A Radiation Transfer Solver for Athena Using Short Characteristics

NASA Astrophysics Data System (ADS)

Davis, Shane W.; Stone, James M.; Jiang, Yan-Fei

2012-03-01

We describe the implementation of a module for the Athena magnetohydrodynamics (MHD) code that solves the time-independent, multi-frequency radiative transfer (RT) equation on multidimensional Cartesian simulation domains, including scattering and non-local thermodynamic equilibrium (LTE) effects. The module is based on well known and well tested algorithms developed for modeling stellar atmospheres, including the method of short characteristics to solve the RT equation, accelerated Lambda iteration to handle scattering and non-LTE effects, and parallelization via domain decomposition. The module serves several purposes: it can be used to generate spectra and images, to compute a variable Eddington tensor (VET) for full radiation MHD simulations, and to calculate the heating and cooling source terms in the MHD equations in flows where radiation pressure is small compared with gas pressure. For the latter case, the module is combined with the standard MHD integrators using operator splitting: we describe this approach in detail, including a new constraint on the time step for stability due to radiation diffusion modes. Implementation of the VET method for radiation pressure dominated flows is described in a companion paper. We present results from a suite of test problems for both the RT solver itself and for dynamical problems that include radiative heating and cooling. These tests demonstrate that the radiative transfer solution is accurate and confirm that the operator split method is stable, convergent, and efficient for problems of interest. We demonstrate there is no need to adopt ad hoc assumptions of questionable accuracy to solve RT problems in concert with MHD: the computational cost for our general-purpose module for simple (e.g., LTE gray) problems can be comparable to or less than a single time step of Athena's MHD integrators, and only few times more expensive than that for more general (non-LTE) problems.

Moving from Batch to Field Using the RT3D Reactive Transport Modeling System

NASA Astrophysics Data System (ADS)

Clement, T. P.; Gautam, T. R.

2002-12-01

The public domain reactive transport code RT3D (Clement, 1997) is a general-purpose numerical code for solving coupled, multi-species reactive transport in saturated groundwater systems. The code uses MODFLOW to simulate flow and several modules of MT3DMS to simulate the advection and dispersion processes. RT3D employs the operator-split strategy which allows the code solve the coupled reactive transport problem in a modular fashion. The coupling between reaction and transport is defined through a separate module where the reaction equations are specified. The code supports a versatile user-defined reaction option that allows users to define their own reaction system through a Fortran-90 subroutine, known as the RT3D-reaction package. Further a utility code, known as BATCHRXN, allows the users to independently test and debug their reaction package. To analyze a new reaction system at a batch scale, users should first run BATCHRXN to test the ability of their reaction package to model the batch data. After testing, the reaction package can simply be ported to the RT3D environment to study the model response under 1-, 2-, or 3-dimensional transport conditions. This paper presents example problems that demonstrate the methods for moving from batch to field-scale simulations using BATCHRXN and RT3D codes. The first example describes a simple first-order reaction system for simulating the sequential degradation of Tetrachloroethene (PCE) and its daughter products. The second example uses a relatively complex reaction system for describing the multiple degradation pathways of Tetrachloroethane (PCA) and its daughter products. References 1) Clement, T.P, RT3D - A modular computer code for simulating reactive multi-species transport in 3-Dimensional groundwater aquifers, Battelle Pacific Northwest National Laboratory Research Report, PNNL-SA-28967, September, 1997. Available at: http://bioprocess.pnl.gov/rt3d.htm.

Light scattering by planetary-regolith analog samples: computational results

NASA Astrophysics Data System (ADS)

Väisänen, Timo; Markkanen, Johannes; Hadamcik, Edith; Levasseur-Regourd, Anny-Chantal; Lasue, Jeremie; Blum, Jürgen; Penttilä, Antti; Muinonen, Karri

