA gene disruption is still unclear, diversity of tRNA structure seems to be co-evolved with their processing enzyme, so-called RNA splicing endonuclease. Metazoan mitochondrial tRNAs (mtRNAs are known for their unique lack of either one or two arms from the typical tRNA cloverleaf structure, while still maintaining functionality. Recently identified nematode-specific V-arm containing tRNAs (nev-tRNAs possess long variable arms that are specific to eukaryotic class II tRNASer and tRNALeu but also decode class I tRNA codons. Moreover, many tRNA-like sequences have been found in the genomes of different organisms and viruses. Thus this review is aimed to cover the latest knowledge on tRNA gene diversity and further recapitulate the evolutionary and biological aspects that caused such uniqueness.

SH2 Domains Serve as Lipid-Binding Modules for pTyr-Signaling Proteins.

Science.gov (United States)

Park, Mi-Jeong; Sheng, Ren; Silkov, Antonina; Jung, Da-Jung; Wang, Zhi-Gang; Xin, Yao; Kim, Hyunjin; Thiagarajan-Rosenkranz, Pallavi; Song, Seohyeon; Yoon, Youngdae; Nam, Wonhee; Kim, Ilshin; Kim, Eui; Lee, Dong-Gyu; Chen, Yong; Singaram, Indira; Wang, Li; Jang, Myoung Ho; Hwang, Cheol-Sang; Honig, Barry; Ryu, Sungho; Lorieau, Justin; Kim, You-Me; Cho, Wonhwa

2016-04-07

The Src-homology 2 (SH2) domain is a protein interaction domain that directs myriad phosphotyrosine (pY)-signaling pathways. Genome-wide screening of human SH2 domains reveals that ∼90% of SH2 domains bind plasma membrane lipids and many have high phosphoinositide specificity. They bind lipids using surface cationic patches separate from pY-binding pockets, thus binding lipids and the pY motif independently. The patches form grooves for specific lipid headgroup recognition or flat surfaces for non-specific membrane binding and both types of interaction are important for cellular function and regulation of SH2 domain-containing proteins. Cellular studies with ZAP70 showed that multiple lipids bind its C-terminal SH2 domain in a spatiotemporally specific manner and thereby exert exquisite spatiotemporal control over its protein binding and signaling activities in T cells. Collectively, this study reveals how lipids control SH2 domain-mediated cellular protein-protein interaction networks and suggest a new strategy for therapeutic modulation of pY-signaling pathways. Copyright © 2016 Elsevier Inc. All rights reserved.

An FFT-accelerated time-domain multiconductor transmission line simulator

KAUST Repository

Bagci, Hakan

2010-02-01

A fast time-domain multiconductor transmission line (MTL) simulator for analyzing general MTL networks is presented. The simulator models the networks as homogeneous MTLs that are excited by external fields and driven/terminated/ connected by potentially nonlinear lumped circuitry. It hybridizes an MTL solver derived from time-domain integral equations (TDIEs) in unknown wave coefficients for each MTL with a circuit solver rooted in modified nodal analysis equations in unknown node voltages and voltage-source currents for each circuit. These two solvers are rigorously interfaced at MTL and circuit terminals, and the resulting coupled system of equations is solved simultaneously for all MTL and circuit unknowns at each time step. The proposed simulator is amenable to hybridization, is fast Fourier transform (FFT)-accelerated, and is highly accurate: 1) It can easily be hybridized with TDIE-based field solvers (in a fully rigorous mathematical framework) for performing electromagnetic interference and compatibility analysis on electrically large and complex structures loaded with MTL networks. 2) It is accelerated by an FFT algorithm that calculates temporal convolutions of time-domain MTL Green functions in only O(Ntlog2 N t) rather than O(Ntt2) operations, where N t is the number of time steps of simulation. Moreover, the algorithm, which operates on temporal samples of MTL Green functions, is indifferent to the method used to obtain them. 3) It approximates MTL voltages, currents, and wave coefficients, using high-order temporal basis functions. Various numerical examples, including the crosstalk analysis of a (twisted) unshielded twisted-pair (UTP)-CAT5 cable and the analysis of field coupling into UTP-CAT5 and RG-58 cables located on an airplane, are presented to demonstrate the accuracy, efficiency, and versatility of the proposed simulator. © 2010 IEEE.

Evolution of the RNase P RNA structural domain in Leptospira spp

NARCIS (Netherlands)

Ravishankar, Vigneshwaran; Ahmed, Ahmed; Sivagnanam, Ulaganathan; Muthuraman, Krishnaraja; Karthikaichamy, Anbarasu; Wilson, Herald A.; Devendran, Ajay; Hartskeerl, Rudy A.; Raj, Stephen M. L.

2014-01-01

We have employed the RNase P RNA (RPR) gene, which is present as single copy in chromosome I of Leptospira spp. to investigate the phylogeny of structural domains present in the RNA subunit of the tRNA processing enzyme, RNase P. RPR gene sequences of 150 strains derived from NCBI database along

Recent Improvements to the IMPACT-T Parallel Particle Tracking Code

International Nuclear Information System (INIS)

Qiang, J.; Pogorelov, I.V.; Ryne, R.

2006-01-01

The IMPACT-T code is a parallel three-dimensional quasi-static beam dynamics code for modeling high brightness beams in photoinjectors and RF linacs. Developed under the US DOE Scientific Discovery through Advanced Computing (SciDAC) program, it includes several key features including a self-consistent calculation of 3D space-charge forces using a shifted and integrated Green function method, multiple energy bins for beams with large energy spread, and models for treating RF standing wave and traveling wave structures. In this paper, we report on recent improvements to the IMPACT-T code including modeling traveling wave structures, short-range transverse and longitudinal wakefields, and longitudinal coherent synchrotron radiation through bending magnets

Application of the risk-informed methodology for APR1400 P-T limits curve

Energy Technology Data Exchange (ETDEWEB)

Kim, K.; Namgung, I. [KEPCO International Nuclear Graduate School, Ulsan (Korea, Republic of)

2014-07-01

A reactor pressure vessel (RPV) in a nuclear power plant has operational limits of pressure and temperature to prevent a potential drastic propagation of cracks due to brittle fracture. We call it a pressure-temperature limits curve (P-T limits curve). Appendix G of the American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel Code, Section XI, provides deterministic procedures to develop the P-T limits curve for the reactor pressure vessel. Recently, an alternative risk-informed methodology has been added in the ASME Code. Risk-informed means that we can consider insights from a probabilistic risk assessment by using this methodology. This alternative methodology provides a simple procedure to develop risk-informed P-T limits for heat up, cool down, and hydrostatic test events. The risk-informed P-T limits curve is known to provide more operational flexibility, particularly for reactor pressure vessels with relatively high irradiation levels and radiation sensitive materials. In this paper, we developed both the deterministic and a risk-informed P-T limits curve for an APR1400 reactor using Appendix G of the ASME Code, Section XI and compare the results in terms of additional operational margin. (author)

Surface potential domains on lamellar P3OT structures

Energy Technology Data Exchange (ETDEWEB)

Perez-GarcIa, B [Departamento Fisica, Facultad de Quimica (Campus Espinardo), Universidad de Murcia, E-30100 Murcia (Spain); Abad, J [Departamento Fisica, Facultad de Quimica (Campus Espinardo), Universidad de Murcia, E-30100 Murcia (Spain); Urbina, A [Departamento Electronica, TecnologIa de Computadoras y Proyectos, Universidad Politecnica de Cartagena, E-30202 Cartagena (Spain); Colchero, J [Departamento Fisica, Facultad de Quimica (Campus Espinardo), Universidad de Murcia, E-30100 Murcia (Spain); Palacios-Lidon, E [Departamento Fisica, Facultad de Quimica (Campus Espinardo), Universidad de Murcia, E-30100 Murcia (Spain)

2008-02-13

In this work the electrostatic properties of poly(3-octylthiophene) thin films have been studied on a nanometer scale by means of electrostatic force microscopy and Kelvin probe microscopy (KPM). The KPM images reveal that different surface contact potential domains coexist on the polymer surface. This result, together with additional capacitance measurements, indicates that the potential domains are related to the existence of dipoles due to different molecular arrangements. Finally, capacitance measurements as a function of the tip-sample bias voltage show that in all regions large band bending effects take place.

Surface potential domains on lamellar P3OT structures

International Nuclear Information System (INIS)

Perez-GarcIa, B; Abad, J; Urbina, A; Colchero, J; Palacios-Lidon, E

2008-01-01

In this work the electrostatic properties of poly(3-octylthiophene) thin films have been studied on a nanometer scale by means of electrostatic force microscopy and Kelvin probe microscopy (KPM). The KPM images reveal that different surface contact potential domains coexist on the polymer surface. This result, together with additional capacitance measurements, indicates that the potential domains are related to the existence of dipoles due to different molecular arrangements. Finally, capacitance measurements as a function of the tip-sample bias voltage show that in all regions large band bending effects take place

Reactions of R(2)P-P(SiMe(3))Li with [(R'(3)P)(2)PtCl(2)]. A general and efficient entry to phosphanylphosphinidene complexes of platinum. Syntheses and structures of [(eta(2)-P=(i)Pr(2))Pt(p-Tol(3)P)(2)], [(eta(2)-P=(t)Bu(2))Pt(p-Tol(3)P)(2)], [{eta(2)-P=(N(i)Pr(2))(2)}Pt(p-Tol(3)P)(2)] and [{(Et(2)PhP)(2)Pt}(2)P(2)].

Science.gov (United States)

Domańska-Babul, Wioleta; Chojnacki, Jaroslaw; Matern, Eberhard; Pikies, Jerzy

2009-01-07

The reactions of lithium derivatives of diphosphanes R(2)P-P(SiMe(3))Li (R = (t)Bu, (i)Pr, Et(2)N and (i)Pr(2)N) with [(R'(3)P)(2)PtCl(2)] (R'(3)P = Et(3)P, Et(2)PhP, EtPh(2)P and p-Tol(3)P) proceed in a facile manner to afford side-on bonded phosphanylphosphinidene complexes of platinum [(eta(2)-P=R(2))Pt(PR'(3))(2)]. The related reactions of Ph(2)P-P(SiMe(3))Li with [(R'(3)P)(2)PtCl(2)] did not yield [(eta(2)-P=PPh(2))Pt(PR'(3))(2)] and resulted mainly in the formation of [{(R'(3)P)(2)Pt}(2)P(2)], Ph(2)P-PLi-PPh(2), (Me(3)Si)(2)PLi and (Me(3)Si)(3)P. Crystallographic data are reported for the compounds [(eta(2)-P=R(2))Pt(p-Tol(3)P)(2)] (R = (t)Bu, (i)Pr, ((i)Pr(2)N)(2)P) and for [{(Et(2)PhP)(2)Pt}(2)P(2)].

Accumulation of raft lipids in T-cell plasma membrane domains engaged in TCR signalling

DEFF Research Database (Denmark)

Zech, Tobias; Ejsing, Christer S.; Gaus, Katharina

2009-01-01

Activating stimuli for T lymphocytes are transmitted through plasma membrane domains that form at T-cell antigen receptor (TCR) signalling foci. Here, we determined the molecular lipid composition of immunoisolated TCR activation domains. We observed that they accumulate cholesterol, sphingomyelin...... and saturated phosphatidylcholine species as compared with control plasma membrane fragments. This provides, for the first time, direct evidence that TCR activation domains comprise a distinct molecular lipid composition reminiscent of liquid-ordered raft phases in model membranes. Interestingly, TCR activation...... domains were also enriched in plasmenyl phosphatidylethanolamine and phosphatidylserine. Modulating the T-cell lipidome with polyunsaturated fatty acids impaired the plasma membrane condensation at TCR signalling foci and resulted in a perturbed molecular lipid composition. These results correlate...

Endoscopic extraperitoneal radical prostatectomy after radical resection of pT1-pT2 rectal cancer: a report of thirty cases.

Science.gov (United States)

Liu, Zhuo; Li, Dechuan; Chen, Yinbo

2017-01-01

Endoscopic extraperitoneal radical prostatectomy (EERPE) has gained popularity for the treatment of localized prostate cancer. However, prior complex lower abdominal or pelvic surgery can complicate subsequent EERPE. To date, there have been few reports on patients who underwent EERPE after radical resection of pT1-pT2 rectal cancer. To present our experience with EERPE in patients after radical resection of pT1-pT2 rectal carcinoma and introduce a simple and effective way to create an extraperitoneal working space. Thirty patients after radical resection of pT1-pT2 rectal carcinoma were treated with EERPE for biopsy-proven localized prostate cancer. Operation time, estimated blood loss, conversion to open surgery rate, transfusion rate and transurethral catheter time were recorded. Meanwhile, functional outcome (continence and potency) and oncological outcome were reviewed. The average operative time was 168 min. Mean blood loss was 195 ml. There was no need for conversion to open surgery or transfusion. The catheter was removed on postoperative day (POD) 7.8. After a mean follow-up time of 53.1 months, 3 patients had a prostate-specific antigen level relapse over 0.1 ng/ml. At the follow-up time, 26 patients were completely continent, and 4 needed 1-2 pads/day. Of the 6 patients who underwent neurovascular bundle preservation, none have experienced return of erections at the last follow-up time. Endoscopic extraperitoneal radical prostatectomy after radical resection of rectal carcinoma appears promising, with feasibility in experienced hands. The operative data, postoperative urinary incontinence and oncological outcomes appear encouraging, but the rate of erectile dysfunction seems to be disappointing.

Development of Adiabatic Doppler Feedback Model in 3D space time analysis Code ARCH

International Nuclear Information System (INIS)

Dwivedi, D.K.; Gupta, Anurag

2015-01-01

Integrated 3D space-time neutron kinetics with thermal-hydraulic feedback code system is being developed for transient analysis of Compact High Temperature Reactor (CHTR) and Advanced Heavy Water Reactor (AHWR). ARCH (code for Analysis of Reactor transients in Cartesian and Hexagon geometries) has been developed with IQS module for efficient 3D space time analysis. Recently, an adiabatic Doppler (fuel temperature) feedback module has been incorporated in this ARCH-IQS version of tile code. In the adiabatic model of fuel temperature feedback, the transfer of the excess heat from the fuel to the coolant during transient is neglected. The viability of Doppler feedback in ARCH-IQS with adiabatic heating has been checked with AER benchmark (Dyn002). Analyses of anticipated transient without scram (ATWS) case in CHTR as well as in AHWR have been performed with adiabatic fuel temperature feedback. The methodology and results have been presented in this paper. (author)

L3.PHI.CTF.P10.02-rev2 Coupling of Subchannel T/H (CTF) and CRUD Chemistry (MAMBA1D)

Energy Technology Data Exchange (ETDEWEB)

Salko, Robert K. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Palmtag, Scott [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Collins, Benjamin S. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Kendrick, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Seker, Jeffrey [Westinghouse Electric Company LLC, Cranberry Township, PA (United States)

2015-05-15

The purpose of this milestone is to create a preliminary capability for modeling light water reactor (LWR) thermal-hydraulic (T/H) and CRUD growth using the CTF subchannel code and the subgrid version of the MAMBA CRUD chemistry code, MAMBA1D. In part, this is a follow-on to Milestone L3.PHI.VCS.P9.01, which is documented in Report CASL-U-2014-0188-000, titled "Development of CTF Capability for Modeling Reactor Operating Cycles with Crud Growth". As the title suggests, the previous milestone set up a framework for modeling reactor operation cycles with CTF. The framework also facilitated coupling to a CRUD chemistry capability for modeling CRUD growth throughout the reactor operating cycle. To demonstrate the capability, a simple CRUD \\surrogate" tool was developed and coupled to CTF; however, it was noted that CRUD growth predictions by the surrogate were not considered realistic. This milestone builds on L3.PHI.VCS.P9.01 by replacing this simple surrogate tool with the more advanced MAMBA1D CRUD chemistry code. Completing this task involves addressing unresolved tasks from Milestone L3.PHI.VCS.P9.01, setting up an interface to MAMBA1D, and extracting new T/H information from CTF that was not previously required in the simple surrogate tool. Speci c challenges encountered during this milestone include (1) treatment of the CRUD erosion model, which requires local turbulent kinetic energy (TKE) (a value that CTF does not calculate) and (2) treatment of the MAMBA1D CRUD chimney boiling model in the CTF rod heat transfer solution. To demonstrate this new T/H, CRUD modeling capability, two sets of simulations were performed: (1) an 18 month cycle simulation of a quarter symmetry model of Watts Bar and (2) a simulation of Assemblies G69 and G70 from Seabrook Cycle 5. The Watts Bar simulation is merely a demonstration of the capability. The simulation of the Seabrook cycle, which had experienced CRUD-related fuel rod failures, had actual CRUD-scrape data to compare with

Mechanistic insights into phosphoprotein-binding FHA domains.

Science.gov (United States)

Liang, Xiangyang; Van Doren, Steven R

2008-08-01

[Structure: see text]. FHA domains are protein modules that switch signals in diverse biological pathways by monitoring the phosphorylation of threonine residues of target proteins. As part of the effort to gain insight into cellular avoidance of cancer, FHA domains involved in the cellular response to DNA damage have been especially well-characterized. The complete protein where the FHA domain resides and the interaction partners determine the nature of the signaling. Thus, a key biochemical question is how do FHA domains pick out their partners from among thousands of alternatives in the cell? This Account discusses the structure, affinity, and specificity of FHA domains and the formation of their functional structure. Although FHA domains share sequence identity at only five loop residues, they all fold into a beta-sandwich of two beta-sheets. The conserved arginine and serine of the recognition loops recognize the phosphorylation of the threonine targeted. Side chains emanating from loops that join beta-strand 4 with 5, 6 with 7, or 10 with 11 make specific contacts with amino acids of the ligand that tailor sequence preferences. Many FHA domains choose a partner in extended conformation, somewhat according to the residue three after the phosphothreonine in sequence (pT + 3 position). One group of FHA domains chooses a short carboxylate-containing side chain at pT + 3. Another group chooses a long, branched aliphatic side chain. A third group prefers other hydrophobic or uncharged polar side chains at pT + 3. However, another FHA domain instead chooses on the basis of pT - 2, pT - 3, and pT + 1 positions. An FHA domain from a marker of human cancer instead chooses a much longer protein fragment that adds a beta-strand to its beta-sheet and that presents hydrophobic residues from a novel helix to the usual recognition surface. This novel recognition site and more remote sites for the binding of other types of protein partners were predicted for the entire family

Cytochrome P450BM-3 reduces aldehydes to alcohols through a direct hydride transfer

International Nuclear Information System (INIS)

Kaspera, Rüdiger; Sahele, Tariku; Lakatos, Kyle; Totah, Rheem A.

2012-01-01

Highlights: ► Cytochrome P450BM-3 reduced aldehydes to alcohols efficiently (k cat ∼ 25 min −1 ). ► Reduction is a direct hydride transfer from R-NADP 2 H to the carbonyl moiety. ► P450 domain variants enhance reduction through potential allosteric/redox interactions. ► Novel reaction will have implications for metabolism of xenobiotics. -- Abstract: Cytochrome P450BM-3 catalyzed the reduction of lipophilic aldehydes to alcohols efficiently. A k cat of ∼25 min −1 was obtained for the reduction of methoxy benzaldehyde with wild type P450BM-3 protein which was higher than in the isolated reductase domain (BMR) alone and increased in specific P450-domain variants. The reduction was caused by a direct hydride transfer from preferentially R-NADP 2 H to the carbonyl moiety of the substrate. Weak substrate-P450-binding of the aldehyde, turnover with the reductase domain alone, a deuterium incorporation in the product from NADP 2 H but not D 2 O, and no inhibition by imidazole suggests the reductase domain of P450BM-3 as the potential catalytic site. However, increased aldehyde reduction by P450 domain variants (P450BM-3 F87A T268A) may involve allosteric or redox mechanistic interactions between heme and reductase domains. This is a novel reduction of aldehydes by P450BM-3 involving a direct hydride transfer and could have implications for the metabolism of endogenous substrates or xenobiotics.

The finite-difference time-domain method for electromagnetics with Matlab simulations

CERN Document Server

Elsherbeni, Atef Z

2016-01-01

This book introduces the powerful Finite-Difference Time-Domain method to students and interested researchers and readers. An effective introduction is accomplished using a step-by-step process that builds competence and confidence in developing complete working codes for the design and analysis of various antennas and microwave devices.

Phosphatidylinositol 3,5-Bisphosphate-Rich Membrane Domains in Endosomes and Lysosomes.

Science.gov (United States)

Takatori, Sho; Tatematsu, Tsuyako; Cheng, Jinglei; Matsumoto, Jun; Akano, Takuya; Fujimoto, Toyoshi

2016-02-01

Phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2 ) has critical functions in endosomes and lysosomes. We developed a method to define nanoscale distribution of PtdIns(3,5)P2 using freeze-fracture electron microscopy. GST-ATG18-4×FLAG was used to label PtdIns(3,5)P2 and its binding to phosphatidylinositol 3-phosphate (PtdIns(3)P) was blocked by an excess of the p40(phox) PX domain. In yeast exposed to hyperosmotic stress, PtdIns(3,5)P2 was concentrated in intramembrane particle (IMP)-deficient domains in the vacuolar membrane, which made close contact with adjacent membranes. The IMP-deficient domain was also enriched with PtdIns(3)P, but was deficient in Vph1p, a liquid-disordered domain marker. In yeast lacking either PtdIns(3,5)P2 or its effector, Atg18p, the IMP-deficient, PtdIns(3)P-rich membranes were folded tightly to make abnormal tubular structures, thus showing where the vacuolar fragmentation process is arrested when PtdIns(3,5)P2 metabolism is defective. In HeLa cells, PtdIns(3,5)P2 was significantly enriched in the vesicular domain of RAB5- and RAB7-positive endosome/lysosomes of the tubulo-vesicular morphology. This biased distribution of PtdIns(3,5)P2 was also observed using fluorescence microscopy, which further showed enrichment of a retromer component, VPS35, in the tubular domain. This is the first report to show segregation of PtdIns(3,5)P2 -rich and -deficient domains in endosome/lysosomes, which should be important for endosome/lysosome functionality. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Insertion of the T3 DNA polymerase thioredoxin binding domain enhances the processivity and fidelity of Taq DNA polymerase

OpenAIRE

Davidson, John F.; Fox, Richard; Harris, Dawn D.; Lyons-Abbott, Sally; Loeb, Lawrence A.

2003-01-01

Insertion of the T3 DNA polymerase thioredoxin binding domain (TBD) into the distantly related thermostable Taq DNA polymerase at an analogous position in the thumb domain, converts the Taq DNA polymerase from a low processive to a highly processive enzyme. Processivity is dependent on the presence of thioredoxin. The enhancement in processivity is 20–50-fold when compared with the wild-type Taq DNA polymerase or to the recombinant polymerase in the absence of thioredoxin. The recombinant Taq...

u-Constacyclic codes over F_p+u{F}_p and their applications of constructing new non-binary quantum codes

Science.gov (United States)

Gao, Jian; Wang, Yongkang

2018-01-01

Structural properties of u-constacyclic codes over the ring F_p+u{F}_p are given, where p is an odd prime and u^2=1. Under a special Gray map from F_p+u{F}_p to F_p^2, some new non-binary quantum codes are obtained by this class of constacyclic codes.

A requiem for AdS4×C P3 fermionic self-T duality

Science.gov (United States)

O'Colgáin, E.; Pittelli, A.

2016-11-01

Strong evidence for dual superconformal symmetry in N =6 superconformal Chern-Simons theory has fueled expectations that the AdS /CFT dual geometry AdS4×C P3 is self-dual under T duality. We revisit the problem to identify commuting bosonic and fermionic isometries in a systematic fashion and show that fermionic T duality, a symmetry originally proposed by Berkovits and Maldacena, inevitably leads to a singularity in the dilaton transformation. We show that TsT deformations commute with fermionic T duality and comment on T duality in the corresponding sigma model. Our results rule out self-duality based on fermionic T duality for AdS4×C P3 or its TsT deformations but leave the door open for new possibilities.

TART 2000: A Coupled Neutron-Photon, 3-D, Combinatorial Geometry, Time Dependent, Monte Carlo Transport Code

International Nuclear Information System (INIS)

Cullen, D.E

2000-01-01

TART2000 is a coupled neutron-photon, 3 Dimensional, combinatorial geometry, time dependent Monte Carlo radiation transport code. This code can run on any modern computer. It is a complete system to assist you with input Preparation, running Monte Carlo calculations, and analysis of output results. TART2000 is also incredibly FAST; if you have used similar codes, you will be amazed at how fast this code is compared to other similar codes. Use of the entire system can save you a great deal of time and energy. TART2000 is distributed on CD. This CD contains on-line documentation for all codes included in the system, the codes configured to run on a variety of computers, and many example problems that you can use to familiarize yourself with the system. TART2000 completely supersedes all older versions of TART, and it is strongly recommended that users only use the most recent version of TART2000 and its data files

TART 2000 A Coupled Neutron-Photon, 3-D, Combinatorial Geometry, Time Dependent, Monte Carlo Transport Code

CERN Document Server

Cullen, D

2000-01-01

TART2000 is a coupled neutron-photon, 3 Dimensional, combinatorial geometry, time dependent Monte Carlo radiation transport code. This code can run on any modern computer. It is a complete system to assist you with input Preparation, running Monte Carlo calculations, and analysis of output results. TART2000 is also incredibly FAST; if you have used similar codes, you will be amazed at how fast this code is compared to other similar codes. Use of the entire system can save you a great deal of time and energy. TART2000 is distributed on CD. This CD contains on-line documentation for all codes included in the system, the codes configured to run on a variety of computers, and many example problems that you can use to familiarize yourself with the system. TART2000 completely supersedes all older versions of TART, and it is strongly recommended that users only use the most recent version of TART2000 and its data files.

T3P- A Novel Catalyst for Aza-Diels-Alder Reaction: One-Pot Synthesis of Pyrano[3,2-c]quinolines and furano[3,2-c]quinolines

Directory of Open Access Journals (Sweden)

T. S. R. Prasanna

2011-01-01

Full Text Available T3P was found to be an efficient catalyst for the Aza-Diels–Alder reactions of aldimines with dihydropyran or dihydrofuran to afford the corresponding pyrano-and furo [3,2-c]quinolines in high yields with high diastereoselectivity in a short period of time.

Validation of full core geometry model of the NODAL3 code in the PWR transient Benchmark problems

International Nuclear Information System (INIS)

T-M Sembiring; S-Pinem; P-H Liem

2015-01-01

The coupled neutronic and thermal-hydraulic (T/H) code, NODAL3 code, has been validated in some PWR static benchmark and the NEACRP PWR transient benchmark cases. However, the NODAL3 code have not yet validated in the transient benchmark cases of a control rod assembly (CR) ejection at peripheral core using a full core geometry model, the C1 and C2 cases. By this research work, the accuracy of the NODAL3 code for one CR ejection or the unsymmetrical group of CRs ejection case can be validated. The calculations by the NODAL3 code have been carried out by the adiabatic method (AM) and the improved quasistatic method (IQS). All calculated transient parameters by the NODAL3 code were compared with the reference results by the PANTHER code. The maximum relative difference of 16 % occurs in the calculated time of power maximum parameter by using the IQS method, while the relative difference of the AM method is 4 % for C2 case. All calculation results by the NODAL3 code shows there is no systematic difference, it means the neutronic and T/H modules are adopted in the code are considered correct. Therefore, all calculation results by using the NODAL3 code are very good agreement with the reference results. (author)

Source Code Vulnerabilities in IoT Software Systems

Directory of Open Access Journals (Sweden)

Saleh Mohamed Alnaeli

2017-08-01

Full Text Available An empirical study that examines the usage of known vulnerable statements in software systems developed in C/C++ and used for IoT is presented. The study is conducted on 18 open source systems comprised of millions of lines of code and containing thousands of files. Static analysis methods are applied to each system to determine the number of unsafe commands (e.g., strcpy, strcmp, and strlen that are well-known among research communities to cause potential risks and security concerns, thereby decreasing a system’s robustness and quality. These unsafe statements are banned by many companies (e.g., Microsoft. The use of these commands should be avoided from the start when writing code and should be removed from legacy code over time as recommended by new C/C++ language standards. Each system is analyzed and the distribution of the known unsafe commands is presented. Historical trends in the usage of the unsafe commands of 7 of the systems are presented to show how the studied systems evolved over time with respect to the vulnerable code. The results show that the most prevalent unsafe command used for most systems is memcpy, followed by strlen. These results can be used to help train software developers on secure coding practices so that they can write higher quality software systems.