2017-04-01

We compute light scattering by a planetary-regolith analog surface. The corresponding experimental work is from Hadamcik et al. [1] with the PROGRA2-surf [2] device measuring the polarization of dust particles. The analog samples are low density (volume fraction 0.15 ± 0.03) agglomerates produced by random ballistic deposition of almost equisized silica spheres (refractive index n=1.5 and diameter 1.45 ± 0.06 µm). Computations are carried out with the recently developed codes entitled Radiative Transfer with Reciprocal Transactions (R2T2) and Radiative Transfer Coherent Backscattering with incoherent interactions (RT-CB-ic). Both codes incorporate the so-called incoherent treatment which enhances the applicability of the radiative transfer as shown by Muinonen et al. [3]. As a preliminary result, we have computed scattering from a large spherical medium with the RT-CB-ic using equal-sized particles with diameters of 1.45 microns. The preliminary results have shown that the qualitative characteristics are similar for the computed and measured intensity and polarization curves but that there are still deviations between the characteristics. We plan to remove the deviations by incorporating a size distribution of particles (1.45 ± 0.02 microns) and detailed information about the volume density profile within the analog surface. Acknowledgments: We acknowledge the ERC Advanced Grant no. 320773 entitled Scattering and Absorption of Electromagnetic Waves in Particulate Media (SAEMPL). Computational resources were provided by CSC - IT Centre for Science Ltd, Finland. References: [1] Hadamcik E. et al. (2007), JQSRT, 106, 74-89 [2] Levasseur-Regourd A.C. et al. (2015), Polarimetry of stars and planetary systems, CUP, 61-80 [3] Muinonen K. et al. (2016), extended abstract for EMTS.

A RADIATION TRANSFER SOLVER FOR ATHENA USING SHORT CHARACTERISTICS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davis, Shane W.; Stone, James M.; Jiang Yanfei

2012-03-01

We describe the implementation of a module for the Athena magnetohydrodynamics (MHD) code that solves the time-independent, multi-frequency radiative transfer (RT) equation on multidimensional Cartesian simulation domains, including scattering and non-local thermodynamic equilibrium (LTE) effects. The module is based on well known and well tested algorithms developed for modeling stellar atmospheres, including the method of short characteristics to solve the RT equation, accelerated Lambda iteration to handle scattering and non-LTE effects, and parallelization via domain decomposition. The module serves several purposes: it can be used to generate spectra and images, to compute a variable Eddington tensor (VET) for full radiationmore » MHD simulations, and to calculate the heating and cooling source terms in the MHD equations in flows where radiation pressure is small compared with gas pressure. For the latter case, the module is combined with the standard MHD integrators using operator splitting: we describe this approach in detail, including a new constraint on the time step for stability due to radiation diffusion modes. Implementation of the VET method for radiation pressure dominated flows is described in a companion paper. We present results from a suite of test problems for both the RT solver itself and for dynamical problems that include radiative heating and cooling. These tests demonstrate that the radiative transfer solution is accurate and confirm that the operator split method is stable, convergent, and efficient for problems of interest. We demonstrate there is no need to adopt ad hoc assumptions of questionable accuracy to solve RT problems in concert with MHD: the computational cost for our general-purpose module for simple (e.g., LTE gray) problems can be comparable to or less than a single time step of Athena's MHD integrators, and only few times more expensive than that for more general (non-LTE) problems.« less

Atmospheric radiance interpolation for the modeling of hyperspectral data

NASA Astrophysics Data System (ADS)

Fuehrer, Perry; Healey, Glenn; Rauch, Brian; Slater, David; Ratkowski, Anthony

2008-04-01

The calibration of data from hyperspectral sensors to spectral radiance enables the use of physical models to predict measured spectra. Since environmental conditions are often unknown, material detection algorithms have emerged that utilize predicted spectra over ranges of environmental conditions. The predicted spectra are typically generated by a radiative transfer (RT) code such as MODTRAN TM. Such techniques require the specification of a set of environmental conditions. This is particularly challenging in the LWIR for which temperature and atmospheric constituent profiles are required as inputs for the RT codes. We have developed an automated method for generating environmental conditions to obtain a desired sampling of spectra in the sensor radiance domain. Our method provides a way of eliminating the usual problems encountered, because sensor radiance spectra depend nonlinearly on the environmental parameters, when model conditions are specified by a uniform sampling of environmental parameters. It uses an initial set of radiance vectors concatenated over a set of conditions to define the mapping from environmental conditions to sensor spectral radiance. This approach enables a given number of model conditions to span the space of desired radiance spectra and improves both the accuracy and efficiency of detection algorithms that rely upon use of predicted spectra.

A Novel Leu92 Mutant of HIV-1 Reverse Transcriptase with a Selective Deficiency in Strand Transfer Causes a Loss of Viral Replication.