Preparation of Proper Immunogen by Cloning and Stable Expression of cDNA coding for Human Hematopoietic Stem Cell Marker CD34 in NIH-3T3 Mouse Fibroblast Cell Line

Science.gov (United States)

Shafaghat, Farzaneh; Abbasi-Kenarsari, Hajar; Majidi, Jafar; Movassaghpour, Ali Akbar; Shanehbandi, Dariush; Kazemi, Tohid

2015-01-01

Purpose: Transmembrane CD34 glycoprotein is the most important marker for identification, isolation and enumeration of hematopoietic stem cells (HSCs). We aimed in this study to clone the cDNA coding for human CD34 from KG1a cell line and stably express in mouse fibroblast cell line NIH-3T3. Such artificial cell line could be useful as proper immunogen for production of mouse monoclonal antibodies. Methods: CD34 cDNA was cloned from KG1a cell line after total RNA extraction and cDNA synthesis. Pfu DNA polymerase-amplified specific band was ligated to pGEMT-easy TA-cloning vector and sub-cloned in pCMV6-Neo expression vector. After transfection of NIH-3T3 cells using 3 μg of recombinant construct and 6 μl of JetPEI transfection reagent, stable expression was obtained by selection of cells by G418 antibiotic and confirmed by surface flow cytometry. Results: 1158 bp specific band was aligned completely to reference sequence in NCBI database corresponding to long isoform of human CD34. Transient and stable expression of human CD34 on transfected NIH-3T3 mouse fibroblast cells was achieved (25% and 95%, respectively) as shown by flow cytometry. Conclusion: Cloning and stable expression of human CD34 cDNA was successfully performed and validated by standard flow cytometric analysis. Due to murine origin of NIH-3T3 cell line, CD34-expressing NIH-3T3 cells could be useful as immunogen in production of diagnostic monoclonal antibodies against human CD34. This approach could bypass the need for purification of recombinant proteins produced in eukaryotic expression systems. PMID:25789221

T2 Relaxation Time Mapping of Proximal Tibiofibular Cartilage by 3-Tesla Magnetic Resonance Imaging

International Nuclear Information System (INIS)

Kwack, Kyu-Sung; Cho, Jae Hyun; Kim, Jun Man; Kim, Sun Yong; Min, Byoung-Hyun; Yoon, Seung-Hyun

2009-01-01

Background: The proximal tibiofibular joint (PTFJ) can be considered the fourth compartment of the knee joint. However, there have been no studies of the T2 values (T2 relaxation time) of PTFJ cartilage. Purpose: To assess the T2 values of PTFJ cartilage at 3T magnetic resonance imaging (MRI), and to show the clinical utility of T2 values of PTFJ cartilage for the diagnosis of osteoarthritis (OA). Material and Methods: 118 patients who had knee MR imaging and knee radiography were enrolled. MRI was performed using a 3T MRI scanner, and T2 maps were calculated from a sagittal multi-echo acquisition. Two regions of interest (ROIs) were positioned within PTFJ cartilage and medial femoral condyle (MFC) cartilage. The average T2 value and standard deviation (SD) of each ROI were recorded. Using PTFJ cartilage as a standard reference, the T2 index ((MFC/PTFJ)x100) and T2SD index ((MFCSD/PTFJSD)x100) were calculated. A paired t test was performed to compare the mean and SD of ROIs within PTFJ and MFC cartilage. Correlation analyses were performed among the parameters age, Kellgren-Lawrence (KL) score, means and SDs of ROIs within PTFJ and MFC cartilage, T2 index, and T2SD index. Results: PTFJ cartilage had a significantly shorter T2 value than did MFC cartilage (P<0.0001). ROIs within PTFJ cartilage showed significantly smaller SDs than did those within MFC cartilage (P<0.0001). The average T2 value and SD of MFC and the T2SD index showed a positive correlation to the KL score (P<0.05). The correlation coefficients for the average T2 value, SD, and T2SD index of MFC were R=0.203, 0.254, and 0.268, respectively. However, there was no significant correlation between T2 values of PTFJ cartilage and KL score (P=0.643). Conclusion: PTFJ cartilage showed shorter and more homogeneous T2 values with a small SD than did MFC cartilage, regardless of the degree of OA at femorotibial compartments. PTFJ cartilage may be a useful internal standard reference to diagnose OA and would be

T2 Relaxation Time Mapping of Proximal Tibiofibular Cartilage by 3-Tesla Magnetic Resonance Imaging

Energy Technology Data Exchange (ETDEWEB)

Kwack, Kyu-Sung; Cho, Jae Hyun; Kim, Jun Man; Kim, Sun Yong (Dept. of Radiology, Ajou Univ. Medical Center, Suwon (Korea)); Min, Byoung-Hyun; Yoon, Seung-Hyun (Cartilage Regeneration Center, Ajou Univ. Medical Center, Suwon (Korea))

2009-11-15

Background: The proximal tibiofibular joint (PTFJ) can be considered the fourth compartment of the knee joint. However, there have been no studies of the T2 values (T2 relaxation time) of PTFJ cartilage. Purpose: To assess the T2 values of PTFJ cartilage at 3T magnetic resonance imaging (MRI), and to show the clinical utility of T2 values of PTFJ cartilage for the diagnosis of osteoarthritis (OA). Material and Methods: 118 patients who had knee MR imaging and knee radiography were enrolled. MRI was performed using a 3T MRI scanner, and T2 maps were calculated from a sagittal multi-echo acquisition. Two regions of interest (ROIs) were positioned within PTFJ cartilage and medial femoral condyle (MFC) cartilage. The average T2 value and standard deviation (SD) of each ROI were recorded. Using PTFJ cartilage as a standard reference, the T2 index ((MFC/PTFJ)x100) and T2SD index ((MFCSD/PTFJSD)x100) were calculated. A paired t test was performed to compare the mean and SD of ROIs within PTFJ and MFC cartilage. Correlation analyses were performed among the parameters age, Kellgren-Lawrence (KL) score, means and SDs of ROIs within PTFJ and MFC cartilage, T2 index, and T2SD index. Results: PTFJ cartilage had a significantly shorter T2 value than did MFC cartilage (P<0.0001). ROIs within PTFJ cartilage showed significantly smaller SDs than did those within MFC cartilage (P<0.0001). The average T2 value and SD of MFC and the T2SD index showed a positive correlation to the KL score (P<0.05). The correlation coefficients for the average T2 value, SD, and T2SD index of MFC were R=0.203, 0.254, and 0.268, respectively. However, there was no significant correlation between T2 values of PTFJ cartilage and KL score (P=0.643). Conclusion: PTFJ cartilage showed shorter and more homogeneous T2 values with a small SD than did MFC cartilage, regardless of the degree of OA at femorotibial compartments. PTFJ cartilage may be a useful internal standard reference to diagnose OA and would be

3D airborne EM modeling based on the spectral-element time-domain (SETD) method

Science.gov (United States)

Cao, X.; Yin, C.; Huang, X.; Liu, Y.; Zhang, B., Sr.; Cai, J.; Liu, L.

2017-12-01

In the field of 3D airborne electromagnetic (AEM) modeling, both finite-difference time-domain (FDTD) method and finite-element time-domain (FETD) method have limitations that FDTD method depends too much on the grids and time steps, while FETD requires large number of grids for complex structures. We propose a time-domain spectral-element (SETD) method based on GLL interpolation basis functions for spatial discretization and Backward Euler (BE) technique for time discretization. The spectral-element method is based on a weighted residual technique with polynomials as vector basis functions. It can contribute to an accurate result by increasing the order of polynomials and suppressing spurious solution. BE method is a stable tine discretization technique that has no limitation on time steps and can guarantee a higher accuracy during the iteration process. To minimize the non-zero number of sparse matrix and obtain a diagonal mass matrix, we apply the reduced order integral technique. A direct solver with its speed independent of the condition number is adopted for quickly solving the large-scale sparse linear equations system. To check the accuracy of our SETD algorithm, we compare our results with semi-analytical solutions for a three-layered earth model within the time lapse 10-6-10-2s for different physical meshes and SE orders. The results show that the relative errors for magnetic field B and magnetic induction are both around 3-5%. Further we calculate AEM responses for an AEM system over a 3D earth model in Figure 1. From numerical experiments for both 1D and 3D model, we draw the conclusions that: 1) SETD can deliver an accurate results for both dB/dt and B; 2) increasing SE order improves the modeling accuracy for early to middle time channels when the EM field diffuses fast so the high-order SE can model the detailed variation; 3) at very late time channels, increasing SE order has little improvement on modeling accuracy, but the time interval plays

Optical image encryption using QR code and multilevel fingerprints in gyrator transform domains

Science.gov (United States)

Wei, Yang; Yan, Aimin; Dong, Jiabin; Hu, Zhijuan; Zhang, Jingtao

2017-11-01

A new concept of GT encryption scheme is proposed in this paper. We present a novel optical image encryption method by using quick response (QR) code and multilevel fingerprint keys in gyrator transform (GT) domains. In this method, an original image is firstly transformed into a QR code, which is placed in the input plane of cascaded GTs. Subsequently, the QR code is encrypted into the cipher-text by using multilevel fingerprint keys. The original image can be obtained easily by reading the high-quality retrieved QR code with hand-held devices. The main parameters used as private keys are GTs' rotation angles and multilevel fingerprints. Biometrics and cryptography are integrated with each other to improve data security. Numerical simulations are performed to demonstrate the validity and feasibility of the proposed encryption scheme. In the future, the method of applying QR codes and fingerprints in GT domains possesses much potential for information security.

Vectorization of DOT3.5 code

International Nuclear Information System (INIS)

Nonomiya, Iwao; Ishiguro, Misako; Tsutsui, Tsuneo

1990-07-01

In this report, we describe the vectorization of two-dimensional Sn-method radiation transport code DOT3.5. Vectorized codes are not only the NEA original version developed at ORNL but also the versions improved by JAERI: DOT3.5 FNS version for fusion neutronics analyses, DOT3.5 FER version for fusion reactor design, and ESPRIT module of RADHEAT-V4 code system for radiation shielding and radiation transport analyses. In DOT3.5, input/output processing time amounts to a great part of the elapsed time when a large number of energy groups and/or a large number of spatial mesh points are used in the calculated problem. Therefore, an improvement has been made for the speedup of input/output processing in the DOT3.5 FNS version, and DOT-DD (Double Differential cross section) code. The total speedup ratio of vectorized version to the original scalar one is 1.7∼1.9 for DOT3.5 NEA version, 2.2∼2.3 fro DOT3.5 FNS version, 1.7 for DOT3.5 FER version, and 3.1∼4.4 for RADHEAT-V4, respectively. The elapsed times for improved DOT3.5 FNS version and DOT-DD are reduced to 50∼65% that of the original version by the input/output speedup. In this report, we describe summary of codes, the techniques used for the vectorization and input/output speedup, verification of computed results, and speedup effect. (author)

Cytochrome P450BM-3 reduces aldehydes to alcohols through a direct hydride transfer

Energy Technology Data Exchange (ETDEWEB)

Kaspera, Ruediger; Sahele, Tariku; Lakatos, Kyle [Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195-7610 (United States); Totah, Rheem A., E-mail: rtotah@u.washington.edu [Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195-7610 (United States)

2012-02-17

Highlights: Black-Right-Pointing-Pointer Cytochrome P450BM-3 reduced aldehydes to alcohols efficiently (k{sub cat} {approx} 25 min{sup -1}). Black-Right-Pointing-Pointer Reduction is a direct hydride transfer from R-NADP{sup 2}H to the carbonyl moiety. Black-Right-Pointing-Pointer P450 domain variants enhance reduction through potential allosteric/redox interactions. Black-Right-Pointing-Pointer Novel reaction will have implications for metabolism of xenobiotics. -- Abstract: Cytochrome P450BM-3 catalyzed the reduction of lipophilic aldehydes to alcohols efficiently. A k{sub cat} of {approx}25 min{sup -1} was obtained for the reduction of methoxy benzaldehyde with wild type P450BM-3 protein which was higher than in the isolated reductase domain (BMR) alone and increased in specific P450-domain variants. The reduction was caused by a direct hydride transfer from preferentially R-NADP{sup 2}H to the carbonyl moiety of the substrate. Weak substrate-P450-binding of the aldehyde, turnover with the reductase domain alone, a deuterium incorporation in the product from NADP{sup 2}H but not D{sub 2}O, and no inhibition by imidazole suggests the reductase domain of P450BM-3 as the potential catalytic site. However, increased aldehyde reduction by P450 domain variants (P450BM-3 F87A T268A) may involve allosteric or redox mechanistic interactions between heme and reductase domains. This is a novel reduction of aldehydes by P450BM-3 involving a direct hydride transfer and could have implications for the metabolism of endogenous substrates or xenobiotics.

Caspase-3-mediated cleavage of p65/RelA results in a carboxy-terminal fragment that inhibits IκBα and enhances HIV-1 replication in human T lymphocytes

Directory of Open Access Journals (Sweden)

Alcamí José

2008-12-01

Full Text Available Abstract Background Degradation of p65/RelA has been involved in both the inhibition of NF-κB-dependent activity and the onset of apoptosis. However, the mechanisms of NF-κB degradation are unclear and can vary depending on the cell type. Cleavage of p65/RelA can produce an amino-terminal fragment that was shown to act as a dominant-negative inhibitor of NF-κB, thereby promoting apoptosis. However, the opposite situation has also been described and the production of a carboxy-terminal fragment that contains two potent transactivation domains has also been related to the onset of apoptosis. In this context, a carboxy-terminal fragment of p65/RelA (ΔNH2p65, detected in non-apoptotic human T lymphocytes upon activation, has been studied. T cells constitute one of the long-lived cellular reservoirs of the human immunodeficiency virus type 1 (HIV-1. Because NF-κB is the most important inducible element involved in initiation of HIV-1 transcription, an adequate control of NF-κB response is of paramount importance for both T cell survival and viral spread. Its major inhibitor IκBα constitutes a master terminator of NF-κB response that is complemented by degradation of p65/RelA. Results and conclusions In this study, the function of a caspase-3-mediated carboxy-terminal fragment of p65/RelA, which was detected in activated human peripheral blood lymphocytes (PBLs, was analyzed. Cells producing this truncated p65/RelA did not undergo apoptosis but showed a high viability, in spite of caspase-3 activation. ΔNH2p65 lacked most of DNA-binding domain but retained the dimerization domain, NLS and transactivation domains. Consequently, it could translocate to the nucleus, associate with NF-κB1/p50 and IκBα, but could not bind -κB consensus sites. However, although ΔNH2p65 lacked transcriptional activity by itself, it could increase NF-κB activity in a dose-dependent manner by hijacking IκBα. Thus, its expression resulted in a persistent

Description of the THYDE-P code

International Nuclear Information System (INIS)

Asahi, Yoshiro

1978-07-01

This paper is a preliminary report about the methods and the models applied to a computer code named THYDE-P which is concerned with thermal-hydraulic transients of a PWR plant following a large or small area break of a primary coolant system pipe, generally referred to as a loss-of-coolant accident (LOCA). The THYDE-P code deals not only with blowdown phase, but also with reflooding phase. What characterizes the THYDE-P code is its entirely new model for the primary loop network. The code user information and the programming detail are not included in this report, but in a future documentation. (auth.)

Calibration of TAMA300 in time domain

International Nuclear Information System (INIS)

Telada, Souichi; Tatsumi, Daisuke; Akutsu, Tomomi; Ando, Masaki; Kanda, Nobuyuki

2005-01-01

We could reconstruct the strain of gravitational wave signals from acquired data in the time domain by using the infinite impulse response filter technique in TAMA300. We would like to analyse the waveform in the time domain for burst-like signal, merger phase waveform of binary neutron stars, and so on. We established the way to make a continuous time-series gravitational wave strain signal. We compared the time-domain reconstruction with the Fourier-space reconstruction. Both coincided within 3% in the observation range. We could also produce the voltage signal which would be recorded by the data-acquisition system from a simulated gravitational wave. This is useful for some analyses of simulations and signal injections. We could extract the waveform of the hardware injection signal in an observational run in the time domain. The extracted waveform was similar to the injection signal

Time reversal violation in the nuclear interaction and p(pol)-/sup 3/He scattering

Energy Technology Data Exchange (ETDEWEB)

Simonius, M [Eidgenoessische Technische Hochschule, Zurich (Switzerland). Lab. fuer Kernphysik; Wyler, D [Carnegie-Mellon Univ., Pittsburgh, Pa. (USA). Dept. of Physics

1977-08-08

Using T-violating boson-exchange interactions T-violating effects in low energy p-/sup 3/He scattering are calculated. The results are below 10/sup -3/ even for full strong (not millistrong) T-violation in the nucleon-nucleon system. It is argued, that the smallness of the effects is not a particularity of the p-/sup 3/He system but a general property of low energy processes.

3-D electromagnetic plasma particle simulations on the Intel Delta parallel computer

International Nuclear Information System (INIS)

Wang, J.; Liewer, P.C.

1994-01-01

A three-dimensional electromagnetic PIC code has been developed on the 512 node Intel Touchstone Delta MIMD parallel computer. This code is based on the General Concurrent PIC algorithm which uses a domain decomposition to divide the computation among the processors. The 3D simulation domain can be partitioned into 1-, 2-, or 3-dimensional sub-domains. Particles must be exchanged between processors as they move among the subdomains. The Intel Delta allows one to use this code for very-large-scale simulations (i.e. over 10 8 particles and 10 6 grid cells). The parallel efficiency of this code is measured, and the overall code performance on the Delta is compared with that on Cray supercomputers. It is shown that their code runs with a high parallel efficiency of ≥ 95% for large size problems. The particle push time achieved is 115 nsecs/particle/time step for 162 million particles on 512 nodes. Comparing with the performance on a single processor Cray C90, this represents a factor of 58 speedup. The code uses a finite-difference leap frog method for field solve which is significantly more efficient than fast fourier transforms on parallel computers. The performance of this code on the 128 node Cray T3D will also be discussed

Analysis of genetic code ambiguity arising from nematode-specific misacylated tRNAs.

Directory of Open Access Journals (Sweden)

Kiyofumi Hamashima

Full Text Available The faithful translation of the genetic code requires the highly accurate aminoacylation of transfer RNAs (tRNAs. However, it has been shown that nematode-specific V-arm-containing tRNAs (nev-tRNAs are misacylated with leucine in vitro in a manner that transgresses the genetic code. nev-tRNA(Gly (CCC and nev-tRNA(Ile (UAU, which are the major nev-tRNA isotypes, could theoretically decode the glycine (GGG codon and isoleucine (AUA codon as leucine, causing GGG and AUA codon ambiguity in nematode cells. To test this hypothesis, we investigated the functionality of nev-tRNAs and their impact on the proteome of Caenorhabditis elegans. Analysis of the nucleotide sequences in the 3' end regions of the nev-tRNAs showed that they had matured correctly, with the addition of CCA, which is a crucial posttranscriptional modification required for tRNA aminoacylation. The nuclear export of nev-tRNAs was confirmed with an analysis of their subcellular localization. These results show that nev-tRNAs are processed to their mature forms like common tRNAs and are available for translation. However, a whole-cell proteome analysis found no detectable level of nev-tRNA-induced mistranslation in C. elegans cells, suggesting that the genetic code is not ambiguous, at least under normal growth conditions. Our findings indicate that the translational fidelity of the nematode genetic code is strictly maintained, contrary to our expectations, although deviant tRNAs with misacylation properties are highly conserved in the nematode genome.

Nonlinear time-domain soil–structure interaction analysis of embedded reactor structures subjected to earthquake loads

Energy Technology Data Exchange (ETDEWEB)

Solberg, Jerome M., E-mail: solberg2@llnl.gov [Methods Development Group, Lawrence Livermore Nat’l Lab, P.O. Box 808, Mailstop L-125, Livermore, CA 94550 (United States); Hossain, Quazi, E-mail: hossain1@llnl.gov [Structural and Applied Mechanics Group, Lawrence Livermore Nat’l Lab, P.O. Box 808, Mailstop L-129, Livermore, CA 94550 (United States); Mseis, George, E-mail: george.mseis@gmail.com [Structural and Applied Mechanics Group, Lawrence Livermore Nat’l Lab, P.O. Box 808, Mailstop L-129, Livermore, CA 94550 (United States)

2016-08-01

Highlights: • Derived modified version of Bielak’s SSI method for nonlinear time-domain analysis. • Utilized a Ramberg–Osgood material with parameters that can be fit to EPRI data. • Matched vertically propagating shear wave results from CARES. • Applied this technique to a representative SMR, compared well with SASSI. • The technique is extensible to other material models and nonlinear effects. - Abstract: A generalized time-domain method for soil–structure interaction analysis is developed, based upon an extension of the work of the domain reduction method of Bielak et al. The methodology is combined with the use of a simple hysteretic soil model based upon the Ramberg–Osgood formulation and applied to a notional Small Modular Reactor. These benchmark results compare well (with some caveats) with those obtained by using the industry-standard frequency-domain code SASSI. The methodology provides a path forward for investigation of other sources of nonlinearity, including those associated with the use of more physically-realistic material models incorporating pore-pressure effects, gap opening/closing, the effect of nonlinear structural elements, and 3D seismic inputs.

Syrthes thermal code and Estet or N3S fluid mechanics codes coupling; Couplage du code de thermique Syrthes et des codes de mecanique des fluides N3S et ou Estet

Energy Technology Data Exchange (ETDEWEB)

Peniguel, C [Electricite de France (EDF), 78 - Chatou (France). Direction des Etudes et Recherches; Rupp, I [SIMULOG, 78 - Guyancourt (France)

1997-06-01

EDF has developed numerical codes for modeling the conductive, radiative and convective thermal transfers and their couplings in complex industrial configurations: the convection in a fluid is solved by Estet in finite volumes or N3S in finite elements, the conduction is solved by Syrthes and the wall-to-wall thermal radiation is modelled by Syrthes with the help of a radiosity method. Syrthes controls the different heat exchanges which may occur between fluid and solid domains, using an explicit iterative method. An extension of Syrthes has been developed in order to allow the consideration of configurations where several fluid codes operate simultaneously, using ``message passing`` tools such as PVM (Parallel Virtual Machine) and the Calcium code coupler developed at EDF. Application examples are given

Female-biased expression of long non-coding RNAs in domains that escape X-inactivation in mouse

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Lu Lu

2010-11-01

Full Text Available Abstract Background Sexual dimorphism in brain gene expression has been recognized in several animal species. However, the relevant regulatory mechanisms remain poorly understood. To investigate whether sex-biased gene expression in mammalian brain is globally regulated or locally regulated in diverse brain structures, and to study the genomic organisation of brain-expressed sex-biased genes, we performed a large scale gene expression analysis of distinct brain regions in adult male and female mice. Results This study revealed spatial specificity in sex-biased transcription in the mouse brain, and identified 173 sex-biased genes in the striatum; 19 in the neocortex; 12 in the hippocampus and 31 in the eye. Genes located on sex chromosomes were consistently over-represented in all brain regions. Analysis on a subset of genes with sex-bias in more than one tissue revealed Y-encoded male-biased transcripts and X-encoded female-biased transcripts known to escape X-inactivation. In addition, we identified novel coding and non-coding X-linked genes with female-biased expression in multiple tissues. Interestingly, the chromosomal positions of all of the female-biased non-coding genes are in close proximity to protein-coding genes that escape X-inactivation. This defines X-chromosome domains each of which contains a coding and a non-coding female-biased gene. Lack of repressive chromatin marks in non-coding transcribed loci supports the possibility that they escape X-inactivation. Moreover, RNA-DNA combined FISH experiments confirmed the biallelic expression of one such novel domain. Conclusion This study demonstrated that the amount of genes with sex-biased expression varies between individual brain regions in mouse. The sex-biased genes identified are localized on many chromosomes. At the same time, sexually dimorphic gene expression that is common to several parts of the brain is mostly restricted to the sex chromosomes. Moreover, the study uncovered

HTLV-1 modulates the frequency and phenotype of FoxP3+CD4+ T cells in virus-infected individuals

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Satou Yorifumi

2012-05-01

Full Text Available Abstract Background HTLV-1 utilizes CD4 T cells as the main host cell and maintains the proviral load via clonal proliferation of infected CD4+ T cells. Infection of CD4+ T cells by HTLV-1 is therefore thought to play a pivotal role in HTLV-1-related pathogenicity, including leukemia/lymphoma of CD4+ T cells and chronic inflammatory diseases. Recently, it has been reported that a proportion of HTLV-1 infected CD4+ T cells express FoxP3, a master molecule of regulatory T cells. However, crucial questions remain unanswered on the relationship between HTLV-1 infection and FoxP3 expression. Results To investigate the effect of HTLV-1 infection on CD4+ T-cell subsets, we used flow cytometry to analyze the T-cell phenotype and HTLV-1 infection in peripheral mononuclear cells (PBMCs of four groups of subjects, including 23 HTLV-1-infected asymptomatic carriers (AC, 10 patients with HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP, 10 patients with adult T-cell leukemia (ATL, and 10 healthy donors. The frequency of FoxP3+ cells in CD4+ T cells in AC with high proviral load and patients with HAM/TSP or ATL was higher than that in uninfected individuals. The proviral load was positively correlated with the percentage of CD4+ T cells that were FoxP3+. The CD4+FoxP3+ T cells, themselves, were frequently infected with HTLV-1. We conclude that FoxP3+ T- cells are disproportionately infected with HTLV-1 during chronic infection. We next focused on PBMCs of HAM/TSP patients. The expression levels of the Treg associated molecules CTLA-4 and GITR were decreased in CD4+FoxP3+ T cells. Further we characterized FoxP3+CD4+ T-cell subsets by staining CD45RA and FoxP3, which revealed an increase in CD45RA−FoxP3low non-suppressive T-cells. These findings can reconcile the inflammatory phenotype of HAM/TSP with the observed increase in frequency of FoxP3+ cells. Finally, we analyzed ATL cells and observed not only a high frequency of FoxP3 expression

Dependence on Temperature, pH, and Cl"− in the Uniform Corrosion of Aluminum Alloys 2024-T3, 6061-T6, and 7075-T6

International Nuclear Information System (INIS)

Huang, I-Wen; Hurley, Belinda L.; Yang, Fan; Buchheit, Rudolph G.

2016-01-01

With regards to localized corrosion, the role of uniform corrosion of aluminum alloys has not always been accounted for in the past. The impact of uniform corrosion on aluminum alloys 2024-T3, 6061-T6, and 7075-T6 is studied here to provide quantitative evidence of its importance. Preliminary weight loss experiments combined with optical profilometry (OP) indicate that corrosion attributed to uniform corrosion is very significant when compared to localized corrosion. A series of free immersion tests were conducted to understand the influence of environmental variables including temperature (20, 40, 60, 80 °C), initial pH without buffering (3, 5, 8, 10) and chloride concentration (0.01, 0.1, 1 M) for 1, 7, and 30 days. With time, uniform corrosion results exhibited a strong dependence on temperature accompanied by variable pH- and temperature-dependent corrosion product formation. Electrochemical approaches including electrochemical impedance spectroscopy (EIS) and cathodic polarization were utilized to characterize the oxygen reduction reaction (ORR) and corrosion product formation as a function of temperature. Electron microscopy was conducted to assess the microstructure and morphology of corrosion products and provide supporting evidence for electrochemical findings.

k-t SENSE-accelerated Myocardial Perfusion MR Imaging at 3.0 Tesla - comparison with 1.5 Tesla

Science.gov (United States)

Plein, Sven; Schwitter, Juerg; Suerder, Daniel; Greenwood, John P.; Boesiger, Peter; Kozerke, Sebastian

2008-01-01

Purpose To determine the feasibility and diagnostic accuracy of high spatial resolution myocardial perfusion MR at 3.0 Tesla using k-space and time domain undersampling with sensitivity encoding (k-t SENSE). Materials and Methods The study was reviewed and approved by the local ethic review board. k-t SENSE perfusion MR was performed at 1.5 Tesla and 3.0 Tesla (saturation recovery gradient echo pulse sequence, repetition time/echo time 3.0ms/1.0ms, flip angle 15°, 5x k-t SENSE acceleration, spatial resolution 1.3×1.3×10mm3). Fourteen volunteers were studied at rest and 37 patients during adenosine stress. In volunteers, comparison was also made with standard-resolution (2.5×2.5×10mm3) 2x SENSE perfusion MR at 3.0 Tesla. Image quality, artifact scores, signal-to-noise ratios (SNR) and contrast-enhancement ratios (CER) were derived. In patients, diagnostic accuracy of visual analysis to detect >50% diameter stenosis on quantitative coronary angiography was determined by receiver-operator-characteristics (ROC). Results In volunteers, image quality and artifact scores were similar for 3.0 Tesla and 1.5 Tesla, while SNR was higher (11.6 vs. 5.6) and CER lower (1.1 vs. 1.5, p=0.012) at 3.0 Tesla. Compared with standard-resolution perfusion MR, image quality was higher for k-t SENSE (3.6 vs. 3.1, p=0.04), endocardial dark rim artifacts were reduced (artifact thickness 1.6mm vs. 2.4mm, pTesla and 1.5 Tesla, respectively. Conclusions k-t SENSE accelerated high-resolution perfusion MR at 3.0 Tesla is feasible with similar artifacts and diagnostic accuracy as at 1.5 Tesla. Compared with standard-resolution perfusion MR, image quality is improved and artifacts are reduced. PMID:18936311

Evolution of the RNase P RNA structural domain in Leptospira spp.

Science.gov (United States)

Ravishankar, Vigneshwaran; Ahmed, Ahmed; Sivagnanam, Ulaganathan; Muthuraman, Krishnaraja; Karthikaichamy, Anbarasu; Wilson, Herald A; Devendran, Ajay; Hartskeerl, Rudy A; Raj, Stephen M L

2014-12-01

We have employed the RNase P RNA (RPR) gene, which is present as single copy in chromosome I of Leptospira spp. to investigate the phylogeny of structural domains present in the RNA subunit of the tRNA processing enzyme, RNase P. RPR gene sequences of 150 strains derived from NCBI database along with sequences determined from 8 reference strains were examined to fathom strain specific structural differences present in leptospiral RPR. Sequence variations in the RPR gene impacted on the configuration of loops, stems and bulges found in the RPR highlighting species and strain specific structural motifs. In vitro transcribed leptospiral RPR ribozymes are demonstrated to process pre-tRNA into mature tRNA in consonance with the positioning of Leptospira in the taxonomic domain of bacteria. RPR sequence datasets used to construct a phylogenetic tree exemplified the segregation of strains into their respective lineages with a (re)speciation of strain SH 9 to Leptospira borgpetersenii, strains Fiocruz LV 3954 and Fiocruz LV 4135 to Leptospira santarosai, strain CBC 613 to Leptospira kirschneri and strain HAI 1536 to Leptospira noguchii. Furthermore, it allowed characterization of an isolate P2653, presumptively characterized as either serovar Hebdomadis, Kremastos or Longnan to Leptospira weilii, serovar Longnan. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

SA-4-1BBL costimulation inhibits conversion of conventional CD4+ T cells into CD4+ FoxP3+ T regulatory cells by production of IFN-γ.

Directory of Open Access Journals (Sweden)

Shravan Madireddi

Full Text Available Tumors convert conventional CD4(+ T cells into induced CD4(+CD25(+FoxP3(+ T regulatory (iTreg cells that serve as an effective means of immune evasion. Therefore, the blockade of conventional CD4(+ T cell conversion into iTreg cells represents an attractive target for improving the efficacy of various immunotherapeutic approaches. Using a novel form of 4-1BBL molecule, SA-4-1BBL, we previously demonstrated that costimulation via 4-1BB receptor renders both CD4(+and CD8(+ T effector (Teff cells refractory to inhibition by Treg cells and increased intratumoral Teff/Treg cell ratio that correlated with therapeutic efficacy in various preclinical tumor models. Building on these studies, we herein show for the first time, to our knowledge, that signaling through 4-1BB inhibits antigen- and TGF-β-driven conversion of naïve CD4(+FoxP3(- T cells into iTreg cells via stimulation of IFN-γ production by CD4(+FoxP3(- T cells. Importantly, treatment with SA-4-1BBL blocked the conversion of CD4(+FoxP3(- T cells into Treg cells by EG.7 tumors. Taken together with our previous studies, these results show that 4-1BB signaling negatively modulate Treg cells by two distinct mechanisms: i inhibiting the conversion of CD4(+FoxP3(- T cells into iTreg cells and ii endowing Teff cells refractory to inhibition by Treg cells. Given the dominant role of Treg cells in tumor immune evasion mechanisms, 4-1BB signaling represents an attractive target for favorably tipping the Teff:Treg balance toward Teff cells with important implications for cancer immunotherapy.

Modeling radiation belt dynamics using a 3-D layer method code

Science.gov (United States)

Wang, C.; Ma, Q.; Tao, X.; Zhang, Y.; Teng, S.; Albert, J. M.; Chan, A. A.; Li, W.; Ni, B.; Lu, Q.; Wang, S.

2017-08-01

A new 3-D diffusion code using a recently published layer method has been developed to analyze radiation belt electron dynamics. The code guarantees the positivity of the solution even when mixed diffusion terms are included. Unlike most of the previous codes, our 3-D code is developed directly in equatorial pitch angle (α0), momentum (p), and L shell coordinates; this eliminates the need to transform back and forth between (α0,p) coordinates and adiabatic invariant coordinates. Using (α0,p,L) is also convenient for direct comparison with satellite data. The new code has been validated by various numerical tests, and we apply the 3-D code to model the rapid electron flux enhancement following the geomagnetic storm on 17 March 2013, which is one of the Geospace Environment Modeling Focus Group challenge events. An event-specific global chorus wave model, an AL-dependent statistical plasmaspheric hiss wave model, and a recently published radial diffusion coefficient formula from Time History of Events and Macroscale Interactions during Substorms (THEMIS) statistics are used. The simulation results show good agreement with satellite observations, in general, supporting the scenario that the rapid enhancement of radiation belt electron flux for this event results from an increased level of the seed population by radial diffusion, with subsequent acceleration by chorus waves. Our results prove that the layer method can be readily used to model global radiation belt dynamics in three dimensions.

Reactor Dosimetry Applications Using RAPTOR-M3G:. a New Parallel 3-D Radiation Transport Code

Science.gov (United States)

Longoni, Gianluca; Anderson, Stanwood L.

2009-08-01

The numerical solution of the Linearized Boltzmann Equation (LBE) via the Discrete Ordinates method (SN) requires extensive computational resources for large 3-D neutron and gamma transport applications due to the concurrent discretization of the angular, spatial, and energy domains. This paper will discuss the development RAPTOR-M3G (RApid Parallel Transport Of Radiation - Multiple 3D Geometries), a new 3-D parallel radiation transport code, and its application to the calculation of ex-vessel neutron dosimetry responses in the cavity of a commercial 2-loop Pressurized Water Reactor (PWR). RAPTOR-M3G is based domain decomposition algorithms, where the spatial and angular domains are allocated and processed on multi-processor computer architectures. As compared to traditional single-processor applications, this approach reduces the computational load as well as the memory requirement per processor, yielding an efficient solution methodology for large 3-D problems. Measured neutron dosimetry responses in the reactor cavity air gap will be compared to the RAPTOR-M3G predictions. This paper is organized as follows: Section 1 discusses the RAPTOR-M3G methodology; Section 2 describes the 2-loop PWR model and the numerical results obtained. Section 3 addresses the parallel performance of the code, and Section 4 concludes this paper with final remarks and future work.

Time domain spectral phase encoding/DPSK data modulation using single phase modulator for OCDMA application.

Science.gov (United States)

Wang, Xu; Gao, Zhensen; Kataoka, Nobuyuki; Wada, Naoya

2010-05-10

A novel scheme using single phase modulator for simultaneous time domain spectral phase encoding (SPE) signal generation and DPSK data modulation is proposed and experimentally demonstrated. Array- Waveguide-Grating and Variable-Bandwidth-Spectrum-Shaper based devices can be used for decoding the signal directly in spectral domain. The effects of fiber dispersion, light pulse width and timing error on the coding performance have been investigated by simulation and verified in experiment. In the experiment, SPE signal with 8-chip, 20GHz/chip optical code patterns has been generated and modulated with 2.5 Gbps DPSK data using single modulator. Transmission of the 2.5 Gbps data over 34km fiber with BEROCDMA) and secure optical communication applications. (c) 2010 Optical Society of America.

Molecular mimicry of human tRNALys anti-codon domain by HIV-1 RNA genome facilitates tRNA primer annealing.

Science.gov (United States)

Jones, Christopher P; Saadatmand, Jenan; Kleiman, Lawrence; Musier-Forsyth, Karin

2013-02-01

The primer for initiating reverse transcription in human immunodeficiency virus type 1 (HIV-1) is tRNA(Lys3). Host cell tRNA(Lys) is selectively packaged into HIV-1 through a specific interaction between the major tRNA(Lys)-binding protein, human lysyl-tRNA synthetase (hLysRS), and the viral proteins Gag and GagPol. Annealing of the tRNA primer onto the complementary primer-binding site (PBS) in viral RNA is mediated by the nucleocapsid domain of Gag. The mechanism by which tRNA(Lys3) is targeted to the PBS and released from hLysRS prior to annealing is unknown. Here, we show that hLysRS specifically binds to a tRNA anti-codon-like element (TLE) in the HIV-1 genome, which mimics the anti-codon loop of tRNA(Lys) and is located proximal to the PBS. Mutation of the U-rich sequence within the TLE attenuates binding of hLysRS in vitro and reduces the amount of annealed tRNA(Lys3) in virions. Thus, LysRS binds specifically to the TLE, which is part of a larger LysRS binding domain in the viral RNA that includes elements of the Psi packaging signal. Our results suggest that HIV-1 uses molecular mimicry of the anti-codon of tRNA(Lys) to increase the efficiency of tRNA(Lys3) annealing to viral RNA.

p21-ras effector domain mutants constructed by "cassette" mutagenesis

DEFF Research Database (Denmark)

Stone, J C; Vass, W C; Willumsen, B M

1988-01-01

A series of mutations encoding single-amino-acid substitutions within the v-rasH effector domain were constructed, and the ability of the mutants to induce focal transformation of NIH 3T3 cells was studied. The mutations, which spanned codons 32 to 40, were made by a "cassette" mutagenesis...

Interoperable domain-specific languages families for code generation

Czech Academy of Sciences Publication Activity Database

Malohlava, M.; Plášil, F.; Bureš, Tomáš; Hnětynka, P.

2013-01-01

Roč. 43, č. 5 (2013), s. 479-499 ISSN 0038-0644 R&D Projects: GA ČR GD201/09/H057 EU Projects: European Commission(XE) ASCENS 257414 Grant - others:GA AV ČR(CZ) GAP103/11/1489 Program:FP7 Institutional research plan: CEZ:AV0Z10300504 Keywords : code generation * domain specific languages * models reuse * extensible languages * specification * program synthesis Subject RIV: JC - Computer Hardware ; Software Impact factor: 1.148, year: 2013

Towards clinical assessment of velopharyngeal closure using MRI: evaluation of real-time MRI sequences at 1.5 and 3 T.

Science.gov (United States)

Scott, A D; Boubertakh, R; Birch, M J; Miquel, M E

2012-11-01

The objective of this study was to demonstrate soft palate MRI at 1.5 and 3 T with high temporal resolution on clinical scanners. Six volunteers were imaged while speaking, using both four real-time steady-state free-precession (SSFP) sequences at 3 T and four balanced SSFP (bSSFP) at 1.5 T. Temporal resolution was 9-20 frames s(-1) (fps), spatial resolution 1.6 × 1.6 × 10.0-2.7 × 2.7 × 10.0 mm(3). Simultaneous audio was recorded. Signal-to-noise ratio (SNR), palate thickness and image quality score (1-4, non-diagnostic-excellent) were evaluated. SNR was higher at 3 T than 1.5 T in the relaxed palate (nasal breathing position) and reduced in the elevated palate at 3 T, but not 1.5 T. Image quality was not significantly different between field strengths or sequences (p=NS). At 3 T, 40% acquisitions scored 2 and 56% scored 3. Most 1.5 T acquisitions scored 1 (19%) or 4 (46%). Image quality was more dependent on subject or field than sequence. SNR in static images was highest with 1.9 × 1.9 × 10.0 mm(3) resolution (10 fps) and measured palate thickness was similar (p=NS) to that at the highest resolution (1.6 × 1.6 × 10.0 mm(3)). SNR in intensity-time plots through the soft palate was highest with 2.7 × 2.7 × 10.0 mm(3) resolution (20 fps). At 3 T, SSFP images are of a reliable quality, but 1.5 T bSSFP images are often better. For geometric measurements, temporal should be traded for spatial resolution (1.9 × 1.9 × 10.0 mm(3), 10 fps). For assessment of motion, temporal should be prioritised over spatial resolution (2.7 × 2.7 × 10.0 mm(3), 20 fps). Advances in knowledge Diagnostic quality real-time soft palate MRI is possible using clinical scanners and optimised protocols have been developed. 3 T SSFP imaging is reliable, but 1.5 T bSSFP often produces better images.

DCOMP Award Lecture (Metropolis): A 3D Spectral Anelastic Hydrodynamic Code for Shearing, Stratified Flows

Science.gov (United States)

Barranco, Joseph

2006-03-01

We have developed a three-dimensional (3D) spectral hydrodynamic code to study vortex dynamics in rotating, shearing, stratified systems (eg, the atmosphere of gas giant planets, protoplanetary disks around newly forming protostars). The time-independent background state is stably stratified in the vertical direction and has a unidirectional linear shear flow aligned with one horizontal axis. Superposed on this background state is an unsteady, subsonic flow that is evolved with the Euler equations subject to the anelastic approximation to filter acoustic phenomena. A Fourier-Fourier basis in a set of quasi-Lagrangian coordinates that advect with the background shear is used for spectral expansions in the two horizontal directions. For the vertical direction, two different sets of basis functions have been implemented: (1) Chebyshev polynomials on a truncated, finite domain, and (2) rational Chebyshev functions on an infinite domain. Use of this latter set is equivalent to transforming the infinite domain to a finite one with a cotangent mapping, and using cosine and sine expansions in the mapped coordinate. The nonlinear advection terms are time integrated explicitly, whereas the Coriolis force, buoyancy terms, and pressure/enthalpy gradient are integrated semi- implicitly. We show that internal gravity waves can be damped by adding new terms to the Euler equations. The code exhibits excellent parallel performance with the Message Passing Interface (MPI). As a demonstration of the code, we simulate vortex dynamics in protoplanetary disks and the Kelvin-Helmholtz instability in the dusty midplanes of protoplanetary disks.

Endothermic decompositions of inorganic monocrystalline thin plates. I. Shape of polycrystalline product domains versus constraints and time

Science.gov (United States)

Bertrand, G.; Comperat, M.; Lallemant, M.; Watelle, G.

1980-03-01

Copper sulfate pentahydrate dehydration into trihydrate was investigated using monocrystalline platelets with varying crystallographic orientations. The morphological and kinetic features of the trihydrate domains were examined. Different shapes were observed: polygons (parallelograms, hexagons) and ellipses; their conditions of occurrence are reported in the (P, T) diagram. At first (for about 2 min), the ratio of the long to the short axes of elliptical domains changes with time; these subsequently develop homothetically and the rate ratio is then only pressure dependent. Temperature influence is inferred from that of pressure. Polygonal shapes are time dependent and result in ellipses. So far, no model can be put forward. Yet, qualitatively, the polygonal shape of a domain may be explained by the prevalence of the crystal arrangement and the elliptical shape by that of the solid tensorial properties. The influence of those factors might be modulated versus pressure, temperature, interface extent, and, thus, time.

Discrete processes modelling and geometry description in RTS and T code

International Nuclear Information System (INIS)

Degtyarev, I.I.; Liashenko, O.A.; Lokhovitskii, A.E.; Yazynin, I.A.; Belyakov-Bodin, V.I.; Blokhin, A.I.

2001-01-01

This paper describes the recent version of the RTS and T code system. RTS and T performs detailed simulations of many types of particles transport in complex 3D geometries in the energy range from a part of eV up to 20 TeV. A description of the main processes is given. (author)

A two-dimensional time domain near zone to far zone transformation

Science.gov (United States)

Luebbers, Raymond J.; Ryan, Deirdre; Beggs, John H.; Kunz, Karl S.

1991-01-01

In a previous paper, a time domain transformation useful for extrapolating 3-D near zone finite difference time domain (FDTD) results to the far zone was presented. In this paper, the corresponding 2-D transform is outlined. While the 3-D transformation produced a physically observable far zone time domain field, this is not convenient to do directly in 2-D, since a convolution would be required. However, a representative 2-D far zone time domain result can be obtained directly. This result can then be transformed to the frequency domain using a Fast Fourier Transform, corrected with a simple multiplicative factor, and used, for example, to calculate the complex wideband scattering width of a target. If an actual time domain far zone result is required it can be obtained by inverse Fourier transform of the final frequency domain result.

Time domain topology optimization of 3D nanophotonic devices

DEFF Research Database (Denmark)

Elesin, Yuriy; Lazarov, Boyan Stefanov; Jensen, Jakob Søndergaard

2014-01-01

We present an efficient parallel topology optimization framework for design of large scale 3D nanophotonic devices. The code shows excellent scalability and is demonstrated for optimization of broadband frequency splitter, waveguide intersection, photonic crystal-based waveguide and nanowire...

Thorax irradiation triggers a local and systemic accumulation of immunosuppressive CD4+ FoxP3+ regulatory T cells

International Nuclear Information System (INIS)

Wirsdörfer, Florian; Cappuccini, Federica; Niazman, Muska; Leve, Simone de; Westendorf, Astrid M; Lüdemann, Lutz; Stuschke, Martin; Jendrossek, Verena

2014-01-01

Lymphocyte infiltration is a common feature of radiation-induced pneumonitis and fibrosis, but their contribution to the pathogenic processes is still unclear. Here, we addressed the impact of thorax irradiation on the T cell compartment with a focus on immunosuppressive regulatory T cells (Treg). C57BL/6 wild type mice (WT) received anesthesia only (sham controls, 0 Gy) or were exposed to a single dose of whole thorax irradiation (15 Gy). Immune cells from lung tissue, spleen, and cervical lymph nodes were collected 10 to 84 days post-irradiation and phenotypically characterized by flow cytometry. Whole thorax irradiation provoked an increased influx of CD3+ T cells at 42 and 84 days post-irradiation. In contrast, local irradiation caused a sustained reduction in CD3+ T cells in peripheral lymphoid tissues. Interestingly, we observed a significant local and systemic increase in the fraction of CD4+ T cells expressing the transcription factor forkhead box P3 (FoxP3), the phenotypic marker for murine Treg, at day 21 post-irradiation. The accumulation of Treg was associated with increased levels of T cells expressing surface proteins characteristic for recruitment and immunosuppressive activity, e.g. CD103, CTLA-4 and CD73. Importantly, Treg isolated at this time point were able to suppress CD4+ effector T cells to a similar extent as Treg isolated from control mice. The response of the adaptive immune system to whole thorax irradiation is characterized by local immunoactivation and systemic immunosuppression. The transient accumulation of immunosuppressive CD4+ FoxP3+ Treg may be required to protect the lung against excessive inflammation-induced tissue damage. Further investigations shall define the mechanisms underlying the accumulation of Treg and their role for the pathogenesis of radiation-induced lung disease

Massively parallel Fokker-Planck code ALLAp

International Nuclear Information System (INIS)

Batishcheva, A.A.; Krasheninnikov, S.I.; Craddock, G.G.; Djordjevic, V.

1996-01-01

The recently developed for workstations Fokker-Planck code ALLA simulates the temporal evolution of 1V, 2V and 1D2V collisional edge plasmas. In this work we present the results of code parallelization on the CRI T3D massively parallel platform (ALLAp version). Simultaneously we benchmark the 1D2V parallel vesion against an analytic self-similar solution of the collisional kinetic equation. This test is not trivial as it demands a very strong spatial temperature and density variation within the simulation domain. (orig.)

Specific phosphopeptide binding regulates a conformational change in the PI 3-kinase SH2 domain associated with enzyme activation.

Science.gov (United States)

Shoelson, S E; Sivaraja, M; Williams, K P; Hu, P; Schlessinger, J; Weiss, M A

1993-01-01

SH2 (src-homology 2) domains define a newly recognized binding motif that mediates the physical association of target phosphotyrosyl proteins with downstream effector enzymes. An example of such phosphoprotein-effector coupling is provided by the association of phosphatidylinositol 3-kinase (PI 3-kinase) with specific phosphorylation sites within the PDGF receptor, the c-Src/polyoma virus middle T antigen complex and the insulin receptor substrate IRS-1. Notably, phosphoprotein association with the SH2 domains of p85 also stimulates an increase in catalytic activity of the PI 3-kinase p110 subunit, which can be mimicked by phosphopeptides corresponding to targeted phosphoprotein phosphorylation sites. To investigate how phosphoprotein binding to the p85 SH2 domain stimulates p110 catalytic activation, we have examined the differential effects of phosphotyrosine and PDGF receptor-, IRS-1- and c-Src-derived phosphopeptides on the conformation of an isolated SH2 domain of PI 3-kinase. Although phosphotyrosine and both activating and non-activating phosphopeptides bind to the SH2 domain, activating phosphopeptides bind with higher affinity and induce a qualitatively distinct conformational change as monitored by CD and NMR spectroscopy. Amide proton exchange and protease protection assays further show that high affinity, specific phosphopeptide binding induces non-local dynamic SH2 domain stabilization. Based on these findings we propose that specific phosphoprotein binding to the p85 subunit induces a change in SH2 domain structure which is transmitted to the p110 subunit and regulates enzymatic activity by an allosteric mechanism. Images PMID:8382612

The MICHELLE 2D/3D ES PIC Code Advances and Applications

CERN Document Server

Petillo, John; De Ford, John F; Dionne, Norman J; Eppley, Kenneth; Held, Ben; Levush, Baruch; Nelson, Eric M; Panagos, Dimitrios; Zhai, Xiaoling

2005-01-01

MICHELLE is a new 2D/3D steady-state and time-domain particle-in-cell (PIC) code* that employs electrostatic and now magnetostatic finite-element field solvers. The code has been used to design and analyze a wide variety of devices that includes multistage depressed collectors, gridded guns, multibeam guns, annular-beam guns, sheet-beam guns, beam-transport sections, and ion thrusters. Latest additions to the MICHELLE/Voyager tool are as follows: 1) a prototype 3D self magnetic field solver using the curl-curl finite-element formulation for the magnetic vector potential, employing edge basis functions and accumulating current with MICHELLE's new unstructured grid particle tracker, 2) the electrostatic field solver now accommodates dielectric media, 3) periodic boundary conditions are now functional on all grids, not just structured grids, 4) the addition of a global optimization module to the user interface where both electrical parameters (such as electrode voltages)can be optimized, and 5) adaptive mesh ref...

TIM-1 glycoprotein binds the adhesion receptor P-selectin and mediates T cell trafficking during inflammation and autoimmunity

Science.gov (United States)

Angiari, Stefano; Donnarumma, Tiziano; Rossi, Barbara; Dusi, Silvia; Pietronigro, Enrica; Zenaro, Elena; Della Bianca, Vittorina; Toffali, Lara; Piacentino, Gennj; Budui, Simona; Rennert, Paul; Xiao, Sheng; Laudanna, Carlo; Casasnovas, Jose M.; Kuchroo, Vijay K.; Constantin, Gabriela

2014-01-01

SUMMARY Selectins play a central role in leukocyte trafficking by mediating tethering and rolling on vascular surfaces. Here we have reported that T cell immunoglobulin and mucin domain 1 (TIM-1) is a P-selectin ligand. We have shown that human and murine TIM-1 binds to P-selectin, and that TIM-1 mediates tethering and rolling of T helper-1 (Th1) and Th17, but not Th2 and regulatory T cells on P-selectin. Th1 and Th17 cells lacking the TIM-1 mucin domain showed reduced rolling in thrombin-activated mesenteric venules and inflamed brain microcirculation. Inhibition of TIM-1 had no effect on naive T cell homing, but reduced T cell recruitment in a skin hypersensitivity model and blocked experimental autoimmune encephalomyelitis. Uniquely, the TIM-1 IgV domain was also required for P-selectin binding. Our data demonstrate that TIM-1 is a major P-selectin ligand with a specialized role in T cell trafficking during inflammatory responses and the induction of autoimmune disease. PMID:24703780

Implementation of a 3D plasma particle-in-cell code on a MIMD parallel computer

International Nuclear Information System (INIS)

Liewer, P.C.; Lyster, P.; Wang, J.

1993-01-01

A three-dimensional plasma particle-in-cell (PIC) code has been implemented on the Intel Delta MIMD parallel supercomputer using the General Concurrent PIC algorithm. The GCPIC algorithm uses a domain decomposition to divide the computation among the processors: A processor is assigned a subdomain and all the particles in it. Particles must be exchanged between processors as they move. Results are presented comparing the efficiency for 1-, 2- and 3-dimensional partitions of the three dimensional domain. This algorithm has been found to be very efficient even when a large fraction (e.g. 30%) of the particles must be exchanged at every time step. On the 512-node Intel Delta, up to 125 million particles have been pushed with an electrostatic push time of under 500 nsec/particle/time step

T3 glottic cancer: an analysis of dose time-volume factors

International Nuclear Information System (INIS)

Harwood, A.R.; Beale, F.A.; Cummings, B.J.; Hawkins, N.V.; Keane, T.J.; Rider, W.D.

1980-01-01

This report analyzes dose-time-volume factors in 112 patients with T3N0M0 glottic cancer who were treated with radical radiotherapy with surgery for salvage between 1963 and 1977. 55% of the patients are alive and well 5 years following treatment; 26% died of glottic cancer and 19% died of intercurrent disease. In the 1965 to 1969 time period, 31% died of tumor as compared to 16% in the 1975 to 1977 time period. Overall local control by radiotherapy was 51%; 2/3 of the failures were surgically salvaged. 44% were locally controlled by radiotherapy in the 1965 to 1969 time period and 57% in the 1975 to 1977 time period. Analysis of dose-time-volume factors reveals that the optimal dose is greater than 1700 ret and a minimal volume of 6 x 8 cm should be used. A dose-cure curve for T3 glottic cancer is constructed and compared with the dose complication curve for the larynx and the dose-cure curve for T1N0M0 glottic cancer. A comparison of cure rates between 112 patients treated with radical radiotherapy and surgery for salvage versus 28 patients treated with combined pre-operative irradiation and surgery reveals no difference in the proportion of patients who died of glottic cancer or in the number of patients alive at 5 years following treatment

Binding of influenza A virus NS1 protein to the inter-SH2 domain of p85 suggests a novel mechanism for phosphoinositide 3-kinase activation.

Science.gov (United States)

Hale, Benjamin G; Batty, Ian H; Downes, C Peter; Randall, Richard E

2008-01-18

Influenza A virus NS1 protein stimulates host-cell phosphoinositide 3-kinase (PI3K) signaling by binding to the p85beta regulatory subunit of PI3K. Here, in an attempt to establish a mechanism for this activation, we report further on the functional interaction between NS1 and p85beta. Complex formation was found to be independent of NS1 RNA binding activity and is mediated by the C-terminal effector domain of NS1. Intriguingly, the primary direct binding site for NS1 on p85beta is the inter-SH2 domain, a coiled-coil structure that acts as a scaffold for the p110 catalytic subunit of PI3K. In vitro kinase activity assays, together with protein binding competition studies, reveal that NS1 does not displace p110 from the inter-SH2 domain, and indicate that NS1 can form an active heterotrimeric complex with PI3K. In addition, it was established that residues at the C terminus of the inter-SH2 domain are essential for mediating the interaction between p85beta and NS1. Equivalent residues in p85alpha have previously been implicated in the basal inhibition of p110. However, such p85alpha residues were unable to substitute for those in p85beta with regards NS1 binding. Overall, these data suggest a model by which NS1 activates PI3K catalytic activity by masking a normal regulatory element specific to the p85beta inter-SH2 domain.