PubMed

Herzig, Eytan; Voronin, Nickolay; Kucherenko, Nataly; Hizi, Amnon

2015-08-01

The process of reverse transcription (RTN) in retroviruses is essential to the viral life cycle. This key process is catalyzed exclusively by the viral reverse transcriptase (RT) that copies the viral RNA into DNA by its DNA polymerase activity, while concomitantly removing the original RNA template by its RNase H activity. During RTN, the combination between DNA synthesis and RNA hydrolysis leads to strand transfers (or template switches) that are critical for the completion of RTN. The balance between these RT-driven activities was considered to be the sole reason for strand transfers. Nevertheless, we show here that a specific mutation in HIV-1 RT (L92P) that does not affect the DNA polymerase and RNase H activities abolishes strand transfer. There is also a good correlation between this complete loss of the RT's strand transfer to the loss of the DNA clamp activity of the RT, discovered recently by us. This finding indicates a mechanistic linkage between these two functions and that they are both direct and unique functions of the RT (apart from DNA synthesis and RNA degradation). Furthermore, when the RT's L92P mutant was introduced into an infectious HIV-1 clone, it lost viral replication, due to inefficient intracellular strand transfers during RTN, thus supporting the in vitro data. As far as we know, this is the first report on RT mutants that specifically and directly impair RT-associated strand transfers. Therefore, targeting residue Leu92 may be helpful in selectively blocking this RT activity and consequently HIV-1 infectivity and pathogenesis. Reverse transcription in retroviruses is essential for the viral life cycle. This multistep process is catalyzed by viral reverse transcriptase, which copies the viral RNA into DNA by its DNA polymerase activity (while concomitantly removing the RNA template by its RNase H activity). The combination and balance between synthesis and hydrolysis lead to strand transfers that are critical for reverse transcription completion. We show here for the first time that a single mutation in HIV-1 reverse transcriptase (L92P) selectively abolishes strand transfers without affecting the enzyme's DNA polymerase and RNase H functions. When this mutation was introduced into an infectious HIV-1 clone, viral replication was lost due to an impaired intracellular strand transfer, thus supporting the in vitro data. Therefore, finding novel drugs that target HIV-1 reverse transcriptase Leu92 may be beneficial for developing new potent and selective inhibitors of retroviral reverse transcription that will obstruct HIV-1 infectivity. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

The VLBA correlator: Real-time in the distributed era

NASA Technical Reports Server (NTRS)

Wells, D. C.

1992-01-01

The correlator is the signal processing engine of the Very Long Baseline Array (VLBA). Radio signals are recorded on special wideband (128 Mb/s) digital recorders at the 10 telescopes, with sampling times controlled by hydrogen maser clocks. The magnetic tapes are shipped to the Array Operations Center in Socorro, New Mexico, where they are played back simultaneously into the correlator. Real-time software and firmware controls the playback drives to achieve synchronization, compute models of the wavefront delay, control the numerous modules of the correlator, and record FITS files of the fringe visibilities at the back-end of the correlator. In addition to the more than 3000 custom VLSI chips which handle the massive data flow of the signal processing, the correlator contains a total of more than 100 programmable computers, 8-, 16- and 32-bit CPUs. Code is downloaded into front-end CPU's dependent on operating mode. Low-level code is assembly language, high-level code is C running under a RT OS. We use VxWorks on Motorola MVME147 CPU's. Code development is on a complex of SPARC workstations connected to the RT CPU's by Ethernet. The overall management of the correlation process is dependent on a database management system. We use Ingres running on a Sparcstation-2. We transfer logging information from the database of the VLBA Monitor and Control System to our database using Ingres/NET. Job scripts are computed and are transferred to the real-time computers using NFS, and correlation job execution logs and status flow back by the route. Operator status and control displays use windows on workstations, interfaced to the real-time processes by network protocols. The extensive network protocol support provided by VxWorks is invaluable. The VLBA Correlator's dependence on network protocols is an example of the radical transformation of the real-time world over the past five years. Real-time is becoming more like conventional computing. Paradoxically, 'conventional' computing is also adopting practices from the real-time world: semaphores, shared memory, light-weight threads, and concurrency. This appears to be a convergence of thinking.