Improved virtual channel noise model for transform domain Wyner-Ziv video coding

DEFF Research Database (Denmark)

Huang, Xin; Forchhammer, Søren

2009-01-01

Distributed video coding (DVC) has been proposed as a new video coding paradigm to deal with lossy source coding using side information to exploit the statistics at the decoder to reduce computational demands at the encoder. A virtual channel noise model is utilized at the decoder to estimate...... the noise distribution between the side information frame and the original frame. This is one of the most important aspects influencing the coding performance of DVC. Noise models with different granularity have been proposed. In this paper, an improved noise model for transform domain Wyner-Ziv video...... coding is proposed, which utilizes cross-band correlation to estimate the Laplacian parameters more accurately. Experimental results show that the proposed noise model can improve the rate-distortion (RD) performance....

Signal to Noise Ratio (SNR Enhancement Comparison of Impulse-, Coding- and Novel Linear-Frequency-Chirp-Based Optical Time Domain Reflectometry (OTDR for Passive Optical Network (PON Monitoring Based on Unique Combinations of Wavelength Selective Mirrors

Directory of Open Access Journals (Sweden)

Christopher M. Bentz

2014-03-01

Full Text Available We compare optical time domain reflectometry (OTDR techniques based on conventional single impulse, coding and linear frequency chirps concerning their signal to noise ratio (SNR enhancements by measurements in a passive optical network (PON with a maximum one-way attenuation of 36.6 dB. A total of six subscribers, each represented by a unique mirror pair with narrow reflection bandwidths, are installed within a distance of 14 m. The spatial resolution of the OTDR set-up is 3.0 m.

Synthesis, purification and characterization of [3,5 - T] p-aminobenzoic acid

International Nuclear Information System (INIS)

Corol-Cucu, Delia-Irina; Chiper, Diana; Mihaila, V.; Negoita, N.

2000-01-01

This paper refers to the synthesis, purification and characterization of [3,5-T] p-aminobenzoic acid (PAB,H' vitamine). The p-aminobenzoic acid is used in the treatment of rheumatic arthritis and dermatological affections. The advantage of tritium labelling of p-aminobenzoic acid is that some biomedical important aspects of collagen's behaviour are made clear. The PAB stimulate the grow of intestinal bacteria so necessary to synthesis of some vitamins (bio tine, pantothenic acid). Tritium is the only radioactive isotope of hydrogen. Several steps have to be carried out in the synthesis of the final product as well as to study its biological behavior. For the labelling of PAB one prefers the substitution of bromine from PAB-3,5-Br with tritium because of simplicity of reaction and the easy synthesis of halogen compound. The first step in synthesis is the protection of NH 2 group through acetylation of PAB. After that PAB is bromated into the 3 and 5 position with elementary bromine. The raw compound is purified and recrystallized and characterized through thin layer chromatography.The tritium labelling is performed through substitution of bromine from bromate derivative, using Pd/C (10% Pd) as catalyst and low basic conditions for the neutralization of HBr resulting from reaction. After the separation of PAB-3,5-T through filtration, the catalyst remains on the filter paper and the labelled compound goes in aqueous solution. PAB-3,5-T is purified through thin layer chromatography with the solvent system n-BuOH:NH 4 OH(25%):H 2 O:EtOH (8:1:2:2,5, v/v) with silica gel GF 254 as support. The determination of activity is carried out with LSC (Liquid Scintillation Counter). A 98% purity was determined through TLC in the same conditions while determination of activity distribution was performed with a 2π Berthold scanner with gas running and without window. The chemical concentration has been measured through UV spectrophotometry and by comparing extinction with

A review of MAAP4 code structure and core T/H model

International Nuclear Information System (INIS)

Song, Yong Mann; Park, Soo Yong

1998-03-01

The modular accident analysis program (MAAP) version 4 is a computer code that can simulate the response of LWR plants during severe accident sequences and includes models for all of the important phenomena which might occur during accident sequences. In this report, MAAP4 code structure and core thermal hydraulic (T/H) model which models the T/H behavior of the reactor core and the response of core components during all accident phases involving degraded cores are specifically reviewed and then reorganized. This reorganization is performed via getting the related models together under each topic whose contents and order are same with other two reports for MELCOR and SCDAP/RELAP5 to be simultaneously published. Major purpose of the report is to provide information about the characteristics of MAAP4 core T/H models for an integrated severe accident computer code development being performed under the one of on-going mid/long-term nuclear developing project. The basic characteristics of the new integrated severe accident code includes: 1) Flexible simulation capability of primary side, secondary side, and the containment under severe accident conditions, 2) Detailed plant simulation, 3) Convenient user-interfaces, 4) Highly modularization for easy maintenance/improvement, and 5) State-of-the-art model selection. In conclusion, MAAP4 code has appeared to be superior for 3) and 4) items but to be somewhat inferior for 1) and 2) items. For item 5), more efforts should be made in the future to compare separated models in detail with not only other codes but also recent world-wide work. (author). 17 refs., 1 tab., 12 figs

T1rho and T2 relaxation times of the normal adult knee meniscus at 3T: analysis of zonal differences.

Science.gov (United States)

Takao, Shoichiro; Nguyen, Tan B; Yu, Hon J; Hagiwara, Shigeo; Kaneko, Yasuhito; Nozaki, Taiki; Iwamoto, Seiji; Otomo, Maki; Schwarzkopf, Ran; Yoshioka, Hiroshi

2017-05-18

Prior studies describe histological and immunohistochemical differences in collagen and proteoglycan content in different meniscal zones. The aim of this study is to evaluate horizontal and vertical zonal differentiation of T1rho and T2 relaxation times of the entire meniscus from volunteers without symptom and imaging abnormality. Twenty volunteers age between 19 and 38 who have no knee-related clinical symptoms, and no history of prior knee surgeries were enrolled in this study. Two T1rho mapping (b-FFE T1rho and SPGR T1rho) and T2 mapping images were acquired with a 3.0-T MR scanner. Each meniscus was divided manually into superficial and deep zones for horizontal zonal analysis. The anterior and posterior horns of each meniscus were divided manually into white, red-white and red zones for vertical zonal analysis. Zonal differences of average relaxation times among each zone, and both inter- and intra-observer reproducibility were statistically analyzed. In horizontal zonal analysis, T1rho relaxation times of the superficial zone tended to be higher than those of the deep zone, and this difference was statistically significant in the medial meniscal segments (84.3 ms vs 76.0 ms on b-FFE, p meniscus (88.4 ms vs 77.1 ms on b-FFE, p meniscus, p = 0.011). T2 relaxation times of the white zone were significantly higher than those of the red zone in the medial meniscus posterior horn (96.8 ms vs 84.3 ms, p meniscus anterior horn (104.6 ms vs 84.2 ms, p 0.74) or good (0.60-0.74) in all meniscal segments on both horizontal and vertical zonal analysis, except for inter-class correlation coefficients of the lateral meniscus on SPGR. Compared with SPGR T1rho images, b-FFE T1rho images demonstrated more significant zonal differentiation with higher inter- and intra-observer reproducibility. There are zonal differences in T1rho and T2 relaxation times of the normal meniscus.

The application of T1 and T2 relaxation time and magnetization transfer ratios to the early diagnosis of patellar cartilage osteoarthritis

Energy Technology Data Exchange (ETDEWEB)

Yao, Weiwu; Qu, Nan; Lu, Zhihua; Yang, Shixun [Shanghai Jiaotong University, Department of Radiology, Shanghai (China)

2009-11-15

We compare the T1 and T2 relaxation times and magnetization transfer ratios (MTRs) of normal subjects and patients with osteoarthritis (OA) to evaluate the ability of these techniques to aid in the early diagnosis and treatment of OA. The knee joints in 11 normal volunteers and 40 patients with OA were prospectively evaluated using T1 relaxation times as measured using delayed gadolinium-enhanced MRI of cartilage (dGEMRIC), T2 relaxation times (multiple spin-echo sequence, T2 mapping), and MTRs. The OA patients were further categorized into mild, moderate, and severe OA. The mean T1 relaxation times of the four groups (normal, mild OA, moderate OA, and severe OA) were: 487.3{+-}27.7, 458.0{+-}55.9, 405.9{+-}57.3, and 357.9{+-}36.7 respectively (p<0.001). The mean T2 relaxation times of the four groups were: 37.8{+-}3.3, 44.0{+-}8.5, 50.9{+-}9.5, and 57.4{+-}4.8 respectively (p<0.001). T1 relaxation time decreased and T2 relaxation time increased with worsening degeneration of patellar cartilage. The result of the covariance analysis showed that the covariate age had a significant influence on T2 relaxation time (p<0.001). No significant differences between the normal and OA groups using MTR were noted. T1 and T2 relaxation times are relatively sensitive to early degenerative changes in the patellar cartilage, whereas the MTR may have some limitations with regard to early detection of OA. In addition, The T1 and T2 relaxation times negatively correlate with each other, which is a novel finding. (orig.)

First Measurement of σ(gg → t$\\bar{t}$)/σ(p$\\bar{p}$ → t$\\bar{t}$)

Energy Technology Data Exchange (ETDEWEB)

Alamdari, Shabnaz Pashapour [Univ. of Toronto, ON (Canada)

2008-01-01

The work presented here is the first measurement of the fraction of top quark pair production through gluon-gluon fusion. We use an integrated luminosity of 0.96 ± 0.06 fb^-1 of p{bar p} collisions at √s of 1.96 TeV collected by the CDF II detector. We select t$\\bar{t}$ candidates by identifying a high-p_T lepton candidate, a large missing E_T as evidence for a neutrino candidate and at least four high E_T jets, one of which has to be identified as originating from a b quark. The challenge is to discriminate between the two production processes with the identical final state, gg → t$\\bar{t}$ and q$\\bar{p}$ → t$\\bar{t}$. We take advantage of the fact that compared to a quark, a gluon is more likely to radiate a low momentum gluon and therefore, one expects a larger number of charged particles with low p_T in a process involving more gluons. Given the large uncertainties associated with the modeling of the low p_T charged particle multiplicity, a data-driven technique was employed. Using calibration data samples, we show there exists a clear correlation between the observed average number of low p_T charged particles and the average number of gluons involved in the production process predicted by Monte Carlo calculations. Given the correlation, one can identify low p_T charged particle multiplicity distributions associated with specific average number of gluons. The W + 0 jet sample and dijets sample with leading jet E_T in the range of 80-100 GeV are used to find no-gluon and gluon-rich low p{sub T} charged particle multiplicity distributions, respectively. Using these no-gluon and gluon-rich distributions in a likelihood fit, we find the fraction of gluon-rich events in t{bar t} candidates. This fraction has contributions from the signal and background events. Taking into account these contributions and the gg → t$\\bar{t}$ and q$\\bar{q}$ → t$\\bar{t

Parallelization of 2-D lattice Boltzmann codes

International Nuclear Information System (INIS)

Suzuki, Soichiro; Kaburaki, Hideo; Yokokawa, Mitsuo.

1996-03-01

Lattice Boltzmann (LB) codes to simulate two dimensional fluid flow are developed on vector parallel computer Fujitsu VPP500 and scalar parallel computer Intel Paragon XP/S. While a 2-D domain decomposition method is used for the scalar parallel LB code, a 1-D domain decomposition method is used for the vector parallel LB code to be vectorized along with the axis perpendicular to the direction of the decomposition. High parallel efficiency of 95.1% by the vector parallel calculation on 16 processors with 1152x1152 grid and 88.6% by the scalar parallel calculation on 100 processors with 800x800 grid are obtained. The performance models are developed to analyze the performance of the LB codes. It is shown by our performance models that the execution speed of the vector parallel code is about one hundred times faster than that of the scalar parallel code with the same number of processors up to 100 processors. We also analyze the scalability in keeping the available memory size of one processor element at maximum. Our performance model predicts that the execution time of the vector parallel code increases about 3% on 500 processors. Although the 1-D domain decomposition method has in general a drawback in the interprocessor communication, the vector parallel LB code is still suitable for the large scale and/or high resolution simulations. (author)

Parallelization of 2-D lattice Boltzmann codes

Energy Technology Data Exchange (ETDEWEB)

Suzuki, Soichiro; Kaburaki, Hideo; Yokokawa, Mitsuo

1996-03-01

Lattice Boltzmann (LB) codes to simulate two dimensional fluid flow are developed on vector parallel computer Fujitsu VPP500 and scalar parallel computer Intel Paragon XP/S. While a 2-D domain decomposition method is used for the scalar parallel LB code, a 1-D domain decomposition method is used for the vector parallel LB code to be vectorized along with the axis perpendicular to the direction of the decomposition. High parallel efficiency of 95.1% by the vector parallel calculation on 16 processors with 1152x1152 grid and 88.6% by the scalar parallel calculation on 100 processors with 800x800 grid are obtained. The performance models are developed to analyze the performance of the LB codes. It is shown by our performance models that the execution speed of the vector parallel code is about one hundred times faster than that of the scalar parallel code with the same number of processors up to 100 processors. We also analyze the scalability in keeping the available memory size of one processor element at maximum. Our performance model predicts that the execution time of the vector parallel code increases about 3% on 500 processors. Although the 1-D domain decomposition method has in general a drawback in the interprocessor communication, the vector parallel LB code is still suitable for the large scale and/or high resolution simulations. (author).

Transformation Algorithm of Dielectric Response in Time-Frequency Domain

Directory of Open Access Journals (Sweden)

Ji Liu

2014-01-01

Full Text Available A transformation algorithm of dielectric response from time domain to frequency domain is presented. In order to shorten measuring time of low or ultralow frequency dielectric response characteristics, the transformation algorithm is used in this paper to transform the time domain relaxation current to frequency domain current for calculating the low frequency dielectric dissipation factor. In addition, it is shown from comparing the calculation results with actual test data that there is a coincidence for both results over a wide range of low frequencies. Meanwhile, the time domain test data of depolarization currents in dry and moist pressboards are converted into frequency domain results on the basis of the transformation. The frequency domain curves of complex capacitance and dielectric dissipation factor at the low frequency range are obtained. Test results of polarization and depolarization current (PDC in pressboards are also given at the different voltage and polarization time. It is demonstrated from the experimental results that polarization and depolarization current are affected significantly by moisture contents of the test pressboards, and the transformation algorithm is effective in ultralow frequency of 10−3 Hz. Data analysis and interpretation of the test results conclude that analysis of time-frequency domain dielectric response can be used for assessing insulation system in power transformer.

Accurate characterization of 3D diffraction gratings using time domain discontinuous Galerkin method with exact absorbing boundary conditions

KAUST Repository

Sirenko, Kostyantyn

2013-07-01

Exact absorbing and periodic boundary conditions allow to truncate grating problems\\' infinite physical domains without introducing any errors. This work presents exact absorbing boundary conditions for 3D diffraction gratings and describes their discretization within a high-order time-domain discontinuous Galerkin finite element method (TD-DG-FEM). The error introduced by the boundary condition discretization matches that of the TD-DG-FEM; this results in an optimal solver in terms of accuracy and computation time. Numerical results demonstrate the superiority of this solver over TD-DG-FEM with perfectly matched layers (PML)-based domain truncation. © 2013 IEEE.

Reconstruction for Time-Domain In Vivo EPR 3D Multigradient Oximetric Imaging—A Parallel Processing Perspective

Directory of Open Access Journals (Sweden)

Christopher D. Dharmaraj

2009-01-01

Full Text Available Three-dimensional Oximetric Electron Paramagnetic Resonance Imaging using the Single Point Imaging modality generates unpaired spin density and oxygen images that can readily distinguish between normal and tumor tissues in small animals. It is also possible with fast imaging to track the changes in tissue oxygenation in response to the oxygen content in the breathing air. However, this involves dealing with gigabytes of data for each 3D oximetric imaging experiment involving digital band pass filtering and background noise subtraction, followed by 3D Fourier reconstruction. This process is rather slow in a conventional uniprocessor system. This paper presents a parallelization framework using OpenMP runtime support and parallel MATLAB to execute such computationally intensive programs. The Intel compiler is used to develop a parallel C++ code based on OpenMP. The code is executed on four Dual-Core AMD Opteron shared memory processors, to reduce the computational burden of the filtration task significantly. The results show that the parallel code for filtration has achieved a speed up factor of 46.66 as against the equivalent serial MATLAB code. In addition, a parallel MATLAB code has been developed to perform 3D Fourier reconstruction. Speedup factors of 4.57 and 4.25 have been achieved during the reconstruction process and oximetry computation, for a data set with 23×23×23 gradient steps. The execution time has been computed for both the serial and parallel implementations using different dimensions of the data and presented for comparison. The reported system has been designed to be easily accessible even from low-cost personal computers through local internet (NIHnet. The experimental results demonstrate that the parallel computing provides a source of high computational power to obtain biophysical parameters from 3D EPR oximetric imaging, almost in real-time.

Reconstruction for time-domain in vivo EPR 3D multigradient oximetric imaging--a parallel processing perspective.

Science.gov (United States)

Dharmaraj, Christopher D; Thadikonda, Kishan; Fletcher, Anthony R; Doan, Phuc N; Devasahayam, Nallathamby; Matsumoto, Shingo; Johnson, Calvin A; Cook, John A; Mitchell, James B; Subramanian, Sankaran; Krishna, Murali C

2009-01-01

Three-dimensional Oximetric Electron Paramagnetic Resonance Imaging using the Single Point Imaging modality generates unpaired spin density and oxygen images that can readily distinguish between normal and tumor tissues in small animals. It is also possible with fast imaging to track the changes in tissue oxygenation in response to the oxygen content in the breathing air. However, this involves dealing with gigabytes of data for each 3D oximetric imaging experiment involving digital band pass filtering and background noise subtraction, followed by 3D Fourier reconstruction. This process is rather slow in a conventional uniprocessor system. This paper presents a parallelization framework using OpenMP runtime support and parallel MATLAB to execute such computationally intensive programs. The Intel compiler is used to develop a parallel C++ code based on OpenMP. The code is executed on four Dual-Core AMD Opteron shared memory processors, to reduce the computational burden of the filtration task significantly. The results show that the parallel code for filtration has achieved a speed up factor of 46.66 as against the equivalent serial MATLAB code. In addition, a parallel MATLAB code has been developed to perform 3D Fourier reconstruction. Speedup factors of 4.57 and 4.25 have been achieved during the reconstruction process and oximetry computation, for a data set with 23 x 23 x 23 gradient steps. The execution time has been computed for both the serial and parallel implementations using different dimensions of the data and presented for comparison. The reported system has been designed to be easily accessible even from low-cost personal computers through local internet (NIHnet). The experimental results demonstrate that the parallel computing provides a source of high computational power to obtain biophysical parameters from 3D EPR oximetric imaging, almost in real-time.

T2 star relaxation times for assessment of articular cartilage at 3 T: a feasibility study

Energy Technology Data Exchange (ETDEWEB)

Mamisch, Tallal Charles [University Bern, Department of Orthopedic Surgery, Inselspital, Bern (Switzerland); University Bern, Magnetic Resonance Spectroscopy and Methodology, Department of Clinical Research, Bern (Switzerland); Hughes, Timothy [Siemens Medical Solutions, Erlangen (Germany); Mosher, Timothy J. [Penn State University College of Medicine, Musculoskeletal Imaging and MRI, Department of Radiology, Hershey, PA (United States); Mueller, Christoph [University of Erlangen, Department of Trauma Surgery, Erlangen (Germany); Trattnig, Siegfried [Medical University of Vienna, MR Center - High Field MR, Department of Radiology, Vienna (Austria); Boesch, Chris [University Bern, Magnetic Resonance Spectroscopy and Methodology, Department of Clinical Research, Bern (Switzerland); Welsch, Goetz Hannes [University of Erlangen, Department of Trauma Surgery, Erlangen (Germany); Medical University of Vienna, MR Center - High Field MR, Department of Radiology, Vienna (Austria)

2012-03-15

T2 mapping techniques use the relaxation constant as an indirect marker of cartilage structure, and the relaxation constant has also been shown to be a sensitive parameter for cartilage evaluation. As a possible additional robust biomarker, T2* relaxation time is a potential, clinically feasible parameter for the biochemical evaluation of articular cartilage. The knees of 15 healthy volunteers and 15 patients after microfracture therapy (MFX) were evaluated with a multi-echo spin-echo T2 mapping technique and a multi-echo gradient-echo T2* mapping sequence at 3.0 Tesla MRI. Inline maps, using a log-linear least squares fitting method, were assessed with respect to the zonal dependency of T2 and T2* relaxation for the deep and superficial regions of healthy articular cartilage and cartilage repair tissue. There was a statistically significant correlation between T2 and T2* values. Both parameters demonstrated similar spatial dependency, with longer values measured toward the articular surface for healthy articular cartilage. No spatial variation was observed for cartilage repair tissue after MFX. Within this feasibility study, both T2 and T2* relaxation parameters demonstrated a similar response in the assessment of articular cartilage and cartilage repair tissue. The potential advantages of T2*-mapping of cartilage include faster imaging times and the opportunity for 3D acquisitions, thereby providing greater spatial resolution and complete coverage of the articular surface. (orig.)

Development of TIME2 code

International Nuclear Information System (INIS)

1986-02-01

The paper reviews the progress on the development of a computer model TIME2, for modelling the long term evolution of shallow burial site environments for low- and intermediate-level radioactive waste disposal. The subject is discussed under the five topic headings: 1) background studies, including geomorphology, climate, human-induced effects, and seismicity, 2) development of the TIME2 code, 3) verification and testing, 4) documentation, and, 5) role of TIME2 in radiological risk assessment. (U.K.)

Development of 3D CFD code based on structured non-orthogonal grids

International Nuclear Information System (INIS)

Vaidya, Abhijeet Mohan; Maheshwari, Naresh Kumar; Rama Rao, A.

2016-01-01

Most of the nuclear industry problems involve complex geometries. Solution of flow and heat transfer over complex geometries is a very important requirement for designing new reactor systems. Hence development of a general purpose three dimensional (3D) CFD code is undertaken. For handling complex shape of computational domain, implementation on structured non-orthogonal coordinates is being done. The code is validated by comparing its results for 3D inclined lid driven cavity at different inclination angles and Reynolds numbers with OpenFOAM results. This paper contains formulation and validation of the new code developed. (author)

A theoretical study of the H-abstraction reactions from HOI by moist air radiolytic products (H, OH, and O (3P)) and iodine atoms (2P(3/2)).

Science.gov (United States)

Hammaecher, Catherine; Canneaux, Sébastien; Louis, Florent; Cantrel, Laurent

2011-06-23

The rate constants of the reactions of HOI molecules with H, OH, O ((3)P), and I ((2)P(3/2)) atoms have been estimated over the temperature range 300-2500 K using four different levels of theory. Geometry optimizations and vibrational frequency calculations are performed using MP2 methods combined with two basis sets (cc-pVTZ and 6-311G(d,p)). Single-point energy calculations are performed with the highly correlated ab initio coupled cluster method in the space of single, double, and triple (pertubatively) electron excitations CCSD(T) using the cc-pVTZ, cc-pVQZ, 6-311+G(3df,2p), and 6-311++G(3df,3pd) basis sets. Reaction enthalpies at 0 K were calculated at the CCSD(T)/cc-pVnZ//MP2/cc-pVTZ (n = T and Q), CCSD(T)/6-311+G(3df,2p)//MP2/6-311G(d,p), and CCSD(T)/6-311++G(3df,3pd)//MP2/6-311G(d,p) levels of theory and compared to the experimental values taken from the literature. Canonical transition-state theory with an Eckart tunneling correction is used to predict the rate constants as a function of temperature. The computational procedure has been used to predict rate constants for H-abstraction elementary reactions because there are actually no literature data to which the calculated rate constants can be directly compared. The final objective is to implement kinetics of gaseous reactions in the ASTEC (accident source term evaluation code) program to improve speciation of fission products, which can be transported along the reactor coolant system (RCS) of a pressurized water reactor (PWR) in the case of a severe accident.

Characterization of activating mutations of NOTCH3 in T-cell acute lymphoblastic leukemia and anti-leukemic activity of NOTCH3 inhibitory antibodies.

Science.gov (United States)

Bernasconi-Elias, P; Hu, T; Jenkins, D; Firestone, B; Gans, S; Kurth, E; Capodieci, P; Deplazes-Lauber, J; Petropoulos, K; Thiel, P; Ponsel, D; Hee Choi, S; LeMotte, P; London, A; Goetcshkes, M; Nolin, E; Jones, M D; Slocum, K; Kluk, M J; Weinstock, D M; Christodoulou, A; Weinberg, O; Jaehrling, J; Ettenberg, S A; Buckler, A; Blacklow, S C; Aster, J C; Fryer, C J

2016-11-24

Notch receptors have been implicated as oncogenic drivers in several cancers, the most notable example being NOTCH1 in T-cell acute lymphoblastic leukemia (T-ALL). To characterize the role of activated NOTCH3 in cancer, we generated an antibody that detects the neo-epitope created upon gamma-secretase cleavage of NOTCH3 to release its intracellular domain (ICD3), and sequenced the negative regulatory region (NRR) and PEST (proline, glutamate, serine, threonine) domain coding regions of NOTCH3 in a panel of cell lines. We also characterize NOTCH3 tumor-associated mutations that result in activation of signaling and report new inhibitory antibodies. We determined the structural basis for receptor inhibition by obtaining the first co-crystal structure of a NOTCH3 antibody with the NRR protein and defined two distinct epitopes for NRR antibodies. The antibodies exhibit potent anti-leukemic activity in cell lines and tumor xenografts harboring NOTCH3 activating mutations. Screening of primary T-ALL samples reveals that 2 of 40 tumors examined show active NOTCH3 signaling. We also identified evidence of NOTCH3 activation in 12 of 24 patient-derived orthotopic xenograft models, 2 of which exhibit activation of NOTCH3 without activation of NOTCH1. Our studies provide additional insights into NOTCH3 activation and offer a path forward for identification of cancers that are likely to respond to therapy with NOTCH3 selective inhibitory antibodies.

A parallel 3D particle-in-cell code with dynamic load balancing

International Nuclear Information System (INIS)

Wolfheimer, Felix; Gjonaj, Erion; Weiland, Thomas

2006-01-01

A parallel 3D electrostatic Particle-In-Cell (PIC) code including an algorithm for modelling Space Charge Limited (SCL) emission [E. Gjonaj, T. Weiland, 3D-modeling of space-charge-limited electron emission. A charge conserving algorithm, Proceedings of the 11th Biennial IEEE Conference on Electromagnetic Field Computation, 2004] is presented. A domain decomposition technique based on orthogonal recursive bisection is used to parallelize the computation on a distributed memory environment of clustered workstations. For problems with a highly nonuniform and time dependent distribution of particles, e.g., bunch dynamics, a dynamic load balancing between the processes is needed to preserve the parallel performance. The algorithm for the detection of a load imbalance and the redistribution of the tasks among the processes is based on a weight function criterion, where the weight of a cell measures the computational load associated with it. The algorithm is studied with two examples. In the first example, multiple electron bunches as occurring in the S-DALINAC [A. Richter, Operational experience at the S-DALINAC, Proceedings of the Fifth European Particle Accelerator Conference, 1996] accelerator are simulated in the absence of space charge fields. In the second example, the SCL emission and electron trajectories in an electron gun are simulated

A parallel 3D particle-in-cell code with dynamic load balancing

Energy Technology Data Exchange (ETDEWEB)

Wolfheimer, Felix [Technische Universitaet Darmstadt, Institut fuer Theorie Elektromagnetischer Felder, Schlossgartenstr.8, 64283 Darmstadt (Germany)]. E-mail: wolfheimer@temf.de; Gjonaj, Erion [Technische Universitaet Darmstadt, Institut fuer Theorie Elektromagnetischer Felder, Schlossgartenstr.8, 64283 Darmstadt (Germany); Weiland, Thomas [Technische Universitaet Darmstadt, Institut fuer Theorie Elektromagnetischer Felder, Schlossgartenstr.8, 64283 Darmstadt (Germany)

2006-03-01

A parallel 3D electrostatic Particle-In-Cell (PIC) code including an algorithm for modelling Space Charge Limited (SCL) emission [E. Gjonaj, T. Weiland, 3D-modeling of space-charge-limited electron emission. A charge conserving algorithm, Proceedings of the 11th Biennial IEEE Conference on Electromagnetic Field Computation, 2004] is presented. A domain decomposition technique based on orthogonal recursive bisection is used to parallelize the computation on a distributed memory environment of clustered workstations. For problems with a highly nonuniform and time dependent distribution of particles, e.g., bunch dynamics, a dynamic load balancing between the processes is needed to preserve the parallel performance. The algorithm for the detection of a load imbalance and the redistribution of the tasks among the processes is based on a weight function criterion, where the weight of a cell measures the computational load associated with it. The algorithm is studied with two examples. In the first example, multiple electron bunches as occurring in the S-DALINAC [A. Richter, Operational experience at the S-DALINAC, Proceedings of the Fifth European Particle Accelerator Conference, 1996] accelerator are simulated in the absence of space charge fields. In the second example, the SCL emission and electron trajectories in an electron gun are simulated.

Heliborne time domain electromagnetic system

International Nuclear Information System (INIS)

Bhattacharya, S.

2009-01-01

Atomic Minerals Directorate (AMD), are using heliborne and ground time domain electromagnetic (TDEM) system for the exploration of deep seated unconformity type uranium deposits. Uranium has been explored in various parts of the world like Athabasca basin using time domain electromagnetic system. AMD has identified some areas in India where such deposits are available. Apart from uranium exploration, the TDEM systems are used for the exploration of deep seated minerals like diamonds. Bhabha Atomic Research Centre (BARC) is involved in the indigenous design of the heliborne time domain system since this system is useful for DAE and also it has a scope of wide application. In this paper we discuss about the principle of time domain electromagnetic systems, their capabilities and the development and problems of such system for various other mineral exploration. (author)

Time-resolved 3D pulmonary perfusion MRI: comparison of different k-space acquisition strategies at 1.5 and 3 T.

Science.gov (United States)

Attenberger, Ulrike I; Ingrisch, Michael; Dietrich, Olaf; Herrmann, Karin; Nikolaou, Konstantin; Reiser, Maximilian F; Schönberg, Stefan O; Fink, Christian

2009-09-01

Time-resolved pulmonary perfusion MRI requires both high temporal and spatial resolution, which can be achieved by using several nonconventional k-space acquisition techniques. The aim of this study is to compare the image quality of time-resolved 3D pulmonary perfusion MRI with different k-space acquisition techniques in healthy volunteers at 1.5 and 3 T. Ten healthy volunteers underwent contrast-enhanced time-resolved 3D pulmonary MRI on 1.5 and 3 T using the following k-space acquisition techniques: (a) generalized autocalibrating partial parallel acquisition (GRAPPA) with an internal acquisition of reference lines (IRS), (b) GRAPPA with a single "external" acquisition of reference lines (ERS) before the measurement, and (c) a combination of GRAPPA with an internal acquisition of reference lines and view sharing (VS). The spatial resolution was kept constant at both field strengths to exclusively evaluate the influences of the temporal resolution achieved with the different k-space sampling techniques on image quality. The temporal resolutions were 2.11 seconds IRS, 1.31 seconds ERS, and 1.07 VS at 1.5 T and 2.04 seconds IRS, 1.30 seconds ERS, and 1.19 seconds VS at 3 T.Image quality was rated by 2 independent radiologists with regard to signal intensity, perfusion homogeneity, artifacts (eg, wrap around, noise), and visualization of pulmonary vessels using a 3 point scale (1 = nondiagnostic, 2 = moderate, 3 = good). Furthermore, the signal-to-noise ratio in the lungs was assessed. At 1.5 T the lowest image quality (sum score: 154) was observed for the ERS technique and the highest quality for the VS technique (sum score: 201). In contrast, at 3 T images acquired with VS were hampered by strong artifacts and image quality was rated significantly inferior (sum score: 137) compared with IRS (sum score: 180) and ERS (sum score: 174). Comparing 1.5 and 3 T, in particular the overall rating of the IRS technique (sum score: 180) was very similar at both field

A parallel code named NEPTUNE for 3D fully electromagnetic and pic simulations

International Nuclear Information System (INIS)

Dong Ye; Yang Wenyuan; Chen Jun; Zhao Qiang; Xia Fang; Ma Yan; Xiao Li; Sun Huifang; Chen Hong; Zhou Haijing; Mao Zeyao; Dong Zhiwei

2010-01-01

A parallel code named NEPTUNE for 3D fully electromagnetic and particle-in-cell (PIC) simulations is introduced, which could run on the Linux system with hundreds to thousand CPUs. NEPTUNE is suitable to simulate entire 3D HPM devices; many HPM devices are simulated and designed by using it. In NEPTUNE code, the electromagnetic fields are updated by using the finite-difference in time domain (FDTD) method of solving Maxwell equations and the particles are moved by using Buneman-Boris advance method of solving relativistic Newton-Lorentz equation. Electromagnetic fields and particles are coupled by using liner weighing interpolation PIC method, and the electric filed components are corrected by using Boris method of solve Poisson equation in order to ensure charge-conservation. NEPTUNE code could construct many complicated geometric structures, such as arbitrary axial-symmetric structures, plane transforming structures, slow-wave-structures, coupling holes, foils, and so on. The boundary conditions used in NEPTUNE code are introduced in brief, including perfectly electric conductor boundary, external wave boundary, and particle boundary. Finally, some typical HPM devices are simulated and test by using NEPTUNE code, including MILO, RBWO, VCO, and RKA. The simulation results are with correct and credible physical images, and the parallel efficiencies are also given. (authors)

Interaction of the p85 subunit of PI 3-kinase and its N-terminal SH2 domain with a PDGF receptor phosphorylation site: structural features and analysis of conformational changes.

Science.gov (United States)

Panayotou, G; Bax, B; Gout, I; Federwisch, M; Wroblowski, B; Dhand, R; Fry, M J; Blundell, T L; Wollmer, A; Waterfield, M D

1992-01-01

Circular dichroism and fluorescence spectroscopy were used to investigate the structure of the p85 alpha subunit of the PI 3-kinase, a closely related p85 beta protein, and a recombinant SH2 domain-containing fragment of p85 alpha. Significant spectral changes, indicative of a conformational change, were observed on formation of a complex with a 17 residue peptide containing a phosphorylated tyrosine residue. The sequence of this peptide is identical to the sequence surrounding Tyr751 in the kinase-insert region of the platelet-derived growth factor beta-receptor (beta PDGFR). The rotational correlation times measured by fluorescence anisotropy decay indicated that phosphopeptide binding changed the shape of the SH2 domain-containing fragment. The CD and fluorescence spectroscopy data support the secondary structure prediction based on sequence analysis and provide evidence for flexible linker regions between the various domains of the p85 proteins. The significance of these results for SH2 domain-containing proteins is discussed. Images PMID:1330535

Three distinct domains contribute to nuclear transport of murine Foxp3.

Directory of Open Access Journals (Sweden)

Wayne W Hancock

2009-11-01

Full Text Available Foxp3, a 47-kDa transcription factor, is necessary for the function of CD4+CD25+ regulatory T cells (Tregs, with an essential role in the control of self-reactive T cells and in preventing autoimmunity. Activation of Tregs by TCR engagement results in upregulation of Foxp3 expression, followed by its rapid nuclear transport and binding to chromatin. Here, we identify three distinct Foxp3 domains that contribute to nuclear transport. The first domain (Domain 1 comprises the C-terminal 12 amino acids. The second domain (Domain 2 is located immediately N-terminal to the forkhead domain (FHD, recently reported to be a binding site for the runt-related transcription factor 1/acute myeloid leukemia 1 (Runx1/AML1. The third domain (Domain 3 is located within the N-terminal first 51 amino acids. Unlike the known nuclear localization signals (NLSs, none of these three regions are rich in basic residues and do not bear any similarity to known monopartite or bipartite NLSs that have one or more clusters of basic amino acids. The basic arginine-lysine-lysine-arginine (RKKR sequence, located 12-aa from the C-terminal end of Foxp3 was previously reported to be a nuclear localization signal (NLS for several proteins, including for a GFP-Foxp3 hybrid. Evidence is provided here that in the full-length native Foxp3 RKKR does not function as an NLS. The data reported in this study indicates that Foxp3 achieves nuclear transport by binding to other nuclear factors and co-transporting with them to the nucleus.

ATP binding to p97/VCP D1 domain regulates selective recruitment of adaptors to its proximal N-domain.

Directory of Open Access Journals (Sweden)

Wei Sheng Chia

Full Text Available p97/Valosin-containing protein (VCP is a member of the AAA-ATPase family involved in many cellular processes including cell division, intracellular trafficking and extraction of misfolded proteins in endoplasmic reticulum-associated degradation (ERAD. It is a homohexamer with each subunit containing two tandem D1 and D2 ATPase domains and N- and C-terminal regions that function as adaptor protein binding domains. p97/VCP is directed to its many different functional pathways by associating with various adaptor proteins. The regulation of the recruitment of the adaptor proteins remains unclear. Two adaptor proteins, Ufd1/Npl4 and p47, which bind exclusively to the p97/VCP N-domain and direct p97/VCP to either ERAD-related processes or homotypic fusion of Golgi fragments, were studied here. Surface plasmon resonance biosensor-based assays allowed the study of binding kinetics in real time. In competition experiments, it was observed that in the presence of ATP, Ufd1/Npl4 was able to compete more effectively with p47 for binding to p97/VCP. By using non-hydrolysable ATP analogues and the hexameric truncated p97/N-D1 fragment, it was shown that binding rather than hydrolysis of ATP to the proximal D1 domain strengthened the Ufd1/Npl4 association with the N-domain, thus regulating the recruitment of either Ufd1/Npl4 or p47. This novel role of ATP and an assigned function to the D1 AAA-ATPase domain link the multiple functions of p97/VCP to the metabolic status of the cell.

ATP binding to p97/VCP D1 domain regulates selective recruitment of adaptors to its proximal N-domain.

Science.gov (United States)

Chia, Wei Sheng; Chia, Diana Xueqi; Rao, Feng; Bar Nun, Shoshana; Geifman Shochat, Susana

2012-01-01

p97/Valosin-containing protein (VCP) is a member of the AAA-ATPase family involved in many cellular processes including cell division, intracellular trafficking and extraction of misfolded proteins in endoplasmic reticulum-associated degradation (ERAD). It is a homohexamer with each subunit containing two tandem D1 and D2 ATPase domains and N- and C-terminal regions that function as adaptor protein binding domains. p97/VCP is directed to its many different functional pathways by associating with various adaptor proteins. The regulation of the recruitment of the adaptor proteins remains unclear. Two adaptor proteins, Ufd1/Npl4 and p47, which bind exclusively to the p97/VCP N-domain and direct p97/VCP to either ERAD-related processes or homotypic fusion of Golgi fragments, were studied here. Surface plasmon resonance biosensor-based assays allowed the study of binding kinetics in real time. In competition experiments, it was observed that in the presence of ATP, Ufd1/Npl4 was able to compete more effectively with p47 for binding to p97/VCP. By using non-hydrolysable ATP analogues and the hexameric truncated p97/N-D1 fragment, it was shown that binding rather than hydrolysis of ATP to the proximal D1 domain strengthened the Ufd1/Npl4 association with the N-domain, thus regulating the recruitment of either Ufd1/Npl4 or p47. This novel role of ATP and an assigned function to the D1 AAA-ATPase domain link the multiple functions of p97/VCP to the metabolic status of the cell.

The element level time domain (ELTD) method for the analysis of nano-optical systems: I. Nondispersive media

Science.gov (United States)

Fallahi, Arya; Oswald, Benedikt; Leidenberger, Patrick

2012-04-01

We study a 3-dimensional, dual-field, fully explicit method for the solution of Maxwell's equations in the time domain on unstructured, tetrahedral grids. The algorithm uses the element level time domain (ELTD) discretization of the electric and magnetic vector wave equations. In particular, the suitability of the method for the numerical analysis of nanometer structured systems in the optical region of the electromagnetic spectrum is investigated. The details of the theory and its implementation as a computer code are introduced and its convergence behavior as well as conditions for stable time domain integration is examined. Here, we restrict ourselves to non-dispersive dielectric material properties since dielectric dispersion will be treated in a subsequent paper. Analytically solvable problems are analyzed in order to benchmark the method. Eventually, a dielectric microlens is considered to demonstrate the potential of the method. A flexible method of 2nd order accuracy is obtained that is applicable to a wide range of nano-optical configurations and can be a serious competitor to more conventional finite difference time domain schemes which operate only on hexahedral grids. The ELTD scheme can resolve geometries with a wide span of characteristic length scales and with the appropriate level of detail, using small tetrahedra where delicate, physically relevant details must be modeled.

Dancing with the Electrons: Time-Domain and CW EPR Imaging

Directory of Open Access Journals (Sweden)

Sankaran Subramanian

2008-01-01

Full Text Available The progress in the development of imaging the distribution of unpaired electrons in living systems and the functional and the potential diagnostic dimensions of such an imaging process, using Electron Paramagnetic Resonance Imaging (EPRI, is traced from its origins with emphasis on our own work. The importance of EPR imaging stems from the fact that many paramagnetic probes show oxygen dependent spectral broadening. Assessment of in vivo oxygen concentration is an important factor in radiation oncology in treatment-planning and monitoring treatment-outcome. The emergence of narrow-line trairylmethyl based, bio-compatible spin probes has enabled the development of radiofrequency time-domain EPRI. Spectral information in time-domain EPRI can be achieved by generating a time sequence of T 2 * or T 2 weighted images. Progress in CW imaging has led to the use of rotating gradients, more recently rapid scan with direct detection, and a combination of all the three. Very low field MRI employing Dynamic Nuclear polarization (Overhauser effect is also employed for monitoring tumor hypoxia, and re-oxygenation in vivo . We have also been working on the co-registration of MRI and time domain EPRI on mouse tumor models at 300 MHz using a specially designed resonator assembly. The mapping of the unpaired electron distribution and unraveling the spectral characteristics by using magnetic resonance in presence of stationary and rotating gradients in indeed ‘dancing with the ( unpaired electrons’, metaphorically speaking.

openPSTD: The open source pseudospectral time-domain method for acoustic propagation

Science.gov (United States)

Hornikx, Maarten; Krijnen, Thomas; van Harten, Louis

2016-06-01

An open source implementation of the Fourier pseudospectral time-domain (PSTD) method for computing the propagation of sound is presented, which is geared towards applications in the built environment. Being a wave-based method, PSTD captures phenomena like diffraction, but maintains efficiency in processing time and memory usage as it allows to spatially sample close to the Nyquist criterion, thus keeping both the required spatial and temporal resolution coarse. In the implementation it has been opted to model the physical geometry as a composition of rectangular two-dimensional subdomains, hence initially restricting the implementation to orthogonal and two-dimensional situations. The strategy of using subdomains divides the problem domain into local subsets, which enables the simulation software to be built according to Object-Oriented Programming best practices and allows room for further computational parallelization. The software is built using the open source components, Blender, Numpy and Python, and has been published under an open source license itself as well. For accelerating the software, an option has been included to accelerate the calculations by a partial implementation of the code on the Graphical Processing Unit (GPU), which increases the throughput by up to fifteen times. The details of the implementation are reported, as well as the accuracy of the code.

FoxP3+CD4+CD25+ T cells with regulatory properties can be cultured from colonic mucosa of patients with Crohn's disease

Science.gov (United States)

Kelsen, J; Agnholt, J; Hoffmann, H J; Rømer, J L; Hvas, C L; Dahlerup, J F

2005-01-01

CD4+CD25+ regulatory T cells (Tregs) are involved in the maintenance of peripheral tolerance and ensure a balanced immune response competent of fighting pathogens and at the same time recognizing commensals as harmless. This feature is lost in Crohn's disease (CD). The forkhead/winged helix transcription factor FoxP3 is a master gene for Treg function and defects in the FoxP3 gene lead to a clinical picture similar to inflammatory bowel disease (IBD). Murine colitis can be cured by adoptive transfer of Tregs and ex vivo-generated gut-specific Tregs represent an attractive option for therapy in CD. Thus, defective Tregs could contribute to the development of CD. We cultured biopsies of colonic mucosa in the presence of high concentrations of interleukin (IL)-2 and IL-4 to overcome the anergic nature of naturally occurring CD4+CD25+ Tregs in the mucosa. We investigated the expression of FoxP3 and regulatory potential of gut-derived CD4+CD25+ T cells cultured from patients with CD and healthy individuals. The FoxP3 expression was analysed by reverse transcriptase polymerase chain reaction (RT-PCR), and the suppressive effect of FoxP3+CD4+CD25+ T cells on proliferation and cytokine production of autologous CD4+ T cells was assessed by flow cytometry. Cultured gut-derived T cells with CD4+CD25+ phenotype expressed FoxP3 and were able as the freshly isolated Tregs from peripheral blood to suppress proliferation and cytokine production of autologous CD4+ T cells. Thus, we demonstrate that FoxP3+CD4+CD25+ T cells with regulatory properties can be propagated in vitro from inflamed mucosa of CD patients, which may be of interest in adoptive immunotherapy. PMID:16045746

Conversion of Dielectric Data from the Time Domain to the Frequency Domain

Directory of Open Access Journals (Sweden)

Vladimir Durman

2005-01-01

Full Text Available Polarisation and conduction processes in dielectric systems can be identified by the time domain or the frequency domain measurements. If the systems is a linear one, the results of the time domain measurements can be transformed into the frequency domain, and vice versa. Commonly, the time domain data of the absorption conductivity are transformed into the frequency domain data of the dielectric susceptibility. In practice, the relaxation are mainly evaluated by the frequency domain data. In the time domain, the absorption current measurement were prefered up to now. Recent methods are based on the recovery voltage measurements. In this paper a new method of the recovery data conversion from the time the frequency domain is proposed. The method is based on the analysis of the recovery voltage transient based on the Maxwell equation for the current density in a dielectric. Unlike the previous published solutions, the Laplace fransform was used to derive a formula suitable for practical purposes. the proposed procedure allows also calculating of the insulation resistance and separating the polarisation and conduction losses.

Effects of shugan jieyu panacea on behavior and levels of ACTH in plasma and T3, T4, TSH and rT3 in serum in depression rats

International Nuclear Information System (INIS)

Li Huijing; Li Yang; Yao Jinghui; Li Youtian

2010-01-01

Objective: To investigate the effects of Shugan Jieyu Panacea (SJP) on behavior and the levels of ACTH in plasma and T 3 , T 4 , TSH, rT 3 in serum in depression model rats and explore the mechanism. Methods: The model rats were lonely fed and received chronic moderate intensive unpredictable stimulation. Normal control group, depressed model group, high dosage SJP group, middle dosage SJP group, low dosage SJP group and fluoxetine group were set up. Different drugs were used in various groups for 21 d, then the body mass, sugar consumption and the behavior changes of the rats were determined and the levels of ACTH in plasma and T 3 , T 4 , TSH, rT 3 in serum were detected with radioimmunoassay. Results: Compared with normal group,the body mass was decreased (P 4 , rT 3 markedly decreased (P 3 was increased (P<0.05) in high, middle, low dosage SJP groups after treatment. At the same time, there was no obvious difference between SJP groups and fluoxetine groups. Conclusion: SJP can significantly improve the depression in rats, its mechanism may be connected with adjusting the function of HPAA and HPTA. (authors)

Chronic levothyroxine and acute T3 treatments enhance the amplitude and time course of uterine contractions in human.

Science.gov (United States)

Corriveau, Stéphanie; Pasquier, Jean-Charles; Blouin, Simon; Bellabarba, Diego; Rousseau, Éric

2013-03-01

This study compares the functional consequences of levothyroxine (T4) treatment during pregnancy as well as the acute affects of triiodothyronine (T3) on spontaneous uterine contractile activities observed in vitro. Uterine biopsies were obtained from consenting women undergoing elective caesarean at term (n = 28). Spontaneous contractile activities from T4-treated pregnant women (n = 8) were compared with control patients (n = 20) by isometric tension measurements. Effects of acute T3 and T4 on control tissues were also monitored. Area under the curve, amplitude, time to peak, duration, and frequency were quantified. In uterine strips from women treated for hypothyroidism, phasic uterine contractions of larger amplitude (+77%) were observed, with a prolonged duration at 90% relaxation (+138%) and reduced frequency (-55%) compared with values of the control group. The addition of exogenous T3 in vitro on control strips induced a significant increase in the duration of the contractions and a significant decrease in frequency (P women. Significant modifications of contractile properties were observed in strips from pregnant women treated with levothyroxine, consistent with those observed with the addition of exogenous T3. Clinical practices of modern obstetrics should take into account the effect of thyroid hormones on uterine contractions' time course to ensure a tighter followup at the end of pregnancy to achieve safer delivery.

Transactivation domain of p53 regulates DNA repair and integrity in human iPS cells.

Science.gov (United States)

Kannappan, Ramaswamy; Mattapally, Saidulu; Wagle, Pooja A; Zhang, Jianyi

2018-05-18

The role of p53 transactivation domain (p53-TAD), a multifunctional and dynamic domain, on DNA repair and retaining DNA integrity in human iPS cells has never been studied. p53-TAD was knocked out in iPS cells using CRISPR/Cas9 and was confirmed by DNA sequencing. p53-TAD KO cells were characterized by: accelerated proliferation, decreased population doubling time, and unaltered Bcl2, BBC3, IGF1R, Bax and altered Mdm2, p21, and PIDD transcripts expression. In p53-TAD KO cells p53 regulated DNA repair proteins XPA, DNA polH and DDB2 expression were found to be reduced compared to p53-WT cells. Exposure to low dose of doxorubicin (Doxo) induced similar DNA damage and DNA damage response (DDR) measured by RAD50 and MRE11 expression, Checkpoint kinase 2 activation and γH2A.X recruitment at DNA strand breaks in both the cell groups indicating silencing p53-TAD do not affect DDR mechanism upstream of p53. Following removal of Doxo p53-WT hiPS cells underwent DNA repair, corrected their damaged DNA and restored DNA integrity. Conversely, p53-TAD KO hiPS cells did not undergo complete DNA repair and failed to restore DNA integrity. More importantly continuous culture of p53-TAD KO hiPS cells underwent G2/M cell cycle arrest and expressed cellular senescent marker p16 INK4a . Our data clearly shows that silencing transactivation domain of p53 did not affect DDR but affected the DNA repair process implying the crucial role of p53 transactivation domain in maintaining DNA integrity. Therefore, activating p53-TAD domain using small molecules may promote DNA repair and integrity of cells and prevent senescence.

A space-time mixed galerkin marching-on-in-time scheme for the time-domain combined field integral equation

KAUST Repository

Beghein, Yves

2013-03-01

The time domain combined field integral equation (TD-CFIE), which is constructed from a weighted sum of the time domain electric and magnetic field integral equations (TD-EFIE and TD-MFIE) for analyzing transient scattering from closed perfect electrically conducting bodies, is free from spurious resonances. The standard marching-on-in-time technique for discretizing the TD-CFIE uses Galerkin and collocation schemes in space and time, respectively. Unfortunately, the standard scheme is theoretically not well understood: stability and convergence have been proven for only one class of space-time Galerkin discretizations. Moreover, existing discretization schemes are nonconforming, i.e., the TD-MFIE contribution is tested with divergence conforming functions instead of curl conforming functions. We therefore introduce a novel space-time mixed Galerkin discretization for the TD-CFIE. A family of temporal basis and testing functions with arbitrary order is introduced. It is explained how the corresponding interactions can be computed efficiently by existing collocation-in-time codes. The spatial mixed discretization is made fully conforming and consistent by leveraging both Rao-Wilton-Glisson and Buffa-Christiansen basis functions and by applying the appropriate bi-orthogonalization procedures. The combination of both techniques is essential when high accuracy over a broad frequency band is required. © 2012 IEEE.

The ubiquitin-homology protein, DAP-1, associates with tumor necrosis factor receptor (p60) death domain and induces apoptosis.

Science.gov (United States)

Liou, M L; Liou, H C

1999-04-09

The tumor necrosis factor receptor, p60 (TNF-R1), transduces death signals via the association of its cytoplasmic domain with several intracellular proteins. By screening a mammalian cDNA library using the yeast two-hybrid cloning technique, we isolated a ubiquitin-homology protein, DAP-1, which specifically interacts with the cytoplasmic death domain of TNF-R1. Sequence analysis reveals that DAP-1 shares striking sequence homology with the yeast SMT3 protein that is essential for the maintenance of chromosome integrity during mitosis (Meluh, P. B., and Koshland, D. (1995) Mol. Biol. Cell 6, 793-807). DAP-1 is nearly identical to PIC1, a protein that interacts with the PML tumor suppressor implicated in acute promyelocytic leukemia (Boddy, M. N., Howe, K., Etkin, L. D., Solomon, E., and Freemont, P. S. (1996) Oncogene 13, 971-982), and the sentrin protein, which associates with the Fas death receptor (Okura, T., Gong, L., Kamitani, T., Wada, T., Okura, I., Wei, C. F., Chang, H. M., and Yeh, E. T. (1996) J. Immunol. 157, 4277-4281). The in vivo interaction between DAP-1 and TNF-R1 was further confirmed in mammalian cells. In transient transfection assays, overexpression of DAP-1 suppresses NF-kappaB/Rel activity in 293T cells, a human kidney embryonic carcinoma cell line. Overexpression of either DAP-1 or sentrin causes apoptosis of TNF-sensitive L929 fibroblast cell line, as well as TNF-resistant osteosarcoma cell line, U2OS. Furthermore, the dominant negative Fas-associated death domain protein (FADD) protein blocks the cell death induced by either DAP-1 or FADD. Collectively, these observations highly suggest a role for DAP-1 in mediating TNF-induced cell death signaling pathways, presumably through the recruitment of FADD death effector.

ORNL probabilistic fracture-mechanics code OCA-P

International Nuclear Information System (INIS)

Cheverton, R.D.; Ball, D.G.

1984-01-01

The computer code OCA-P was developed at the request of the USNRC for the purpose of helping to evaluate the integrity of PWR pressure vessels during overcooling accidents (OCA's). The code can be used for both deterministic and probabilistic fracture-mechanics calculations, and consists essentially of OCA-II and a Monte Carlo routine similar to that developed by Strosnider et al. In the probabilistic mode OCA-P generates a large number of vessels (10 6 more or less), each with a different combination of the various values of the different parameters involved in the analysis of flaw behavior. For each of these vessels a deterministic fracture-mechanics analysis is performed (calculation of K/sub I/, K/sub Ic/, K/sub Ia/) to determine whether vessel failure takes place. The conditional probability of failure is simply the number of vessels that fail divided by the number of vessels generated. OCA-II is used for the deterministic analysis. Basic input to OCA-II includes, among other things, the primry-system pressure transient and the temperature transient for the coolant in the reactor-vessel downcomer. With this and additional information available OCA-II performs a one-dimensional thermal analysis to obtain the temperature distribution in the wall as a function of time and then a one-dimensional linear-elastic stress analysis. OCA-P has been checked against similar codes and is presently being used in the Integrated Pressurized Thermal Shock Program for specific PWR plants

Organization of functional domains in the docking protein p130Cas

International Nuclear Information System (INIS)

Nasertorabi, Fariborz; Garcia-Guzman, Miguel; Briknarova, Klara; Larsen, Elise; Havert, Marnie L.; Vuori, Kristiina; Ely, Kathryn R.

2004-01-01

The docking protein p130Cas becomes phosphorylated upon cell adhesion to extracellular matrix proteins, and is thought to play an essential role in cell transformation. Cas transmits signals through interactions with the Src-homology 3 (SH3) and Src-homology 2 domains of FAK or v-Crk signaling molecules, or with 14-3-3 protein, as well as phosphatases PTP1B and PTP-PEST. The large (130 kDa), multi-domain Cas molecule contains an SH3 domain, a Src-binding domain, a serine-rich protein interaction region, and a C-terminal region that participates in protein interactions implicated in antiestrogen resistance in breast cancer. In this study, as part of a long-term goal to examine the protein interactions of Cas by X-ray crystallography and nuclear magnetic resonance spectroscopy, molecular constructs were designed to express two adjacent domains, the serine-rich domain and the Src-binding domain, that each participate in intermolecular contacts dependent on protein phosphorylation. The protein products are soluble, homogeneous, monodisperse, and highly suitable for structural studies to define the role of Cas in integrin-mediated cell signaling

Simulation of Time-Dependent P3 Equations Using a Semi-Analog Medium

International Nuclear Information System (INIS)

Hadad, K.; Pirouzmand, A.; Suh, Kune Y.