A simple model for molecular hydrogen chemistry coupled to radiation hydrodynamics

NASA Astrophysics Data System (ADS)

Nickerson, Sarah; Teyssier, Romain; Rosdahl, Joakim

2018-06-01

We introduce non-equilibrium molecular hydrogen chemistry into the radiation-hydrodynamics code RAMSES-RT. This is an adaptive mesh refinement grid code with radiation hydrodynamics that couples the thermal chemistry of hydrogen and helium to moment-based radiative transfer with the Eddington tensor closure model. The H2 physics that we include are formation on dust grains, gas phase formation, formation by three-body collisions, collisional destruction, photodissociation, photoionisation, cosmic ray ionisation and self-shielding. In particular, we implement the first model for H2 self-shielding that is tied locally to moment-based radiative transfer by enhancing photo-destruction. This self-shielding from Lyman-Werner line overlap is critical to H2 formation and gas cooling. We can now track the non-equilibrium evolution of molecular, atomic, and ionised hydrogen species with their corresponding dissociating and ionising photon groups. Over a series of tests we show that our model works well compared to specialised photodissociation region codes. We successfully reproduce the transition depth between molecular and atomic hydrogen, molecular cooling of the gas, and a realistic Strömgren sphere embedded in a molecular medium. In this paper we focus on test cases to demonstrate the validity of our model on small scales. Our ultimate goal is to implement this in large-scale galactic simulations.

Extending the NASA Ames Mars General Circulation Model to Explore Mars’ Middle Atmosphere

NASA Astrophysics Data System (ADS)

Brecht, Amanda; Hollingsworth, J.; Kahre, M.; Schaeffer, J.

2013-10-01

The NASA Ames Mars General Circulation Model (MGCM) upper boundary has been extended to ~120 km altitude (p ~10-5 mbar). The extension of the MGCM upper boundary initiates the ability to understand the connection between the lower and upper atmosphere of Mars through the middle atmosphere 70 - 120 km). Moreover, it provides the opportunity to support future missions (i.e. the 2013 MAVEN mission). A major factor in this extension is the incorporation of the Non-Local Thermodynamic Equilibrium (NLTE) heating (visible) and cooling (infrared). This modification to the radiative transfer forcing (i.e., RT code) has been significantly tested in a 1D vertical column and now has been ported to the full 3D Mars GCM. Initial results clearly show the effects of NLTE in the upper middle atmosphere. Diagnostic of seasonal mean fields and large-scale wave activity will be shown with insight into circulation patterns in the middle atmosphere. Furthermore, sensitivity tests with the resolution of the pressure and temperature grids, in which the k-coefficients are calculated upon, have been performed in the 1D RT code. Our progress on this research will be presented. Brecht is supported by NASA’s Postdoctoral Program at the Ames Research Center, administered by Oak Ridge Associated Universities through a contract with NASA.

Numerical modeling of the fracture process in a three-unit all-ceramic fixed partial denture.

PubMed

Kou, Wen; Kou, Shaoquan; Liu, Hongyuan; Sjögren, Göran

2007-08-01

The main objectives were to examine the fracture mechanism and process of a ceramic fixed partial denture (FPD) framework under simulated mechanical loading using a recently developed numerical modeling code, the R-T(2D) code, and also to evaluate the suitability of R-T(2D) code as a tool for this purpose. Using the recently developed R-T(2D) code the fracture mechanism and process of a 3U yttria-tetragonal zirconia polycrystal ceramic (Y-TZP) FPD framework was simulated under static loading. In addition, the fracture pattern obtained using the numerical simulation was compared with the fracture pattern obtained in a previous laboratory test. The result revealed that the framework fracture pattern obtained using the numerical simulation agreed with that observed in a previous laboratory test. Quasi-photoelastic stress fringe pattern and acoustic emission showed that the fracture mechanism was tensile failure and that the crack started at the lower boundary of the framework. The fracture process could be followed both in step-by-step and step-in-step. Based on the findings in the current study, the R-T(2D) code seems suitable for use as a complement to other tests and clinical observations in studying stress distribution, fracture mechanism and fracture processes in ceramic FPD frameworks.