2010-01-01

A wide variety of numerical methods have been introduced to solve the neutron transport equation for reactor calculations. With the state-of-the-art computer technology, successful implementation of higher-order approximation of transport methods (P N , S N , MOC, etc.) may now be feasible. Although these methods have been adaptable to code parallelization techniques, the computational expense remains a significant obstacle and thwarts their implementation in a whole-core, time-dependent methodology. A novel method to remove this problem is based on the method of cellular neural networks (CNN) coupling with the PN method. Parallel data processing in CNN reduces the processing time and makes it possible to solve the time dependent models of neutron transport equation in real time

Complementary roles of Fas-associated death domain (FADD) and receptor interacting protein kinase-3 (RIPK3) in T-cell homeostasis and antiviral immunity.

Science.gov (United States)

Lu, Jennifer V; Weist, Brian M; van Raam, Bram J; Marro, Brett S; Nguyen, Long V; Srinivas, Prathna; Bell, Bryan D; Luhrs, Keith A; Lane, Thomas E; Salvesen, Guy S; Walsh, Craig M

2011-09-13

Caspase-8 (casp8) is required for extrinsic apoptosis, and mice deficient in casp8 fail to develop and die in utero while ultimately failing to maintain the proliferation of T cells, B cells, and a host of other cell types. Paradoxically, these failures are not caused by a defect in apoptosis, but by a presumed proliferative function of this protease. Indeed, following mitogenic stimulation, T cells lacking casp8 or its adaptor protein FADD (Fas-associated death domain protein) develop a hyperautophagic morphology, and die a programmed necrosis-like death process termed necroptosis. Recent studies have demonstrated that receptor-interacting protein kinases (RIPKs) RIPK1 and RIPK3 together facilitate TNF-induced necroptosis, but the precise role of RIPKs in the demise of T cells lacking FADD or casp8 activity is unknown. Here we demonstrate that RIPK3 and FADD have opposing and complementary roles in promoting T-cell clonal expansion and homeostasis. We show that the defective proliferation of T cells bearing an interfering form of FADD (FADDdd) is rescued by crossing with RIPK3(-/-) mice, although such rescue ultimately leads to lymphadenopathy. Enhanced recovery of these double-mutant T cells following stimulation demonstrates that FADD, casp8, and RIPK3 are all essential for clonal expansion, contraction, and antiviral responses. Finally, we demonstrate that caspase-mediated cleavage of RIPK1-containing necrosis inducing complexes (necrosomes) is sufficient to prevent necroptosis in the face of death receptor signaling. These studies highlight the "two-faced" nature of casp8 activity, promoting clonal expansion in some situations and apoptotic demise in others.

The time-dependent 3D discrete ordinates code TORT-TD with thermal-hydraulic feedback by ATHLET models

International Nuclear Information System (INIS)

Seubert, A.; Velkov, K.; Langenbuch, S.

2008-01-01

This paper describes the time-dependent 3D discrete ordinates transport code TORT-TD. Thermal-hydraulic feedback is considered by coupling TORT-TD with the thermal-hydraulics system code ATHLET. The coupled code TORT-TD/ATHLET allows 3D pin-by-pin analyses of transients in few energy groups and anisotropic scattering by solving the time-dependent transport equation using the unconditionally stable implicit method. The nuclear cross sections are interpolated between pre-calculated table values of fuel temperature, moderator density and boron concentration. For verification of the implementation, selected test cases have been calculated by TORT-TD/ATHLET. They include a control rod ejection transient in a small PWR fuel assembly arrangement and a local boron concentration change in a single PWR fuel assembly. In the latter, special attention has been paid to study the influence of the thermal-hydraulic feedback modelling in ATHLET. The results obtained for a control rod ejection accident in a PWR quarter core demonstrate the applicability of TORT-TD/ATHLET. (authors)

Transformation and radiosensitivity of human diploid skin fibroblasts transfected with SV40 T-antigen mutants defective in RB and P53 binding domains

International Nuclear Information System (INIS)

LingNah Su; Little, J.B.

1992-01-01

A series of human diploid fibroblast cell clones were developed by DNA transfection with either wild-type SV40 T-antigen (SV40T) or T-antigen mutants defective in its various functional domains. Cell clones expressing the wild-type SV40 T were significantly radioresistant as compared with clones transfected with the neo gene only (D o 192 ± 13 vs 127 ± 19). This radioresistance persisted in post-crisis, immortalized cell lines. A series of mutants with point or deletion mutations within each functionally active domain of SV40 T were also examined for their ability to alter radiosensitivity and induce morphological transformation. Cell clones transfected with T-antigen mutants defective in nuclear localization or origin binding showed increased radioresistance similar to clones transfected with wild-type T-antigen, and expressed morphological changes characteristic of SV40 T-transfected cells. (author)

Comparison of WDM/Pulse-Position-Modulation (WDM/PPM) with Code/Pulse-Position-Swapping (C/PPS) Based on Wavelength/Time Codes

Energy Technology Data Exchange (ETDEWEB)

Mendez, A J; Hernandez, V J; Gagliardi, R M; Bennett, C V

2009-06-19

Pulse position modulation (PPM) signaling is favored in intensity modulated/direct detection (IM/DD) systems that have average power limitations. Combining PPM with WDM over a fiber link (WDM/PPM) enables multiple accessing and increases the link's throughput. Electronic bandwidth and synchronization advantages are further gained by mapping the time slots of PPM onto a code space, or code/pulse-position-swapping (C/PPS). The property of multiple bits per symbol typical of PPM can be combined with multiple accessing by using wavelength/time [W/T] codes in C/PPS. This paper compares the performance of WDM/PPM and C/PPS for equal wavelengths and bandwidth.

Effects of Mutations in the Substrate-Binding Domain of Poly[(R)-3-Hydroxybutyrate] (PHB) Depolymerase from Ralstonia pickettii T1 on PHB Degradation▿

OpenAIRE

Hiraishi, Tomohiro; Hirahara, Yoko; Doi, Yoshiharu; Maeda, Mizuo; Taguchi, Seiichi

2006-01-01

Poly[(R)-3-hydroxybutyrate] (PHB) depolymerase from Ralstonia pickettii T1 (PhaZRpiT1) adsorbs to denatured PHB (dPHB) via its substrate-binding domain (SBD) to enhance dPHB degradation. To evaluate the amino acid residues participating in dPHB adsorption, PhaZRpiT1 was subjected to a high-throughput screening system consisting of PCR-mediated random mutagenesis targeted to the SBD gene and a plate assay to estimate the effects of mutations in the SBD on dPHB degradation by PhaZRpiT1. Genetic...

Time-domain calculation of sub-nanosecond pulse launched by a proton beam

International Nuclear Information System (INIS)

Chan, Kwok-Chi Dominic; Cooper, R.K.

1990-01-01

Using the finite-difference time-domain code TBCI, we have numerically calculated the radiation from a sub-nanosecond 800-MeV proton bunch as it is launched into space. The calculation is compared to measurements of the time history of the radiated fields and good agreement is found. A movie showing the development of the radiation pattern will be shown during the presentation at this conference, namely, the First Los Alamos Symposium on Ultra-Wideband Radar. 6 refs., 7 figs

Space-charge-dominated beam dynamics simulations using the massively parallel processors (MPPs) of the Cray T3D

International Nuclear Information System (INIS)

Liu, H.

1996-01-01

Computer simulations using the multi-particle code PARMELA with a three-dimensional point-by-point space charge algorithm have turned out to be very helpful in supporting injector commissioning and operations at Thomas Jefferson National Accelerator Facility (Jefferson Lab, formerly called CEBAF). However, this algorithm, which defines a typical N 2 problem in CPU time scaling, is very time-consuming when N, the number of macro-particles, is large. Therefore, it is attractive to use massively parallel processors (MPPs) to speed up the simulations. Motivated by this, the authors modified the space charge subroutine for using the MPPs of the Cray T3D. The techniques used to parallelize and optimize the code on the T3D are discussed in this paper. The performance of the code on the T3D is examined in comparison with a Parallel Vector Processing supercomputer of the Cray C90 and an HP 735/15 high-end workstation

Mutiple LDPC Decoding using Bitplane Correlation for Transform Domain Wyner-Ziv Video Coding

DEFF Research Database (Denmark)

Luong, Huynh Van; Huang, Xin; Forchhammer, Søren

2011-01-01

Distributed video coding (DVC) is an emerging video coding paradigm for systems which fully or partly exploit the source statistics at the decoder to reduce the computational burden at the encoder. This paper considers a Low Density Parity Check (LDPC) based Transform Domain Wyner-Ziv (TDWZ) video...... codec. To improve the LDPC coding performance in the context of TDWZ, this paper proposes a Wyner-Ziv video codec using bitplane correlation through multiple parallel LDPC decoding. The proposed scheme utilizes inter bitplane correlation to enhance the bitplane decoding performance. Experimental results...

Fast Convolutional Sparse Coding in the Dual Domain

KAUST Repository

Affara, Lama Ahmed; Ghanem, Bernard; Wonka, Peter

2017-01-01

Convolutional sparse coding (CSC) is an important building block of many computer vision applications ranging from image and video compression to deep learning. We present two contributions to the state of the art in CSC. First, we significantly speed up the computation by proposing a new optimization framework that tackles the problem in the dual domain. Second, we extend the original formulation to higher dimensions in order to process a wider range of inputs, such as color inputs, or HOG features. Our results show a significant speedup compared to the current state of the art in CSC.

Fast Convolutional Sparse Coding in the Dual Domain

KAUST Repository

Affara, Lama Ahmed

2017-09-27

Convolutional sparse coding (CSC) is an important building block of many computer vision applications ranging from image and video compression to deep learning. We present two contributions to the state of the art in CSC. First, we significantly speed up the computation by proposing a new optimization framework that tackles the problem in the dual domain. Second, we extend the original formulation to higher dimensions in order to process a wider range of inputs, such as color inputs, or HOG features. Our results show a significant speedup compared to the current state of the art in CSC.

Measurement of electron paramagnetic resonance using terahertz time-domain spectroscopy.

Science.gov (United States)

Kozuki, Kohei; Nagashima, Takeshi; Hangyo, Masanori

2011-12-05

We present a frequency-domain electron spin resonance (ESR) measurement system using terahertz time-domain spectroscopy. A crossed polarizer technique is utilized to increase the sensitivity in detecting weak ESR signals of paramagnets caused by magnetic dipole transitions between magnetic sublevels. We demonstrate the measurements of ESR signal of paramagnetic copper(II) sulfate pentahydrate with uniaxial anisotropy of the g-factor under magnetic fields up to 10 T. The lineshape of the obtained ESR signals agrees well with the theoretical predictions for a powder sample with the uniaxial anisotropy.

VALIDATION OF FULL CORE GEOMETRY MODEL OF THE NODAL3 CODE IN THE PWR TRANSIENT BENCHMARK PROBLEMS

Directory of Open Access Journals (Sweden)

Tagor Malem Sembiring

2015-10-01

Full Text Available ABSTRACT VALIDATION OF FULL CORE GEOMETRY MODEL OF THE NODAL3 CODE IN THE PWR TRANSIENT BENCHMARK PROBLEMS. The coupled neutronic and thermal-hydraulic (T/H code, NODAL3 code, has been validated in some PWR static benchmark and the NEACRP PWR transient benchmark cases. However, the NODAL3 code have not yet validated in the transient benchmark cases of a control rod assembly (CR ejection at peripheral core using a full core geometry model, the C1 and C2 cases.  By this research work, the accuracy of the NODAL3 code for one CR ejection or the unsymmetrical group of CRs ejection case can be validated. The calculations by the NODAL3 code have been carried out by the adiabatic method (AM and the improved quasistatic method (IQS. All calculated transient parameters by the NODAL3 code were compared with the reference results by the PANTHER code. The maximum relative difference of 16% occurs in the calculated time of power maximum parameter by using the IQS method, while the relative difference of the AM method is 4% for C2 case.  All calculation results by the NODAL3 code shows there is no systematic difference, it means the neutronic and T/H modules are adopted in the code are considered correct. Therefore, all calculation results by using the NODAL3 code are very good agreement with the reference results. Keywords: nodal method, coupled neutronic and thermal-hydraulic code, PWR, transient case, control rod ejection.   ABSTRAK VALIDASI MODEL GEOMETRI TERAS PENUH PAKET PROGRAM NODAL3 DALAM PROBLEM BENCHMARK GAYUT WAKTU PWR. Paket program kopel neutronik dan termohidraulika (T/H, NODAL3, telah divalidasi dengan beberapa kasus benchmark statis PWR dan kasus benchmark gayut waktu PWR NEACRP.  Akan tetapi, paket program NODAL3 belum divalidasi dalam kasus benchmark gayut waktu akibat penarikan sebuah perangkat batang kendali (CR di tepi teras menggunakan model geometri teras penuh, yaitu kasus C1 dan C2. Dengan penelitian ini, akurasi paket program

GAPCON-THERMAL-3 code description

International Nuclear Information System (INIS)

Lanning, D.D.; Mohr, C.L.; Panisko, F.E.; Stewart, K.B.

1978-01-01

GAPCON-3 is a computer program that predicts the thermal and mechanical behavior of an operating fuel rod during its normal lifetime. The code calculates temperatures, dimensions, stresses, and strains for the fuel and the cladding in both the radial and axial directions for each step of the user specified power history. The method of weighted residuals is for the steady state temperature calculation, and is combined with a finite difference approximation of the time derivative for transient conditions. The stress strain analysis employs an iterative axisymmetric finite element procedure that includes plasticity and creep for normal and pellet-clad mechanical interaction loads. GAPCON-3 can solve steady state and operational transient problems. Comparisons of GAPCON-3 predictions to both closed form analytical solutions and actual inpile instrumented fuel rod data have demonstrated the ability of the code to calculate fuel rod behavior. GAPCON-3 features a restart capability and an associated plot package unavailable in previous GAPCON series codes

GAPCON-THERMAL-3 code description

Energy Technology Data Exchange (ETDEWEB)

Lanning, D.D.; Mohr, C.L.; Panisko, F.E.; Stewart, K.B.

1978-01-01

GAPCON-3 is a computer program that predicts the thermal and mechanical behavior of an operating fuel rod during its normal lifetime. The code calculates temperatures, dimensions, stresses, and strains for the fuel and the cladding in both the radial and axial directions for each step of the user specified power history. The method of weighted residuals is for the steady state temperature calculation, and is combined with a finite difference approximation of the time derivative for transient conditions. The stress strain analysis employs an iterative axisymmetric finite element procedure that includes plasticity and creep for normal and pellet-clad mechanical interaction loads. GAPCON-3 can solve steady state and operational transient problems. Comparisons of GAPCON-3 predictions to both closed form analytical solutions and actual inpile instrumented fuel rod data have demonstrated the ability of the code to calculate fuel rod behavior. GAPCON-3 features a restart capability and an associated plot package unavailable in previous GAPCON series codes.

An Energy-Efficient Compressive Image Coding for Green Internet of Things (IoT).

Science.gov (United States)

Li, Ran; Duan, Xiaomeng; Li, Xu; He, Wei; Li, Yanling

2018-04-17

Aimed at a low-energy consumption of Green Internet of Things (IoT), this paper presents an energy-efficient compressive image coding scheme, which provides compressive encoder and real-time decoder according to Compressive Sensing (CS) theory. The compressive encoder adaptively measures each image block based on the block-based gradient field, which models the distribution of block sparse degree, and the real-time decoder linearly reconstructs each image block through a projection matrix, which is learned by Minimum Mean Square Error (MMSE) criterion. Both the encoder and decoder have a low computational complexity, so that they only consume a small amount of energy. Experimental results show that the proposed scheme not only has a low encoding and decoding complexity when compared with traditional methods, but it also provides good objective and subjective reconstruction qualities. In particular, it presents better time-distortion performance than JPEG. Therefore, the proposed compressive image coding is a potential energy-efficient scheme for Green IoT.

An Energy-Efficient Compressive Image Coding for Green Internet of Things (IoT

Directory of Open Access Journals (Sweden)

Ran Li

2018-04-01

Full Text Available Aimed at a low-energy consumption of Green Internet of Things (IoT, this paper presents an energy-efficient compressive image coding scheme, which provides compressive encoder and real-time decoder according to Compressive Sensing (CS theory. The compressive encoder adaptively measures each image block based on the block-based gradient field, which models the distribution of block sparse degree, and the real-time decoder linearly reconstructs each image block through a projection matrix, which is learned by Minimum Mean Square Error (MMSE criterion. Both the encoder and decoder have a low computational complexity, so that they only consume a small amount of energy. Experimental results show that the proposed scheme not only has a low encoding and decoding complexity when compared with traditional methods, but it also provides good objective and subjective reconstruction qualities. In particular, it presents better time-distortion performance than JPEG. Therefore, the proposed compressive image coding is a potential energy-efficient scheme for Green IoT.

Ab initio dynamics trajectory study of the heterolytic cleavage of H2 by a Lewis acid [B(C6F5)3] and a Lewis base [P(tBu)3

Science.gov (United States)

Pu, Maoping; Privalov, Timofei

2013-04-01

Activation of H2 by a "frustrated Lewis pair" (FLP) composed of B(C6F5)3 and P(tBu)3 species has been explored with high level direct ab initio molecular dynamics (AIMD) simulations at finite temperature (T = 300 K) in gas phase. The initial geometrical conditions for the AIMD trajectory calculations, i.e., the near attack conformations of FLP + H2, were devised using the host-guest model in which suitable FLP conformations were obtained from the dynamics of the B(C6F5)3/P(tBu)3 pair in gas phase. AIMD trajectory calculations yielded microscopic insight into effects which originate from nuclear motion in the reacting complex, e.g., the alternating compression/elongation of the boron-phosphorous distance and the change of the pyramidality of boron in B(C6F5)3. The ensemble averaged trajectory analysis has been compared with the minimum energy path (MEP) description of the reaction. Similar to MEP, AIMD shows that an attack of the acid/base pair on the H-H bond gives rise to the polarization of the H2 molecule and as a consequence generates a large dipole moment of the reacting complex. The MEP and AIMD portrayals of the reaction are fundamentally different in terms of the magnitude of the motion of nuclei in B(C6F5)3 and P(tBu)3 during the H2 cleavage. In the AIMD trajectory simulations, geometries of B(C6F5)3 and P(tBu)3 appear as nearly "frozen" on the short time scale of the H2 cleavage. This is contrary to the MEP picture. Several of the concepts which arise from this work, e.g., separation of time scales of nuclear motion and the time-dependence of the donor-acceptor interactions in the reacting complex, are important for the understanding of chemical reactivity and catalysis.

(p, {rho}, T, x) properties for CO{sub 2}/isobutane binary mixtures at T = (280 to 440) K and (3 to 200) MPa

Energy Technology Data Exchange (ETDEWEB)

Sugiyama, T. [Master' s Programs of Mechanical Systems Engineering, Toyama Prefectural University (Japan); Orita, S. [Department of Mechanical Systems Engineering, Toyama Prefectural University (Japan); Miyamoto, H., E-mail: miyamoto@pu-toyama.ac.jp [Department of Mechanical Systems Engineering, Toyama Prefectural University (Japan)

2011-12-15

Highlights: > The p{rho}Tx properties for CO{sub 2}/isobutane were measured in the compressed liquid phase. > A total of 283 points data were obtained from T = (280 to 440) K and (3 to 200) MPa. > The data were compared with the available equation of state. > The excess molar volumes were calculated and plotted as a function of T and P. - Abstract: The (p, {rho}, T, x) properties for binary mixtures of CO{sub 2} (volume fraction purity 0.99999) and isobutane (mole fraction purity 0.99988) {l_brace}x{sub 1} CO{sub 2} + x{sub 2} isobutane (x{sub 1} = 0.2482, 0.4718, and 0.7506){r_brace} were measured in the compressed liquid phase using a metal-bellows variable volumometer. Measurements were conducted from T = (280 to 440) K and (3 to 200) MPa. The expanded uncertainties (k = 2) were estimated to be: temperature, <3 mK; pressure, 1.5 kPa (p {<=} 7 MPa), 0.06% (7 MPa < p {<=} 50 MPa), 0.1% (50 MPa < p {<=} 150 MPa), 0.2% (p > 150 MPa); density, 0.10%; and composition, 4.4 . 10{sup -4}. At >100 MPa and T = (280 or 440) K, the uncertainties in the density measurements increased to 0.14% and 0.22%, respectively. The data are compared with the available equation of state. The excess molar volumes, v{sub m}{sup E}, of the mixtures were calculated and plotted as a function of temperature and pressure.

Evaluation of the FRAPCON-3 Computer Code

Energy Technology Data Exchange (ETDEWEB)

Jernkvist, Lars Olof; Massih, Ali [Quantum Technologies AB, Uppsala (Sweden)

2002-03-01

The FRAPCON-3 computer code has been evaluated with respect to its applicability, modeling capability, user friendliness, source code structure and supporting experimental database. The code is intended for thermo-mechanical analyses of light water reactor nuclear fuel rods under steady-state operational conditions and moderate power excursions. It is applicable to both boiling- and pressurized water reactor fuel rods with UO{sub 2} fuel, ranging up to about 65 MWd/kg U in rod average burnup. The models and numerical methods in FRAPCON-3 are relatively simple, which makes the code transparent and also fairly easy to modify and extend for the user. The fundamental equations for heat transfer, structural analysis and fuel fission gas release are solved in one-dimensional (radial) and stationary (time-independent) form, and interaction between axial segments of the rod is confined to calculations of coolant axial flow and rod internal gas pressure. The code is fairly easy to use; fuel rod design data and time histories of fuel rod power and coolant inlet conditions are input via a single text file, and the corresponding calculated variation with time of important fuel rod parameters are printed to a single output file in textual form. The results can also be presented in graphical form through an interface to the general graphics program xmgr. FRAPCON-3 also provides the possibility to export calculated results to the transient fuel rod analysis code FRAPTRAN, where the data can be used as burnup-dependent initial conditions to a postulated transient. Most of the source code to FRAPCON-3 is written in Fortran-IV, which is an archaic, non-standard dialect of the Fortran programming language. Since Fortran-IV is not accepted by all compilers for the latest standard of the language, Fortran-95, there is a risk that the source code must be partly rewritten in the future. Documentation of the code comprises (i) a general code description, which briefly presents models

Evaluation of the FRAPCON-3 Computer Code

International Nuclear Information System (INIS)

Jernkvist, Lars Olof; Massih, Ali

2002-03-01

The FRAPCON-3 computer code has been evaluated with respect to its applicability, modeling capability, user friendliness, source code structure and supporting experimental database. The code is intended for thermo-mechanical analyses of light water reactor nuclear fuel rods under steady-state operational conditions and moderate power excursions. It is applicable to both boiling- and pressurized water reactor fuel rods with UO 2 fuel, ranging up to about 65 MWd/kg U in rod average burnup. The models and numerical methods in FRAPCON-3 are relatively simple, which makes the code transparent and also fairly easy to modify and extend for the user. The fundamental equations for heat transfer, structural analysis and fuel fission gas release are solved in one-dimensional (radial) and stationary (time-independent) form, and interaction between axial segments of the rod is confined to calculations of coolant axial flow and rod internal gas pressure. The code is fairly easy to use; fuel rod design data and time histories of fuel rod power and coolant inlet conditions are input via a single text file, and the corresponding calculated variation with time of important fuel rod parameters are printed to a single output file in textual form. The results can also be presented in graphical form through an interface to the general graphics program xmgr. FRAPCON-3 also provides the possibility to export calculated results to the transient fuel rod analysis code FRAPTRAN, where the data can be used as burnup-dependent initial conditions to a postulated transient. Most of the source code to FRAPCON-3 is written in Fortran-IV, which is an archaic, non-standard dialect of the Fortran programming language. Since Fortran-IV is not accepted by all compilers for the latest standard of the language, Fortran-95, there is a risk that the source code must be partly rewritten in the future. Documentation of the code comprises (i) a general code description, which briefly presents models

Numeral series hidden in the distribution of atomic mass of amino acids to codon domains in the genetic code.

Science.gov (United States)

Wohlin, Åsa

2015-03-21

The distribution of codons in the nearly universal genetic code is a long discussed issue. At the atomic level, the numeral series 2x(2) (x=5-0) lies behind electron shells and orbitals. Numeral series appear in formulas for spectral lines of hydrogen. The question here was if some similar scheme could be found in the genetic code. A table of 24 codons was constructed (synonyms counted as one) for 20 amino acids, four of which have two different codons. An atomic mass analysis was performed, built on common isotopes. It was found that a numeral series 5 to 0 with exponent 2/3 times 10(2) revealed detailed congruency with codon-grouped amino acid side-chains, simultaneously with the division on atom kinds, further with main 3rd base groups, backbone chains and with codon-grouped amino acids in relation to their origin from glycolysis or the citrate cycle. Hence, it is proposed that this series in a dynamic way may have guided the selection of amino acids into codon domains. Series with simpler exponents also showed noteworthy correlations with the atomic mass distribution on main codon domains; especially the 2x(2)-series times a factor 16 appeared as a conceivable underlying level, both for the atomic mass and charge distribution. Furthermore, it was found that atomic mass transformations between numeral systems, possibly interpretable as dimension degree steps, connected the atomic mass of codon bases with codon-grouped amino acids and with the exponent 2/3-series in several astonishing ways. Thus, it is suggested that they may be part of a deeper reference system. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

Validation of Westinghouse integrated code POLCA-T against OECD NEACRP-L-335 rod ejection benchmark

Energy Technology Data Exchange (ETDEWEB)

Panayotov, Dobromir [Westinghouse Electric Sweden AB, Vaesteraas, SE-721 63 (Sweden)

2008-07-01

This paper describes the work performed and results obtained in the validation of the POLCA-T code against NEACRP PWR Rod Ejection Transients Benchmark. Presented work is a part of the POLCA-T licensing Assessment Data Base for BWR Control Rod Drop Accident (CRDA) Application. The validation against a PWR Rod Ejection Accidents (REA) Benchmark is relevant for the validation of the code for BWR CRDA, as the analyses of both transients require identical phenomena to be modelled. All six benchmark cases have been analyzed in the presented work. Initial state steady-state calculations including boron search, control rod worth, and final state power search have been performed by POLCA7 code. Initial state boron adjustment and steady-state CR worth as well as the transient analyses were performed by POLCA-T code. Benchmark results including 3D transient power distributions are compared with reference PANTHER solutions and published results of other codes. Given the similarity of the kinetics modelling for a BWR CRDA and a PWR REA and the fact that POLCA-T accurately predicts the local transient power and thus, the resulting fuel enthalpy, it is concluded that POLCA-T is a state-of-art tool also for BWR CRDA analysis. (author)

Validation of Westinghouse integrated code POLCA-T against OECD NEACRP-L-335 rod ejection benchmark

International Nuclear Information System (INIS)

Panayotov, Dobromir

2008-01-01

This paper describes the work performed and results obtained in the validation of the POLCA-T code against NEACRP PWR Rod Ejection Transients Benchmark. Presented work is a part of the POLCA-T licensing Assessment Data Base for BWR Control Rod Drop Accident (CRDA) Application. The validation against a PWR Rod Ejection Accidents (REA) Benchmark is relevant for the validation of the code for BWR CRDA, as the analyses of both transients require identical phenomena to be modelled. All six benchmark cases have been analyzed in the presented work. Initial state steady-state calculations including boron search, control rod worth, and final state power search have been performed by POLCA7 code. Initial state boron adjustment and steady-state CR worth as well as the transient analyses were performed by POLCA-T code. Benchmark results including 3D transient power distributions are compared with reference PANTHER solutions and published results of other codes. Given the similarity of the kinetics modelling for a BWR CRDA and a PWR REA and the fact that POLCA-T accurately predicts the local transient power and thus, the resulting fuel enthalpy, it is concluded that POLCA-T is a state-of-art tool also for BWR CRDA analysis. (author)

A novel domain overlapping strategy for the multiscale coupling of CFD with 1D system codes with applications to transient flows

International Nuclear Information System (INIS)

Grunloh, T.P.; Manera, A.