Tunneling nanotubes promote intercellular mitochondria transfer followed by increased invasiveness in bladder cancer cells

PubMed Central

Lu, Jinjin; Zheng, Xiufen; Li, Fan; Yu, Yang; Chen, Zhong; Liu, Zheng; Wang, Zhihua; Xu, Hua; Yang, Weimin

2017-01-01

Intercellular transfer of organelles via tunneling nanotubes (TNTs) is a novel means of cell-to-cell communication. Here we demonstrate the existence of TNTs between co-cultured RT4 and T24 bladder cancer cells using light microscopy, fluorescence imaging, and scanning electron microscopy (SEM). Spontaneous unidirectional transfer of mitochondria from T24 to RT4 cells was detected using fluorescence imaging and flow cytometry. The distribution of mitochondria migrated from T24 cells was in good agreement with the original mitochondria in RT4 cells, which may imply mitochondrial fusion. We detected cytoskeleton reconstruction in RT4-Mito-T24 cells by observing F-actin redistribution. Akt, mTOR, and their downstream mediators were activated and increased. The resultant increase in the invasiveness of bladder cancer cells was detected in vitro and in vivo. These data indicate that TNTs promote intercellular mitochondrial transfer between heterogeneous cells, followed by an increase in the invasiveness of bladder cancer cells. PMID:28107184

The impact of Lyman-α radiative transfer on large-scale clustering in the Illustris simulation

NASA Astrophysics Data System (ADS)

Behrens, C.; Byrohl, C.; Saito, S.; Niemeyer, J. C.

2018-06-01

Context. Lyman-α emitters (LAEs) are a promising probe of the large-scale structure at high redshift, z ≳ 2. In particular, the Hobby-Eberly Telescope Dark Energy Experiment aims at observing LAEs at 1.9 < z < 3.5 to measure the baryon acoustic oscillation (BAO) scale and the redshift-space distortion (RSD). However, it has been pointed out that the complicated radiative transfer (RT) of the resonant Lyman-α emission line generates an anisotropic selection bias in the LAE clustering on large scales, s ≳ 10 Mpc. This effect could potentially induce a systematic error in the BAO and RSD measurements. Also, there exists a recent claim to have observational evidence of the effect in the Lyman-α intensity map, albeit statistically insignificant. Aims: We aim at quantifying the impact of the Lyman-α RT on the large-scale galaxy clustering in detail. For this purpose, we study the correlations between the large-scale environment and the ratio of an apparent Lyman-α luminosity to an intrinsic one, which we call the "observed fraction", at 2 < z < 6. Methods: We apply our Lyman-α RT code by post-processing the full Illustris simulations. We simply assume that the intrinsic luminosity of the Lyman-α emission is proportional to the star formation rate of galaxies in Illustris, yielding a sufficiently large sample of LAEs to measure the anisotropic selection bias. Results: We find little correlation between large-scale environment and the observed fraction induced by the RT, and hence a smaller anisotropic selection bias than has previously been claimed. We argue that the anisotropy was overestimated in previous work due to insufficient spatial resolution; it is important to keep the resolution such that it resolves the high-density region down to the scale of the interstellar medium, that is, 1 physical kpc. We also find that the correlation can be further enhanced by assumptions in modeling intrinsic Lyman-α emission.

Molecular cloning, recombinant expression, and antifungal functional characterization of the lipid transfer protein from Panax ginseng.

PubMed

Cai, Kexin; Wang, Jiawen; Wang, Min; Zhang, Hui; Wang, Siming; Zhao, Yu

2016-07-01

To establish an efficient expression system for a fusion protein GST-pgLTP (Lipid Transfer Protein) and to test its antifungal activity. The nucleotide sequence of LTP gene was obtained from Panax ginseng using RT-PCR. The ORF of the cDNA is 363 bp, codING for a protein OF 120 amino acids with a calculated MW of 12.09 kDa. The pgLTP gene with a His6-tag at the C-terminus was cloned into the pGEX-6p1 vector to generate a GST-fusion pgLTP protein construct that was expressed in Escherichia coli Rosetta. Following purification by Ni-NTA, the fusion protein exhibited antifungal activity against five fungi found in ginseng. The fusion protein GST-pgLTP has activity against a broad spectrum of phytopathogenic fungi, and can potentially be adapted for production to combat fungal diseases that affect P. ginseng.

SU-F-BRD-02: Application of ARCHERRT-- A GPU-Based Monte Carlo Dose Engine for Radiation Therapy -- to Tomotherapy and Patient-Independent IMRT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Su, L; Du, X; Liu, T

Purpose: As a module of ARCHER -- Accelerated Radiation-transport Computations in Heterogeneous EnviRonments, ARCHER{sub RT} is designed for RadioTherapy (RT) dose calculation. This paper describes the application of ARCHERRT on patient-dependent TomoTherapy and patient-independent IMRT. It also conducts a 'fair' comparison of different GPUs and multicore CPU. Methods: The source input used for patient-dependent TomoTherapy is phase space file (PSF) generated from optimized plan. For patient-independent IMRT, the open filed PSF is used for different cases. The intensity modulation is simulated by fluence map. The GEANT4 code is used as benchmark. DVH and gamma index test are employed to evaluatemore » the accuracy of ARCHER{sub RT} code. Some previous studies reported misleading speedups by comparing GPU code with serial CPU code. To perform a fairer comparison, we write multi-thread code with OpenMP to fully exploit computing potential of CPU. The hardware involved in this study are a 6-core Intel E5-2620 CPU and 6 NVIDIA M2090 GPUs, a K20 GPU and a K40 GPU. Results: Dosimetric results from ARCHER{sub RT} and GEANT4 show good agreement. The 2%/2mm gamma test pass rates for different clinical cases are 97.2% to 99.7%. A single M2090 GPU needs 50~79 seconds for the simulation to achieve a statistical error of 1% in the PTV. The K40 card is about 1.7∼1.8 times faster than M2090 card. Using 6 M2090 card, the simulation can be finished in about 10 seconds. For comparison, Intel E5-2620 needs 507∼879 seconds for the same simulation. Conclusion: We successfully applied ARCHER{sub RT} to Tomotherapy and patient-independent IMRT, and conducted a fair comparison between GPU and CPU performance. The ARCHER{sub RT} code is both accurate and efficient and may be used towards clinical applications.« less

Numerical Electromagnetic Code (NEC)-Basic Scattering Code. Part I. User’s Manual.

DTIC Science & Technology

1979-09-01

Command RT : 29 I. Command PG: 32 J. Command GP: 35 K. Command CG: 36 L. Command SG: 39 M. Command AM: 44 N. Conumand PR: 48 0. Command NP: 49 P...these points and con- firm the validity of the solution. 1 0 1 -.- ’----.- ... The source presently considered in the computer code is an Plec - tric...Range Input 28 * RT : Translate and/or Rotate Coordinates 29 SG: Source Geometry Input IQ TO: Test Data Generation Options 17 [IN: Units of Input U)S

3-D Inhomogeous Radiative Transfer Model using a Planar-stratified Forward RT Model and Horizontal Perturbation Series

NASA Astrophysics Data System (ADS)

Zhang, K.; Gasiewski, A. J.

2017-12-01

A horizontally inhomogeneous unified microwave radiative transfer (HI-UMRT) model based upon a nonspherical hydrometeor scattering model is being developed at the University of Colorado at Boulder to facilitate forward radiative simulations for 3-dimensionally inhomogeneous clouds in severe weather. The HI-UMRT 3-D analytical solution is based on incorporating a planar-stratified 1-D UMRT algorithm within a horizontally inhomogeneous iterative perturbation scheme. Single-scattering parameters are computed using the Discrete Dipole Scattering (DDSCAT v7.3) program for hundreds of carefully selected nonspherical complex frozen hydrometeors from the NASA/GSFC DDSCAT database. The required analytic factorization symmetry of transition matrix in a normalized RT equation was analytically proved and validated numerically using the DDSCAT-based full Stokes matrix of randomly oriented hydrometeors. The HI-UMRT model thus inherits the properties of unconditional numerical stability, efficiency, and accuracy from the UMRT algorithm and provides a practical 3-D two-Stokes parameter radiance solution with Jacobian to be used within microwave retrievals and data assimilation schemes. In addition, a fast forward radar reflectivity operator with Jacobian based on DDSCAT backscatter efficiency computed for large hydrometeors is incorporated into the HI-UMRT model to provide applicability to active radar sensors. The HI-UMRT will be validated strategically at two levels: 1) intercomparison of brightness temperature (Tb) results with those of several 1-D and 3-D RT models, including UMRT, CRTM and Monte Carlo models, 2) intercomparison of Tb with observed data from combined passive and active spaceborne sensors (e.g. GPM GMI and DPR). The precise expression for determining the required number of 3-D iterations to achieve an error bound on the perturbation solution will be developed to facilitate the numerical verification of the HI-UMRT code complexity and computation performance.