2016-01-01

Highlights: • A novel domain overlapping coupling method is presented. • Method calculates closure coefficients for system codes based on CFD results. • Convergence and stability are compared with a domain decomposition implementation. • Proposed method is tested in several 1D cases. • Proposed method found to exhibit more favorable convergence and stability behavior. - Abstract: A novel multiscale coupling methodology based on a domain overlapping approach has been developed to couple a computational fluid dynamics code with a best-estimate thermal hydraulic code. The methodology has been implemented in the coupling infrastructure code Janus, developed at the University of Michigan, providing methods for the online data transfer between the commercial computational fluid dynamics code STAR-CCM+ and the US NRC best-estimate thermal hydraulic system code TRACE. Coupling between these two software packages is motivated by the desire to extend the range of applicability of TRACE to scenarios in which local momentum and energy transfer are important, such as three-dimensional mixing. These types of flows are relevant, for example, in the simulation of passive safety systems including large containment pools, or for flow mixing in the reactor pressure vessel downcomer of current light water reactors and integral small modular reactors. The intrafluid shear forces neglected by TRACE equations of motion are readily calculated from computational fluid dynamics solutions. Consequently, the coupling methods used in this study are built around correcting TRACE solutions with data from a corresponding STAR-CCM+ solution. Two coupling strategies are discussed in the paper: one based on a novel domain overlapping approach specifically designed for transient operation, and a second based on the well-known domain decomposition approach. In the present paper, we discuss the application of the two coupling methods to the simulation of open and closed loops in both steady

An explicit marching on-in-time solver for the time domain volume magnetic field integral equation

KAUST Repository

Sayed, Sadeed Bin

2014-07-01

Transient scattering from inhomogeneous dielectric objects can be modeled using time domain volume integral equations (TDVIEs). TDVIEs are oftentimes solved using marching on-in-time (MOT) techniques. Classical MOT-TDVIE solvers expand the field induced on the scatterer using local spatio-temporal basis functions. Inserting this expansion into the TDVIE and testing the resulting equation in space and time yields a system of equations that is solved by time marching. Depending on the type of the basis and testing functions and the time step, the time marching scheme can be implicit (N. T. Gres, et al., Radio Sci., 36(3), 379-386, 2001) or explicit (A. Al-Jarro, et al., IEEE Trans. Antennas Propag., 60(11), 5203-5214, 2012). Implicit MOT schemes are known to be more stable and accurate. However, under low-frequency excitation, i.e., when the time step size is large, they call for inversion of a full matrix system at very time step.

An explicit marching on-in-time solver for the time domain volume magnetic field integral equation

KAUST Repository

Sayed, Sadeed Bin; Ulku, Huseyin Arda; Bagci, Hakan

2014-01-01

Transient scattering from inhomogeneous dielectric objects can be modeled using time domain volume integral equations (TDVIEs). TDVIEs are oftentimes solved using marching on-in-time (MOT) techniques. Classical MOT-TDVIE solvers expand the field induced on the scatterer using local spatio-temporal basis functions. Inserting this expansion into the TDVIE and testing the resulting equation in space and time yields a system of equations that is solved by time marching. Depending on the type of the basis and testing functions and the time step, the time marching scheme can be implicit (N. T. Gres, et al., Radio Sci., 36(3), 379-386, 2001) or explicit (A. Al-Jarro, et al., IEEE Trans. Antennas Propag., 60(11), 5203-5214, 2012). Implicit MOT schemes are known to be more stable and accurate. However, under low-frequency excitation, i.e., when the time step size is large, they call for inversion of a full matrix system at very time step.

Activation of phosphatidylinositol-3 kinase by nerve growth factor involves indirect coupling of the trk proto-oncogene with src homology 2 domains.

Science.gov (United States)

Ohmichi, M; Decker, S J; Saltiel, A R

1992-10-01

Growth factor receptor tyrosine kinases can form stable associations with intracellular proteins that contain src homology (SH) 2 domains, including the p85 regulatory subunit of phosphatidylinositol (PI)-3 kinase. The activation of this enzyme by growth factors is evaluated in PC12 pheochromocytoma cells and NIH 3T3 fibroblasts expressing the pp140c-trk nerve growth factor (NGF) receptor (3T3-c-trk). NGF causes the rapid stimulation of PI-3 kinase activity detected in anti-phosphotyrosine, but not in anti-trk, immunoprecipitates. This effect coincides with the tyrosine phosphorylation of two proteins, with molecular masses of of 100 kd and 110 kd, that coimmunoprecipitate with p85. Similar phosphorylation patterns are induced when an immobilized fusion protein containing the amino-terminal SH2 domain of p85 is used to precipitate tyrosine-phosphorylated proteins. Thus, although NGF produces the rapid activation of PI-3 kinase through a mechanism that involves tyrosine phosphorylation, there is no evidence for tyrosine phosphorylation of p85, or for its ligand-dependent association with the NGF receptor. Perhaps another phosphoprotein may link the NGF receptor to this enzyme.

Membrane fusion by VAMP3 and plasma membrane t-SNAREs

International Nuclear Information System (INIS)

Hu Chuan; Hardee, Deborah; Minnear, Fred

2007-01-01

Pairing of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins on vesicles (v-SNAREs) and SNARE proteins on target membranes (t-SNAREs) mediates intracellular membrane fusion. VAMP3/cellubrevin is a v-SNARE that resides in recycling endosomes and endosome-derived transport vesicles. VAMP3 has been implicated in recycling of transferrin receptors, secretion of α-granules in platelets, and membrane trafficking during cell migration. Using a cell fusion assay, we examined membrane fusion capacity of the ternary complexes formed by VAMP3 and plasma membrane t-SNAREs syntaxin1, syntaxin4, SNAP-23 and SNAP-25. VAMP3 forms fusogenic pairing with t-SNARE complexes syntaxin1/SNAP-25, syntaxin1/SNAP-23 and syntaxin4/SNAP-25, but not with syntaxin4/SNAP-23. Deletion of the N-terminal domain of syntaxin4 enhanced membrane fusion more than two fold, indicating that the N-terminal domain negatively regulates membrane fusion. Differential membrane fusion capacities of the ternary v-/t-SNARE complexes suggest that transport vesicles containing VAMP3 have distinct membrane fusion kinetics with domains of the plasma membrane that present different t-SNARE proteins

Parallel Implementation of the Multi-Dimensional Spectral Code SPECT3D on large 3D grids.

Science.gov (United States)

Golovkin, Igor E.; Macfarlane, Joseph J.; Woodruff, Pamela R.; Pereyra, Nicolas A.

2006-10-01

The multi-dimensional collisional-radiative, spectral analysis code SPECT3D can be used to study radiation from complex plasmas. SPECT3D can generate instantaneous and time-gated images and spectra, space-resolved and streaked spectra, which makes it a valuable tool for post-processing hydrodynamics calculations and direct comparison between simulations and experimental data. On large three dimensional grids, transporting radiation along lines of sight (LOS) requires substantial memory and CPU resources. Currently, the parallel option in SPECT3D is based on parallelization over photon frequencies and allows for a nearly linear speed-up for a variety of problems. In addition, we are introducing a new parallel mechanism that will greatly reduce memory requirements. In the new implementation, spatial domain decomposition will be utilized allowing transport along a LOS to be performed only on the mesh cells the LOS crosses. The ability to operate on a fraction of the grid is crucial for post-processing the results of large-scale three-dimensional hydrodynamics simulations. We will present a parallel implementation of the code and provide a scalability study performed on a Linux cluster.

CD147 (Basigin/Emmprin) identifies FoxP3+CD45RO+CTLA4+-activated human regulatory T cells.

Science.gov (United States)

Solstad, Therese; Bains, Simer Jit; Landskron, Johannes; Aandahl, Einar Martin; Thiede, Bernd; Taskén, Kjetil; Torgersen, Knut Martin

2011-11-10

Human CD4(+)FoxP3(+) T cells are functionally and phenotypically heterogeneous providing plasticity to immune activation and regulation. To better understand the functional dynamics within this subset, we first used a combined strategy of subcellular fractionation and proteomics to describe differences at the protein level between highly purified human CD4(+)CD25(+) and CD4(+)CD25(-) T-cell populations. This identified a set of membrane proteins highly expressed on the cell surface of human regulatory T cells (Tregs), including CD71, CD95, CD147, and CD148. CD147 (Basigin or Emmprin) divided CD4(+)CD25(+) cells into distinct subsets. Furthermore, CD147, CD25, FoxP3, and in particular CTLA-4 expression correlated. Phenotypical and functional analyses suggested that CD147 marks the switch between resting (CD45RA(+)) and activated (CD45RO(+)) subsets within the FoxP3(+) T-cell population. Sorting of regulatory T cells into CD147(-) and CD147(+) populations demonstrated that CD147 identifies an activated and highly suppressive CD45RO(+) Treg subset. When analyzing CD4(+) T cells for their cytokine producing potential, CD147 levels grouped the FoxP3(+) subset into 3 categories with different ability to produce IL-2, TNF-α, IFN-γ, and IL-17. Together, this suggests that CD147 is a direct marker for activated Tregs within the CD4(+)FoxP3(+) subset and may provide means to manipulate cells important for immune homeostasis.

C -P -T anomaly matching in bosonic quantum field theory and spin chains

Science.gov (United States)

Sulejmanpasic, Tin; Tanizaki, Yuya

2018-04-01

We consider the O (3 ) nonlinear sigma model with the θ term and its linear counterpart in 1+1D. The model has discrete time-reflection and space-reflection symmetries at any θ , and enjoys the periodicity in θ →θ +2 π . At θ =0 ,π it also has a charge-conjugation C symmetry. Gauging the discrete space-time reflection symmetries is interpreted as putting the theory on the nonorientable R P2 manifold, after which the 2 π periodicity of θ and the C symmetry at θ =π are lost. We interpret this observation as a mixed 't Hooft anomaly among charge-conjugation C , parity P , and time-reversal T symmetries when θ =π . Anomaly matching implies that in this case the ground state cannot be trivially gapped, as long as C ,P , and T are all good symmetries of the theory. We make several consistency checks with various semiclassical regimes, and with the exactly solvable XYZ model. We interpret this anomaly as an anomaly of the corresponding spin-half chains with translational symmetry, parity, and time reversal [but not involving the SO(3)-spin symmetry], requiring that the ground state is never trivially gapped, even if SO(3) spin symmetry is explicitly and completely broken. We also consider generalizations to C PN -1 models and show that the C -P -T anomaly exists for even N .

The C2 domain of PKCalpha is a Ca2+ -dependent PtdIns(4,5)P2 sensing domain: a new insight into an old pathway.

Science.gov (United States)

Sánchez-Bautista, Sonia; Marín-Vicente, Consuelo; Gómez-Fernández, Juan C; Corbalán-García, Senena

2006-10-06

The C2 domain is a targeting domain that responds to intracellular Ca2+ signals in classical protein kinases (PKCs) and mediates the translocation of its host protein to membranes. Recent studies have revealed a new motif in the C2 domain, named the lysine-rich cluster, that interacts with acidic phospholipids. The purpose of this work was to characterize the molecular mechanism by which PtdIns(4,5)P2 specifically interacts with this motif. Using a combination of isothermal titration calorimetry, fluorescence resonance energy transfer and time-lapse confocal microscopy, we show here that Ca2+ specifically binds to the Ca2+ -binding region, facilitating PtdIns(4,5)P2 access to the lysine-rich cluster. The magnitude of PtdIns(4,5)P2 binding is greater than in the case of other polyphosphate phosphatidylinositols. Very importantly, the residues involved in PtdIns(4,5)P2 binding are essential for the plasma membrane localization of PKCalpha when RBL-2H3 cells are stimulated through their IgE receptors. Additionally, CFP-PH and CFP-C1 domains were used as bioprobes to demonstrate the co-existence of PtdIns(4,5)P2 and diacylglycerol in the plasma membrane, and it was shown that although a fraction of PtdIns(4,5)P2 is hydrolyzed to generate diacylglycerol and IP3, an important amount still remains in the membrane where it is available to activate PKCalpha. These findings entail revision of the currently accepted model of PKCalpha recruitment to the membrane and its activation.

Crystallization and preliminary X-ray diffraction analysis of the P3 RNA domain of yeast ribonuclease MRP in a complex with RNase P/MRP protein components Pop6 and Pop7

International Nuclear Information System (INIS)

Perederina, Anna; Esakova, Olga; Quan, Chao; Khanova, Elena; Krasilnikov, Andrey S.

2009-01-01

This article describes the first successful crystallization of components of eukaryotic ribonucleases P/MRP. Yeast RNase MRP RNA domain P3 was crystallized in a complex with the proteins Pop6 and Pop7; the crystals diffracted to 3.25 Å resolution. Eukaryotic ribonucleases P and MRP are closely related RNA-based enzymes which contain a catalytic RNA component and several protein subunits. The roles of the protein subunits in the structure and function of eukaryotic ribonucleases P and MRP are not clear. Crystals of a complex that included a circularly permuted 46-nucleotide-long P3 domain of the RNA component of Saccharomyces cerevisiae ribonuclease MRP and selenomethionine derivatives of the shared ribonuclease P/MRP protein components Pop6 (18.2 kDa) and Pop7 (15.8 kDa) were obtained using the sitting-drop vapour-diffusion method. The crystals belonged to space group P4 2 22 (unit-cell parameters a = b = 127.2, c = 76.8 Å, α = β = γ = 90°) and diffracted to 3.25 Å resolution

Evaluation of articular cartilage in patients with femoroacetabular impingement (FAI) using T2* mapping at different time points at 3.0 Tesla MRI: a feasibility study

International Nuclear Information System (INIS)

Apprich, S.; Mamisch, T.C.; Welsch, G.H.; Bonel, H.; Siebenrock, K.A.; Dudda, M.; Kim, Y.J.; Trattnig, S.

2012-01-01

To define the feasibility of utilizing T2* mapping for assessment of early cartilage degeneration prior to surgery in patients with symptomatic femoroacetabular impingement (FAI), we compared cartilage of the hip joint in patients with FAI and healthy volunteers using T2* mapping at 3.0 Tesla over time. Twenty-two patients (13 females and 9 males; mean age 28.1 years) with clinical signs of FAI and Toennis grade ≤ 1 on anterior-posterior x-ray and 35 healthy age-matched volunteers were examined at a 3 T MRI using a flexible body coil. T2* maps were calculated from sagittal- and coronal-oriented gradient-multi-echo sequences using six echoes (TR 125, TE 4.41/8.49/12.57/16.65/20.73/24.81, scan time 4.02 min), both measured at beginning and end of the scan (45 min time span between measurements). Region of interest analysis was manually performed on four consecutive slices for superior and anterior cartilage. Mean T2* values were compared among patients and volunteers, as well as over time using analysis of variance and Student's t-test. Whereas quantitative T2* values for the first measurement did not reveal significant differences between patients and volunteers, either for sagittal (p = 0.644) or coronal images (p = 0.987), at the first measurement, a highly significant difference (p ≤ 0.004) was found for both measurements with time after unloading of the joint. Over time we found decreasing mean T2* values for patients, in contrast to increasing mean T2* relaxation times in volunteers. The study proved the feasibility of utilizing T2* mapping for assessment of early cartilage degeneration in the hip joint in FAI patients at 3 Tesla to predict possible success of joint-preserving surgery. However, we suggest the time point for measuring T2* as an MR biomarker for cartilage and the changes in T2* over time to be of crucial importance for designing an MR protocol in patients with FAI. (orig.)

Identification of candidates for postmastectomy radiotherapy in patients with pT3N0M0 breast cancer

International Nuclear Information System (INIS)

Hamamoto, Yasushi; Ohsumi, Shozo; Aogi, Kenjiro; Takashima, Shigemitsu; Shinohara, Shuichi; Nakajima, Naomi; Kataoka, Masaaki

2013-01-01

There is still controversy concerning the indication of postmastectomy radiotherapy (PMRT) for pT3N0M0 breast cancer. To identify the candidates for PMRT in this subset, we investigated failure patterns, and searched for risk factors for isolated locoregional failure in pT3N0M0 breast cancer after mastectomy without PMRT. Among 1,176 patients who received mastectomy without PMRT for untreated unilateral breast cancer between 1990 and 2002, 64 patients (5%) had pT3N0M0 breast cancer (age 30-81 years; median 52.5 years). Isolated locoregional failure as the initial failure occurred in three patients. For all 64 patients, the 8-year failure-free survival rate, the isolated locoregional failure-free rate, and the distant failure-free rate were 76, 93, and 82%, respectively. Incidence of isolated locoregional failure as the initial failure was 18% (2/11) for patients 40 years or younger and 2% (1/53) for patients older than 40 years. The 8-year isolated locoregional failure-free rates were 73% for patients 40 years or younger and 98% for patients older than 40 years (p=0.0135). Concerning pT3N0M0 breast cancer, incidence of isolated locoregional failure was comparatively low after mastectomy without PMRT. Routine use of PMRT for all pT3N0M0 patients seemed to be unacceptable. PMRT may be useful for younger patients because of the comparatively high incidence of isolated locoregional failure. Because of the small number of cases in our series, further studies are necessary to determine the usefulness of PMRT for younger patients with pT3N0M0 breast cancer. (author)

Mutation of CD2AP and SH3KBP1 Binding Motif in Alphavirus nsP3 Hypervariable Domain Results in Attenuated Virus.

Science.gov (United States)

Mutso, Margit; Morro, Ainhoa Moliner; Smedberg, Cecilia; Kasvandik, Sergo; Aquilimeba, Muriel; Teppor, Mona; Tarve, Liisi; Lulla, Aleksei; Lulla, Valeria; Saul, Sirle; Thaa, Bastian; McInerney, Gerald M; Merits, Andres; Varjak, Margus

2018-04-27

Infection by Chikungunya virus (CHIKV) of the Old World alphaviruses (family Togaviridae) in humans can cause arthritis and arthralgia. The virus encodes four non-structural proteins (nsP) (nsP1, nsp2, nsP3 and nsP4) that act as subunits of the virus replicase. These proteins also interact with numerous host proteins and some crucial interactions are mediated by the unstructured C-terminal hypervariable domain (HVD) of nsP3. In this study, a human cell line expressing EGFP tagged with CHIKV nsP3 HVD was established. Using quantitative proteomics, it was found that CHIKV nsP3 HVD can bind cytoskeletal proteins, including CD2AP, SH3KBP1, CAPZA1, CAPZA2 and CAPZB. The interaction with CD2AP was found to be most evident; its binding site was mapped to the second SH3 ligand-like element in nsP3 HVD. Further assessment indicated that CD2AP can bind to nsP3 HVDs of many different New and Old World alphaviruses. Mutation of the short binding element hampered the ability of the virus to establish infection. The mutation also abolished ability of CD2AP to co-localise with nsP3 and replication complexes of CHIKV; the same was observed for Semliki Forest virus (SFV) harbouring a similar mutation. Similar to CD2AP, its homolog SH3KBP1 also bound the identified motif in CHIKV and SFV nsP3.

Computationally Efficient Amplitude Modulated Sinusoidal Audio Coding using Frequency-Domain Linear Prediction

DEFF Research Database (Denmark)

Christensen, M. G.; Jensen, Søren Holdt

2006-01-01

A method for amplitude modulated sinusoidal audio coding is presented that has low complexity and low delay. This is based on a subband processing system, where, in each subband, the signal is modeled as an amplitude modulated sum of sinusoids. The envelopes are estimated using frequency......-domain linear prediction and the prediction coefficients are quantized. As a proof of concept, we evaluate different configurations in a subjective listening test, and this shows that the proposed method offers significant improvements in sinusoidal coding. Furthermore, the properties of the frequency...

The effect of tRNA levels on decoding times of mRNA codons.

Science.gov (United States)

Dana, Alexandra; Tuller, Tamir

2014-08-01

The possible effect of transfer ribonucleic acid (tRNA) concentrations on codons decoding time is a fundamental biomedical research question; however, due to a large number of variables affecting this process and the non-direct relation between them, a conclusive answer to this question has eluded so far researchers in the field. In this study, we perform a novel analysis of the ribosome profiling data of four organisms which enables ranking the decoding times of different codons while filtering translational phenomena such as experimental biases, extreme ribosomal pauses and ribosome traffic jams. Based on this filtering, we show for the first time that there is a significant correlation between tRNA concentrations and the codons estimated decoding time both in prokaryotes and in eukaryotes in natural conditions (-0.38 to -0.66, all P values decoding times are not correlated with aminoacyl-tRNA levels. The reported results support the conjecture that translation efficiency is directly influenced by the tRNA levels in the cell. Thus, they should help to understand the evolution of synonymous aspects of coding sequences via the adaptation of their codons to the tRNA pool. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Isolation and characterization of NIH 3T3 cells expressing polyomavirus small T antigen

International Nuclear Information System (INIS)

Noda, T.; Satake, M.; Robins, T.; Ito, Y.

1986-01-01

The polyomavirus small T-antigen gene, together with the polyomavirus promoter, was inserted into retrovirus vector pGV16 which contains the Moloney sarcoma virus long terminal repeat and neomycin resistance gene driven by the simian virus 40 promoter. This expression vector, pGVST, was packaged into retrovirus particles by transfection of PSI2 cells which harbor packaging-defective murine retrovirus genome. NIH 3T3 cells were infected by this replication-defective retrovirus containing pGVST. Of the 15 G418-resistant cell clones, 8 express small T antigen at various levels as revealed by immunoprecipitation. A cellular protein with an apparent molecular weight of about 32,000 coprecipitates with small T antigen. Immunofluorescent staining shows that small T antigen is mainly present in the nuclei. Morphologically, cells expressing small T antigen are indistinguishable from parental NIH 3T3 cells and have a microfilament pattern similar to that in parental NIH 3T3 cells. Cells expressing small T antigen form a flat monolayer but continue to grow beyond the saturation density observed for parental NIH 3T3 cells and eventually come off the culture plate as a result of overconfluency. There is some correlation between the level of expression of small T antigen and the growth rate of the cells. Small T-antigen-expressing cells form small colonies in soft agar. However, the proportion of cells which form these small colonies is rather small. A clone of these cells tested did not form tumors in nude mice within 3 months after inoculation of 10 6 cells per animal. Thus, present studies establish that the small T antigen of polyomavirus is a second nucleus-localized transforming gene product of the virus (the first one being large T antigen) and by itself has a function which is to stimulate the growth of NIH 3T3 cells beyond their saturation density in monolayer culture

Stroke code improves intravenous thrombolysis administration in acute ischemic stroke.

Directory of Open Access Journals (Sweden)

Chih-Hao Chen

Full Text Available Timely intravenous (IV thrombolysis for acute ischemic stroke is associated with better clinical outcomes. Acute stroke care implemented with "Stroke Code" (SC may increase IV tissue plasminogen activator (tPA administration. The present study aimed to investigate the impact of SC on thrombolysis.The study period was divided into the "pre-SC era" (January 2006 to July 2010 and "SC era" (August 2010 to July 2013. Demographics, critical times (stroke symptom onset, presentation to the emergency department, neuroimaging, thrombolysis, stroke severity, and clinical outcomes were recorded and compared between the two eras.During the study period, 5957 patients with acute ischemic stroke were admitted; of these, 1301 (21.8% arrived at the emergency department within 3 h of stroke onset and 307 (5.2% received IV-tPA. The number and frequency of IV-tPA treatments for patients with an onset-to-door time of <3 h increased from the pre-SC era (n = 91, 13.9% to the SC era (n = 216, 33.3% (P<0.001. SC also improved the efficiency of IV-tPA administration; the median door-to-needle time decreased (88 to 51 min, P<0.001 and the percentage of door-to-needle times ≤60 min increased (14.3% to 71.3%, P<0.001. The SC era group tended to have more patients with good outcome (modified Rankin Scale ≤2 at discharge (49.5 vs. 39.6%, P = 0.11, with no difference in symptomatic hemorrhage events or in-hospital mortality.The SC protocol increases the percentage of acute ischemic stroke patients receiving IV-tPA and decreases door-to-needle time.

Development of backward equations T(p,h), T(p,s) and p(h,s) for heavy water liquid and vapor

International Nuclear Information System (INIS)

Nick P Petropoulos; Simos E Simopoulos

2005-01-01

Full text of publication follows: Backward equations for heavy water (a) temperature as a function of pressure and enthalpy T(p,h), (b) temperature as a function of pressure and entropy T(p,s) and (c) pressure as a function of enthalpy and entropy p(h,s) presented in this work, are based on the 'IAPS Formulation 1984 for the Thermodynamic Properties of Heavy Water Substance' [1], and also on the respective equations for the ordinary water substance as presented in 'The IAPWS Industrial Formulation 1997 for the Thermodynamic Properties of Water and Steam' [2]. Heavy water and steam thermodynamic properties can be calculated using the basic equations and saturation equations that are included in [1]. However, [1] does not contain any backward functions T(p,h), T(p,s) and p(h,s), which are needed for heavy water thermodynamic process modeling. The development of the two temperature backward functions efficiently increases computational speed for temperature calculations more than three times as pointed out in the similar case problem for ordinary water, addressed successfully in [2]. Without these temperature backward functions calculations may be performed only iteratively using the heavy water state equations at a much greater computing cost. Moreover, the development of the pressure backward function saves even more computing time in modeling problems since two-dimensional iterations from the h(p,T) and s(p,T) heavy water functions may by effectively avoided. In addition, given the pressure function p(h,s), the heavy water temperature T(h,s) can be calculated by the temperature function T(p,h). The numerical consistencies of calculated T and p to the state equations included in [1] are sufficient for most applications in the heavy water nuclear reactors heat cycles. For applications, where the demands on numerical consistency and accuracy are rather high, iterations with the approved state equations may be necessary. In these cases both temperature and pressure

Performance of a neutron transport code with full phase space decomposition on the Cray Research T3D

International Nuclear Information System (INIS)

Dorr, M.R.; Salo, E.M.

1995-01-01

We present performance results obtained on a 128-node Cray Research T3D computer by a neutron transport code implementing a standard mtiltigroup, discrete ordinates algorithm on a three-dimensional Cartesian grid. After summarizing the implementation strategy used to obtain a full decomposition of phase space (i.e., simultaneous parallelization of the neutron energy, directional and spatial variables), we investigate the scalability of the fundamental source iteration step with respect to each phase space variable. We also describe enhancements that have enabled performance rates approaching 10 gigaflops on the full 128-node machine

Symmetrical refolding of protein domains and subunits: example of the dimeric two-domain 3-isopropylmalate dehydrogenases.

Science.gov (United States)

Gráczer, Eva; Varga, Andrea; Melnik, Bogdan; Semisotnov, Gennady; Závodszky, Péter; Vas, Mária

2009-02-10

The refolding mechanism of the homodimeric two-domain 3-isopropylmalate dehydrogenase (IPMDH) from the organisms adapted to different temperatures, Thermus thermophilus (Tt), Escherichia coli (Ec), and Vibrio sp. I5 (Vib), is described. In all three cases, instead of a self-template mechanism, the high extent of symmetry and cooperativity in folding of subunits and domains have been concluded from the following experimental findings: The complex time course of refolding, monitored by Trp fluorescence, consists of a fast (the rate constant varies as 16.5, 25.0, and 11.7 min-1 in the order of Tt, Ec, and Vib IPMDHs) and a slow (the rate constants are 0.11, 0.80, and 0.23 min-1 for the three different species) first-order process. However, a burst increase of Trp fluorescence anisotropy to the value of the native states indicates that in all three cases the association of the two polypeptide chains occurs at the beginning of refolding. This dimeric species binds the substrate IPM, but the native-like interactions of the tertiary and quaternary structures are only formed during the slow phase of refolding, accompanied by further increase of protein fluorescence and appearance of FRET between Trp side chain(s) and the bound NADH. Joining the contacting arms of each subunit also takes place exclusively during this slow phase. To monitor refolding of each domain within the intact molecule of T. thermophilus IPMDH, Trp's (located in separate domains) were systematically replaced with Phe's. The refolding processes of the mutants were followed by measuring changes in Trp fluorescence and in FRET between the particular Trp and NADH. The high similarity of time courses (both in biphasicity and in their rates) strongly suggests cooperative folding of the domains during formation of the native three-dimensional structure of IPMDH.

Distributed space-time coding

CERN Document Server

Jing, Yindi

2014-01-01

Distributed Space-Time Coding (DSTC) is a cooperative relaying scheme that enables high reliability in wireless networks. This brief presents the basic concept of DSTC, its achievable performance, generalizations, code design, and differential use. Recent results on training design and channel estimation for DSTC and the performance of training-based DSTC are also discussed.