Risk of Cerebrovascular Events in Elderly Patients After Radiation Therapy Versus Surgery for Early-Stage Glottic Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hong, Julian C.; Kruser, Tim J.; Gondi, Vinai

Purpose: Comprehensive neck radiation therapy (RT) has been shown to increase cerebrovascular disease (CVD) risk in advanced-stage head-and-neck cancer. We assessed whether more limited neck RT used for early-stage (T1-T2 N0) glottic cancer is associated with increased CVD risk, using the Surveillance, Epidemiology, and End Results (SEER)-Medicare linked database. Methods and Materials: We identified patients ≥66 years of age with early-stage glottic laryngeal cancer from SEER diagnosed from 1992 to 2007. Patients treated with combined surgery and RT were excluded. Medicare CPT codes for carotid interventions, Medicare ICD-9 codes for cerebrovascular events, and SEER data for stroke as the causemore » of death were collected. Similarly, Medicare CPT and ICD-9 codes for peripheral vascular disease (PVD) were assessed to serve as an internal control between treatment groups. Results: A total of 1413 assessable patients (RT, n=1055; surgery, n=358) were analyzed. The actuarial 10-year risk of CVD was 56.5% (95% confidence interval 51.5%-61.5%) for the RT cohort versus 48.7% (41.1%-56.3%) in the surgery cohort (P=.27). The actuarial 10-year risk of PVD did not differ between the RT (52.7% [48.1%-57.3%]) and surgery cohorts (52.6% [45.2%-60.0%]) (P=.89). Univariate analysis showed an increased association of CVD with more recent diagnosis (P=.001) and increasing age (P=.001). On multivariate Cox analysis, increasing age (P<.001) and recent diagnosis (P=.002) remained significantly associated with a higher CVD risk, whereas the association of RT and CVD remained not statistically significant (HR=1.11 [0.91-1.37,] P=.31). Conclusions: Elderly patients with early-stage laryngeal cancer have a high burden of cerebrovascular events after surgical management or RT. RT and surgery are associated with comparable risk for subsequent CVD development after treatment in elderly patients.« less

Room temperature deintercalation of alkali metal atoms from epitaxial graphene by formation of charge-transfer complexes

NASA Astrophysics Data System (ADS)

Shin, H.-C.; Ahn, S. J.; Kim, H. W.; Moon, Y.; Rai, K. B.; Woo, S. H.; Ahn, J. R.

2016-08-01

Atom (or molecule) intercalations and deintercalations have been used to control the electronic properties of graphene. In general, finite energies above room temperature (RT) thermal energy are required for the intercalations and deintercalations. Here, we demonstrate that alkali metal atoms can be deintercalated from epitaxial graphene on a SiC substrate at RT, resulting in the reduction in density of states at the Fermi level. The change in density of states at the Fermi level at RT can be applied to a highly sensitive graphene sensor operating at RT. Na atoms, which were intercalated at a temperature of 80 °C, were deintercalated at a high temperature above 1000 °C when only a thermal treatment was used. In contrast to the thermal treatment, the intercalated Na atoms were deintercalated at RT when tetrafluorotetracyanoquinodimethane (F4-TCNQ) molecules were adsorbed on the surface. The RT deintercalation occurred via the formation of charge-transfer complexes between Na atoms and F4-TCNQ molecules.

Development and Implementation of Dynamic Scripts to Execute Cycled GSI/WRF Forecasts

NASA Technical Reports Server (NTRS)

Zavodsky, Bradley; Srikishen, Jayanthi; Berndt, Emily; Li, Xuanli; Watson, Leela

2014-01-01

The Weather Research and Forecasting (WRF) numerical weather prediction (NWP) model and Gridpoint Statistical Interpolation (GSI) data assimilation (DA) are the operational systems that make up the North American Mesoscale (NAM) model and the NAM Data Assimilation System (NDAS) analysis used by National Weather Service forecasters. The Developmental Testbed Center (DTC) manages and distributes the code for the WRF and GSI, but it is up to individual researchers to link the systems together and write scripts to run the systems, which can take considerable time for those not familiar with the code. The objective of this project is to develop and disseminate a set of dynamic scripts that mimic the unique cycling configuration of the operational NAM to enable researchers to develop new modeling and data assimilation techniques that can be easily transferred to operations. The current version of the SPoRT GSI/WRF Scripts (v3.0.1) is compatible with WRF v3.3 and GSI v3.0.