An Atmospheric General Circulation Model with Chemistry for the CRAY T3E: Design, Performance Optimization and Coupling to an Ocean Model

Science.gov (United States)

Farrara, John D.; Drummond, Leroy A.; Mechoso, Carlos R.; Spahr, Joseph A.

1998-01-01

The design, implementation and performance optimization on the CRAY T3E of an atmospheric general circulation model (AGCM) which includes the transport of, and chemical reactions among, an arbitrary number of constituents is reviewed. The parallel implementation is based on a two-dimensional (longitude and latitude) data domain decomposition. Initial optimization efforts centered on minimizing the impact of substantial static and weakly-dynamic load imbalances among processors through load redistribution schemes. Recent optimization efforts have centered on single-node optimization. Strategies employed include loop unrolling, both manually and through the compiler, the use of an optimized assembler-code library for special function calls, and restructuring of parts of the code to improve data locality. Data exchanges and synchronizations involved in coupling different data-distributed models can account for a significant fraction of the running time. Therefore, the required scattering and gathering of data must be optimized. In systems such as the T3E, there is much more aggregate bandwidth in the total system than in any particular processor. This suggests a distributed design. The design and implementation of a such distributed 'Data Broker' as a means to efficiently couple the components of our climate system model is described.

Quantifying NMR relaxation correlation and exchange in articular cartilage with time domain analysis

Science.gov (United States)

Mailhiot, Sarah E.; Zong, Fangrong; Maneval, James E.; June, Ronald K.; Galvosas, Petrik; Seymour, Joseph D.

2018-02-01

Measured nuclear magnetic resonance (NMR) transverse relaxation data in articular cartilage has been shown to be multi-exponential and correlated to the health of the tissue. The observed relaxation rates are dependent on experimental parameters such as solvent, data acquisition methods, data analysis methods, and alignment to the magnetic field. In this study, we show that diffusive exchange occurs in porcine articular cartilage and impacts the observed relaxation rates in T1-T2 correlation experiments. By using time domain analysis of T2-T2 exchange spectroscopy, the diffusive exchange time can be quantified by measurements that use a single mixing time. Measured characteristic times for exchange are commensurate with T1 in this material and so impacts the observed T1 behavior. The approach used here allows for reliable quantification of NMR relaxation behavior in cartilage in the presence of diffusive fluid exchange between two environments.

Durations and domains of daily aerobic activity: evidence from the 2010 Canadian time-use survey.

Science.gov (United States)

Millward, Hugh; Spinney J, E L; Scott, Darren

2014-07-01

This study employs national time-diary data to evaluate how much aerobic activity Canadians engage in on a daily basis, how that activity is apportioned by activity domain, and how subgroups within the population vary in their aerobic attainment. The study employs time-use data from the 2010 General Social Survey of Canada, for 15,390 respondents aged 15 and older. To estimate effort levels, the authors harmonized survey codes with those in the Compendium of Physical Activities. Aerobic activity was defined as moderate or vigorous effort at 3.5 Metabolic Equivalent of Task (MET) or higher. Among the 4 activity domains, aerobic participation is highest in leisure activities, followed by chores, paid work, and active transportation (AT). Only a minority (42%) of respondents recorded at least 20 mins/day of aerobic activity. Aerobic totals were particularly low for women and those in poor or fair health, and low for students, 15- to 24-year-olds, and those residing in Quebec, Ontario, and larger cities. The majority of Canadian adults are failing to meet recommended aerobic activity levels. However, there is considerable opportunity to increase aerobic participation for some groups, particularly women and young adults, especially in the leisure and AT domains.

Implementation of Unsplit Perfectly Matched Layer Absorbing Boundary Condition in 3 Dimensional Finite Difference Time Domain Method

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B. U. Musa

2017-04-01

Full Text Available The C++ programming language was used to implement three-dimensional (3-D finite-difference time-domain (FDTD technique to simulate radiation of high frequency electromagnetic waves in free space. To achieve any meaningful results the computational domain of interest should have to be truncated in some way and this is achieved by applying absorbing boundary conditions. A uniaxial perfectly matched layer (UPML absorbing boundary condition is used in this work. The discretised equations of the UPML in FDTD time stepping scheme were derived and has been successfully implemented using the computer program. Simulation results showed that the UPML behaves as an absorber. This was confirmed by comparing the results with another boundary condition, the Mur ABC.

T-Cell-Specific Loss of the PI-3-Kinase p110α Catalytic Subunit Results in Enhanced Cytokine Production and Antitumor Response

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Laura Aragoneses-Fenoll

2018-02-01

Full Text Available Class IA phosphatidylinositol 3-kinase (PI3K catalytic subunits p110α and p110δ are targets in cancer therapy expressed at high levels in T lymphocytes. The role of p110δ PI3K in normal or pathological immune responses is well established, yet the importance of p110α subunits in T cell-dependent immune responses is not clear. To address this problem, mice with p110α conditionally deleted in CD4+ and CD8+ T lymphocytes (p110α−/−ΔT were used. p110α−/−ΔT mice show normal development of T cell subsets, but slightly reduced numbers of CD4+ T cells in the spleen. “In vitro,” TCR/CD3 plus CD28 activation of naive CD4+ and CD8+ p110α−/−ΔT T cells showed enhanced effector function, particularly IFN-γ secretion, T-bet induction, and Akt, Erk, or P38 activation. Tfh derived from p110α−/−ΔT cells also have enhanced responses when compared to normal mice, and IL-2 expanded p110α−/−ΔT CD8+ T cells had enhanced levels of LAMP-1 and Granzyme B. By contrast, the expansion of p110α−/−ΔT iTreg cells was diminished. Also, p110α−/−ΔT mice had enhanced anti-keyhole limpet hemocyanin (KLH IFN-γ, or IL-4 responses and IgG1 and IgG2b anti-KLH antibodies, using CFA or Alum as adjuvant, respectively. When compared to WT mice, p110α−/−ΔT mice inoculated with B16.F10 melanoma showed delayed tumor progression. The percentage of CD8+ T lymphocytes was higher and the percentage of Treg cells lower in the spleen of tumor-bearing p110α−/−ΔT mice. Also, IFN-γ production in tumor antigen-activated spleen cells was enhanced. Thus, PI3K p110α plays a significant role in antigen activation and differentiation of CD4+ and CD8+ T lymphocytes modulating antitumor immunity.

Improvement of the MEDUSA code for one-dimensional laser fusion analysis (MEDUSA-P) and sensitivity analysis of the energy gain

International Nuclear Information System (INIS)

Takano, Hideki; Nakano, Ko.

1976-07-01

The MEDUSA-P code is a revised version of MEDUSA which was developed for calculation of the hydrodynamic behaviour (implosion process and thermonuclear reaction) of plasmas irradiated by an intense laser light. In conversion of MEDUSA for JAERI's computer, some programming errors were corrected. In order to express the violent space variation of plasmas, the number of region meshes is increased and the variables are expressed in double precision. And further, graphical representations of the main physical variables, i.e. rho (density), u (velocity), Tsub(i) (ion temperature), Tsub(e) (electron temperature) and P (pressure), are programmed to understand the complex time and space dependence of the plasma fluid with ease. The MEDUSA-P code is available for both computer FACOM 230/75 and CDC 6600. In this report, the calculations for spherical D-T pellets are performed with MEDUSA-P. The relation between several initial conditions and energy gain is described, and also phenomenology of the fuel implosion process. (auth.)

Structure of lipid kinase p110β/p85β elucidates an unusual SH2-domain-mediated inhibitory mechanism.

Science.gov (United States)

Zhang, Xuxiao; Vadas, Oscar; Perisic, Olga; Anderson, Karen E; Clark, Jonathan; Hawkins, Phillip T; Stephens, Len R; Williams, Roger L

2011-03-04

Phosphoinositide 3-kinases (PI3Ks) are essential for cell growth, migration, and survival. The structure of a p110β/p85β complex identifies an inhibitory function for the C-terminal SH2 domain (cSH2) of the p85 regulatory subunit. Mutagenesis of a cSH2 contact residue activates downstream signaling in cells. This inhibitory contact ties up the C-terminal region of the p110β catalytic subunit, which is essential for lipid kinase activity. In vitro, p110β basal activity is tightly restrained by contacts with three p85 domains: the cSH2, nSH2, and iSH2. RTK phosphopeptides relieve inhibition by nSH2 and cSH2 using completely different mechanisms. The binding site for the RTK's pYXXM motif is exposed on the cSH2, requiring an extended RTK motif to reach and disrupt the inhibitory contact with p110β. This contrasts with the nSH2 where the pY-binding site itself forms the inhibitory contact. This establishes an unusual mechanism by which p85 SH2 domains contribute to RTK signaling specificities. Copyright © 2011 Elsevier Inc. All rights reserved.

Investigation of the (p,p'), (p,d) and (p,t) reactions on some light Sn isotopes

International Nuclear Information System (INIS)

Blankert, P.J.

1979-01-01

The results are presented of the 112 Sn(p,p') 112 Sn reaction. Apart from the usual distorted-wave analysis the excitation of some states is described in the coupled-channels formalism. The results of the 112 Sn(p,d) 111 Sn and the 112 Sn(p,t) 110 Sn reactions are also reported. From the (p,d) reaction quasi-particle energies and occupation numbers are determined. Two-step DWBA calculations are performed for some states that are assumed to result from the coupling of a quasiparticle to the 2 + 1 or 3 - 1 state of the even core. In the gross structure above 3 MeV of excitation, pickup strength from deeply-bound hole states is observed. The (p,t) reaction provided spin and parity of a number of levels in 110 Sn. A two-step DWBA analysis of the excitation of the ground state and first excited 2 + state shows the importance of second-order processes. The combined results of the (p,t) reactions on 112 Sn, 114 Sn and 116 Sn are given with some emphasis on the systematic features. The derivation is given of some expressions for spectroscopic amplitudes necessary in the two-step DWBA calculations for the (p,t) reactions. For all reactions a comparison is made with other existing data and with the results of model calculations. (Auth.)

Mutation of CD2AP and SH3KBP1 Binding Motif in Alphavirus nsP3 Hypervariable Domain Results in Attenuated Virus

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Margit Mutso

2018-04-01

Full Text Available Infection by Chikungunya virus (CHIKV of the Old World alphaviruses (family Togaviridae in humans can cause arthritis and arthralgia. The virus encodes four non-structural proteins (nsP (nsP1, nsp2, nsP3 and nsP4 that act as subunits of the virus replicase. These proteins also interact with numerous host proteins and some crucial interactions are mediated by the unstructured C-terminal hypervariable domain (HVD of nsP3. In this study, a human cell line expressing EGFP tagged with CHIKV nsP3 HVD was established. Using quantitative proteomics, it was found that CHIKV nsP3 HVD can bind cytoskeletal proteins, including CD2AP, SH3KBP1, CAPZA1, CAPZA2 and CAPZB. The interaction with CD2AP was found to be most evident; its binding site was mapped to the second SH3 ligand-like element in nsP3 HVD. Further assessment indicated that CD2AP can bind to nsP3 HVDs of many different New and Old World alphaviruses. Mutation of the short binding element hampered the ability of the virus to establish infection. The mutation also abolished ability of CD2AP to co-localise with nsP3 and replication complexes of CHIKV; the same was observed for Semliki Forest virus (SFV harbouring a similar mutation. Similar to CD2AP, its homolog SH3KBP1 also bound the identified motif in CHIKV and SFV nsP3.

Validation and applicability of the 3D core kinetics and thermal hydraulics coupled code SPARKLE

International Nuclear Information System (INIS)

Miyata, Manabu; Maruyama, Manabu; Ogawa, Junto; Otake, Yukihiko; Miyake, Shuhei; Tabuse, Shigehiko; Tanaka, Hirohisa

2009-01-01

The SPARKLE code is a coupled code system based on three individual codes whose physical models have already been verified and validated. Mitsubishi Heavy Industries (MHI) confirmed the coupling calculation, including data transfer and the total reactor coolant system (RCS) behavior of the SPARKLE code. The confirmation uses the OECD/NEA MSLB benchmark problem, which is based on Three Mile Island Unit 1 (TMI-1) nuclear power plant data. This benchmark problem has been used to verify coupled codes developed and used by many organizations. Objectives of the benchmark program are as follows. Phase 1 is to compare the results of the system transient code using point kinetics. Phase 2 is to compare the results of the coupled three-dimensional (3D) core kinetics code and 3D core thermal-hydraulics (T/H) code, and Phase 3 is to compare the results of the combined coupled system transient code, 3D core kinetics code, and 3D core T/H code as a total validation of the coupled calculation. The calculation results of the SPARKLE code indicate good agreement with other benchmark participants' results. Therefore, the SPARKLE code is validated through these benchmark problems. In anticipation of applying the SPARKLE code to licensing analyses, MHI and Japanese PWR utilities have established a safety analysis method regarding the calculation conditions such as power distributions, reactivity coefficients, and event-specific features. (author)

Electromagnetic Pulse Excitation of Finite-Long Dissipative Conductors over a Conducting Ground Plane in the Time Domain

Energy Technology Data Exchange (ETDEWEB)

Campione, Salvatore [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Warne, Larry K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Schiek, Richard [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Basilio, Lorena I. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2017-09-01

This report details the modeling results for the response of a finite-length dissipative conductor interacting with a conducting ground to a hypothetical nuclear device with the same output energy spectrum as the Fat Man device. We use a time-domain method based on transmission line theory that allows accounting for time-varying air conductivities. We implemented such method in a code we call ATLOG - Analytic Transmission Line Over Ground. Results are compared the frequency-domain version of ATLOG previously developed and to the circuit simulator Xyce in some instances. Intentionally Left Blank

In vivo estimation of transverse relaxation time constant (T2 ) of 17 human brain metabolites at 3T.

Science.gov (United States)

Wyss, Patrik O; Bianchini, Claudio; Scheidegger, Milan; Giapitzakis, Ioannis A; Hock, Andreas; Fuchs, Alexander; Henning, Anke

2018-08-01

The transverse relaxation times T 2 of 17 metabolites in vivo at 3T is reported and region specific differences are addressed. An echo-time series protocol was applied to one, two, or three volumes of interest with different fraction of white and gray matter including a total number of 106 healthy volunteers and acquiring a total number of 128 spectra. The data were fitted with the 2D fitting tool ProFit2, which included individual line shape modeling for all metabolites and allowed the T 2 calculation of 28 moieties of 17 metabolites. The T 2 of 10 metabolites and their moieties have been reported for the first time. Region specific T 2 differences in white and gray matter enriched tissue occur in 16 of 17 metabolites examined including single resonance lines and coupled spin systems. The relaxation time T 2 is regions specific and has to be considered when applying tissue composition correction for internal water referencing. Magn Reson Med 80:452-461, 2018. © 2018 International Society for Magnetic Resonance in Medicine. © 2018 International Society for Magnetic Resonance in Medicine.

Risk of biochemical recurrence and timing of radiotherapy in pT3a N0 prostate cancer with positive surgical margin. A single center experience

International Nuclear Information System (INIS)

Hegemann, Nina-Sophie; Morcinek, Sebastian; Corradini, Stefanie; Li, Minglun; Belka, Claus; Ganswindt, Ute; Buchner, Alexander; Karl, Alexander; Stief, Christian; Knuechel, Ruth

2016-01-01

Despite improved biochemical recurrence-free survival rates by the use of immediate adjuvant radiotherapy (RT) in patients with locally advanced prostate cancer, disagreement about the need and timing of RT remains. From 2005-2009, 94 patients presenting with a stage pT3a N0 and microscopic positive resection margin were retrospectively analyzed after radical prostatectomy. Special attention was given to patients' outcome, the frequency of additive RT, and its efficacy. Median follow-up was 80 months. A total of 71 patients had a negative postoperative prostate-specific antigen (PSA) level (<0.07 ng/ml). Thirty-six of them did not experience any PSA relapse (subgroup 1). Fourteen of them received additive RT and during follow-up all 36 patients remained PSA negative. Of 71 initially PSA-negative patients, 35 had a biochemical relapse (subgroup 2); 28 patients underwent salvage RT. The median PSA value before salvage RT was 0.24 ng/ml and was subsequently negative (<0.07 ng/ml) in 23 patients after RT. Of the entire cohort, 23 patients had persisting PSA after surgery (subgroup 3). Of these, 18 patients received salvage RT at a median PSA level of 0.4 ng/ml. One patient in subgroup 1, 5 patients in subgroup 2, and 9 patients in subgroup 3 had ongoing androgen deprivation therapy. The present study of 94 pT3a N0 R1 prostate cancer patients provides insight into medical care of this patient cohort and underlines the need for additive RT for the majority of patients to achieve long-term biochemical control. Although immediate adjuvant RT was applied with restraint (20 %), during the observation period 60 of 94 patients (63.8 %) received RT - highlighting the need of postoperative treatment. (orig.) [de

Evaluating the Training, Responsibilities, and Practices of P&T Committee Members and Nonmember Contributors.

Science.gov (United States)

Rodriguez, Ryan; Kelly, Brett J; Moody, Mary

2017-08-01

use any criteria for author selection. When authoring documents, primary literature was routinely consulted by 89.5% of the respondents. Most of the respondents (84.1%) used an organization-specific document template, while 5.8% of the respondents indicated that they prepared documents with no defined process. The most highly ranked factor that could have a perceived beneficial effect on P&T committee functions were guidelines on the authoring and reviewing of P&T committee documents. The survey of P&T committee members and nonmember contributors used in this study identified current training, responsibilities, and practices that can inform recommendations for standards in these domains. Findings suggest opportunities for improvement in achieving best practice recommendations to ensure evidence-based decision making by P&T committees. No outside funding supported this study. At the time of this study, Kelly was employed by Global Account Management Group (GAMG), which provides consulting services to the hospital and health services industry. As an employee of GAMG, Kelly has served on various advisory boards. All fees for consulting work were paid to GAMG and were primarily related to training or the federal market (e.g., Department of Defense or the Department of Veterans Affairs) and have no association with this study. Rodriguez and Moody report no conflicts of interest. All authors contributed to study concept and design. Rodriguez took the lead in data collection, assisted by the other authors. Data interpretation was performed by Rodriguez, along with Kelly and Moody. The manuscript was written and revised primarily by Rodriguez, along with the other authors.

Research of time-domain equivalent circuit method in solving dispersion of coupled-cavity traveling-wave tube

International Nuclear Information System (INIS)

Li Wenjun; China Academy of Engineering Physics, Mianyang; Xu Zhou; Li Ming; Yang Xingfan; Chen Yanan; Liu Jie; Jin Xiao; Lin Yuzheng

2008-01-01

In this paper, a time-domain equivalent circuit method is applied to solve dispersion of coupled-cavity travelling-wave tube (CCTWT). First, the time-domain circuit equations of CCTWT coupled-cavity chain are deduced from the equivalent circuit model. Then, the equations are solved numerically by fourth-order Runge-Kutta method and a program CTTDCP is developed using MATLAB. Last, a L-band CCTWT is calculated using CTTDCP and the cavity pass-band of this tube is computed to be 1.08-1.48 GHz, which is consistent with the experimental results and the simulation results of electromagnetic code and demonstrates the validity of the time-domain equivalent circuit method. In addition, a new design method which uses the equivalent circuit method and electromagnetic simulation together to optimize the cold cavity characteristics of CCTWT is proposed. (authors)

3T MRI of the knee with optimised isotropic 3D sequences. Accurate delineation of intra-articular pathology without prolonged acquisition times

Energy Technology Data Exchange (ETDEWEB)

Abdulaal, Osamah M.; Rainford, Louise; Galligan, Marie; McGee, Allison [University College Dublin, Radiography and Diagnostic Imaging, School of Medicine, Belfield, Dublin (Ireland); MacMahon, Peter; Kavanagh, Eoin [Mater Misericordiae University Hospital, Department of Radiology, Dublin (Ireland); University College Dublin, School of Medicine, Dublin (Ireland); Cashman, James [Mater Misericordiae University Hospital, Department of Orthopaedics, Dublin (Ireland); University College Dublin, School of Medicine, Dublin (Ireland)

2017-11-15

To investigate optimised isotropic 3D turbo spin echo (TSE) and gradient echo (GRE)-based pulse sequences for visualisation of articular cartilage lesions within the knee joint. Optimisation of experimental imaging sequences was completed using healthy volunteers (n=16) with a 3-Tesla (3T) MRI scanner. Imaging of patients with knee cartilage abnormalities (n=57) was then performed. Acquired sequences included 3D proton density-weighted (PDW) TSE (SPACE) with and without fat-suppression (FS), and T2*W GRE (TrueFISP) sequences, with acquisition times of 6:51, 6:32 and 5:35 min, respectively. One hundred sixty-one confirmed cartilage lesions were detected and categorised (Grade II n=90, Grade III n=71). The highest sensitivity and specificity for detecting cartilage lesions were obtained with TrueFISP with values of 84.7% and 92%, respectively. Cartilage SNR mean for PDW SPACE-FS was the highest at 72.2. TrueFISP attained the highest CNR means for joint fluid/cartilage (101.5) and joint fluid/ligament (156.5), and the lowest CNR for cartilage/meniscus (48.5). Significant differences were identified across the three sequences for all anatomical structures with respect to SNR and CNR findings (p-value <0.05). Isotropic TrueFISP at 3T, optimised for acquisition time, accurately detects cartilage defects, although it demonstrated the lowest contrast between cartilage and meniscus. (orig.)

Murine K2P5.1 Deficiency Has No Impact on Autoimmune Neuroinflammation due to Compensatory K2P3.1- and KV1.3-Dependent Mechanisms

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Stefan Bittner

2015-07-01

Full Text Available Lymphocytes express potassium channels that regulate physiological cell functions, such as activation, proliferation and migration. Expression levels of K2P5.1 (TASK2; KCNK5 channels belonging to the family of two-pore domain potassium channels have previously been correlated to the activity of autoreactive T lymphocytes in patients with multiple sclerosis and rheumatoid arthritis. In humans, K2P5.1 channels are upregulated upon T cell stimulation and influence T cell effector functions. However, a further clinical translation of targeting K2P5.1 is currently hampered by a lack of highly selective inhibitors, making it necessary to evaluate the impact of KCNK5 in established preclinical animal disease models. We here demonstrate that K2P5.1 knockout (K2P5.1−/− mice display no significant alterations concerning T cell cytokine production, proliferation rates, surface marker molecules or signaling pathways. In an experimental model of autoimmune neuroinflammation, K2P5.1−/− mice show a comparable disease course to wild-type animals and no major changes in the peripheral immune system or CNS compartment. A compensatory upregulation of the potassium channels K2P3.1 and KV1.3 seems to counterbalance the deletion of K2P5.1. As an alternative model mimicking autoimmune neuroinflammation, experimental autoimmune encephalomyelitis in the common marmoset has been proposed, especially for testing the efficacy of new potential drugs. Initial experiments show that K2P5.1 is functionally expressed on marmoset T lymphocytes, opening up the possibility for assessing future K2P5.1-targeting drugs.

Nuclear GUI: a Graphical User Interface for 3D discrete ordinates neutral particle transport codes in the doors and BOT3P packages

International Nuclear Information System (INIS)

Saintagne, P.W.; Azmy, Y.Y.

2005-01-01

A GUI (Graphical User Interface) provides a graphical, interactive and intuitive link between the user and the software. It translates the user'actions into information, e.g; input data that is interpretable by the software. In order to develop an efficient GUI, it is important to master the target computational code. An initial version of a complete GUI for the DOORS and BOT3P packages for solving neutral particle transport problems in 3-dimensional geometry has been completed. This GUI is made of 4 components. The first component GipGui aims at handling cross-sections by mixing microscopic cross-sections from different libraries. The second component TORT-GUI provides the user a simple way to create or modify input files for the TORT codes that is a general purpose neutral transport code able to solve large problems with complex configurations. The third component GGTM-GUI prepares the data describing the problem configuration like the geometrical data, material assignment or key flux positions. The fourth component DTM3-GUI helps the user to visualize TORT results by providing data for a graphics post-processor

FRAP-T1: a computer code for the transient analysis of oxide fuel rods

International Nuclear Information System (INIS)

Dearien, J.A.; Miller, R.L.; Hobbins, R.R.; Siefken, L.J.; Baston, V.F.; Coleman, D.R.

1977-02-01

FRAP-T is a FORTRAN IV computer code which can be used to solve for the transient response of a light water reactor (LWR) fuel rod during accident transients such as loss-of-coolant accident (LOCA) or a power-cooling-mismatch (PCM). The coupled effects of mechanical, thermal, internal gas, and material property response on the behavior of the fuel rod are considered. FRAP-T is a modular code with each major computational model isolated within the code and coupled to the main code by subroutine calls and data transfer through argument lists. FRAP-T is coupled to a materials properties subcode (MATPRO) which is used to provide gas, fuel, and cladding properties to the FRAP-T computational subcodes. No material properties need be supplied by the code user. The needed water properties are stored in tables built into the code. Critical heat flux (CHF) and heat transfer correlations for a wide range of coolant conditions are contained in modular subroutines. FRAP-T has been evaluated by making extensive comparisons between predictions of the code and experimental data. Comparison of predicted and experimental results are presented for a range of FRAP-T calculated parameters. The code is presently programmed and running on an IBM-360/75 and a CDC 7600 computer

Carotid Artery Stenosis: Comparison of 3D Time-of-Flight MR Angiography and Contrast-Enhanced MR Angiography at 3T

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Ivan Platzek

2014-01-01

Full Text Available Purpose. The aim of this study was to assess the correlation of 3D time-of-flight MR angiography (TOF MRA and contrast-enhanced MR angiography (CEMRA for carotid artery stenosis evaluation at 3T. Material and Methods. Twenty-three patients (5 f, 18 m; mean age 61 y, age range 45–78 y with internal carotid artery stenosis detected with ultrasonography were examined on a 3.0T MR system. The MR examination included both 3D TOF MRA and CEMRA of the carotid arteries. MR images were evaluated independently by two board-certified radiologists. Stenosis evaluation was based on a five-point scale. Stenosis grades determined by TOF and CEMRA were compared using Spearman’s rank correlation coefficient and the Wilcoxon test. Cohen’s Kappa was used to evaluate interrater reliability. Results. CEMRA detected stenosis in 24 (52% of 46 carotids evaluated, while TOF detected stenosis in 27 (59% of 46 carotids. TOF MRA yielded significantly higher results for stenosis grade in comparison to CEMRA (P=0.014. Interrater agreement was very good for both TOF MRA (κ=0.93 and CEMRA (κ=0.93. Conclusion. At 3T, 3D TOF MRA should not be used as replacement for contrast-enhanced MRA of the carotid arteries, as it results in significantly higher stenosis grades.

T P Sharma

Indian Academy of Sciences (India)

Home; Journals; Bulletin of Materials Science. T P Sharma. Articles written in Bulletin of Materials Science. Volume 26 Issue 4 June 2003 pp 387-389 Magnetic Materials. Band gap determination of Ni–Zn ferrites · G P Joshi N S Saxena R Mangal A Mishra T P Sharma · More Details Abstract Fulltext PDF. Nanocomposites of ...

Stevioside from Stevia rebaudiana Bertoni Increases Insulin Sensitivity in 3T3-L1 Adipocytes

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Nabilatul Hani Mohd-Radzman

2013-01-01

Full Text Available Stevioside from Stevia rebaudiana has been reported to exert antihyperglycemic effects in both rat and human subjects. There have been few studies on these effects in vitro. In this paper, radioactive glucose uptake assay was implemented in order to assess improvements in insulin sensitivity in 3T3-L1 cells by elevation of glucose uptake following treatment with stevioside. Oil Red-O staining and MTT assay were utilized to confirm adipocyte differentiation and cell viability, respectively. Findings from this research showed a significant increase in absorbance values in mature adipocytes following Oil Red-O staining, confirming the differentiation process. Stevioside was noncytotoxic to 3T3-L1 cells as cell viability was reduced by a maximum of 17%, making it impossible to determine its IC50. Stevioside increased glucose uptake activities by 2.1 times (p<0.001 in normal conditions and up to 4.4 times (p<0.001 in insulin-resistant states. At times, this increase was higher than that seen in positive control group treated with rosiglitazone maleate, an antidiabetic agent. Expressions of pY20 and p-IRS1 which were measured via Western blot were improved by stevioside treatment. In conclusion, stevioside has direct effects on 3T3-L1 insulin sensitivity via increase in glucose uptake and enhanced expression of proteins involved in insulin-signalling pathway.