Multidimensional radiative transfer with multilevel atoms. II. The non-linear multigrid method.

NASA Astrophysics Data System (ADS)

Fabiani Bendicho, P.; Trujillo Bueno, J.; Auer, L.

1997-08-01

A new iterative method for solving non-LTE multilevel radiative transfer (RT) problems in 1D, 2D or 3D geometries is presented. The scheme obtains the self-consistent solution of the kinetic and RT equations at the cost of only a few (<10) formal solutions of the RT equation. It combines, for the first time, non-linear multigrid iteration (Brandt, 1977, Math. Comp. 31, 333; Hackbush, 1985, Multi-Grid Methods and Applications, springer-Verlag, Berlin), an efficient multilevel RT scheme based on Gauss-Seidel iterations (cf. Trujillo Bueno & Fabiani Bendicho, 1995ApJ...455..646T), and accurate short-characteristics formal solution techniques. By combining a valid stopping criterion with a nested-grid strategy a converged solution with the desired true error is automatically guaranteed. Contrary to the current operator splitting methods the very high convergence speed of the new RT method does not deteriorate when the grid spatial resolution is increased. With this non-linear multigrid method non-LTE problems discretized on N grid points are solved in O(N) operations. The nested multigrid RT method presented here is, thus, particularly attractive in complicated multilevel transfer problems where small grid-sizes are required. The properties of the method are analyzed both analytically and with illustrative multilevel calculations for Ca II in 1D and 2D schematic model atmospheres.

Gaps, rings, and non-axisymmetric structures in protoplanetary disks. From simulations to ALMA observations

NASA Astrophysics Data System (ADS)

Flock, M.; Ruge, J. P.; Dzyurkevich, N.; Henning, Th.; Klahr, H.; Wolf, S.

2015-02-01

Aims: Recent observations by the Atacama Large Millimeter/submillimeter Array (ALMA) of disks around young stars revealed distinct asymmetries in the dust continuum emission. In this work we wish to study axisymmetric and non-axisymmetric structures that are generated by the magneto-rotational instability in the outer regions of protoplanetary disks. We combine the results of state-of-the-art numerical simulations with post-processing radiative transfer (RT) to generate synthetic maps and predictions for ALMA. Methods: We performed non-ideal global 3D magneto-hydrodynamic (MHD) stratified simulations of the dead-zone outer edge using the FARGO MHD code PLUTO. The stellar and disk parameters were taken from a parameterized disk model applied for fitting high-angular resolution multi-wavelength observations of various circumstellar disks. We considered a stellar mass of M∗ = 0.5 M⊙ and a total disk mass of about 0.085 M∗. The 2D initial temperature and density profiles were calculated consistently from a given surface density profile and Monte Carlo radiative transfer. The 2D Ohmic resistivity profile was calculated using a dust chemistry model. We considered two values for the dust-to-gas mass ratio, 10-2 and 10-4, which resulted in two different levels of magnetic coupling. The initial magnetic field was a vertical net flux field. The radiative transfer simulations were performed with the Monte Carlo-based 3D continuum RT code MC3D. The resulting dust reemission provided the basis for the simulation of observations with ALMA. Results: All models quickly turned into a turbulent state. The fiducial model with a dust-to-gas mass ratio of 10-2 developed a large gap followed by a jump in surface density located at the dead-zone outer edge. The jump in density and pressure was strong enough to stop the radial drift of particles at this location. In addition, we observed the generation of vortices by the Rossby wave instability at the jump location close to 60 AU. The vortices were steadily generated and destroyed at a cycle of 40 local orbits. The RT results and simulated ALMA observations predict that it is feasible to observe these large-scale structures that appear in magnetized disks without planets. Neither the turbulent fluctuations in the disk nor specific times of the model can be distinguished on the basis of high-angular resolution submillimeter observations alone. The same applies to the distinction between gaps at the dead-zone edges and planetary gaps, to the distinction between turbulent and simple unperturbed disks, and to the asymmetry created by the vortex.

Efficient Optical Logic, Interconnections and Processing Using Quantum Confined Structures

DTIC Science & Technology

1993-05-20

mnounced D ELECTE j LL.,iicEtion ......... -..................- JUN 14 1993 B y .. . ........ . . . . . .. Di~t ibution l Availability Codes Avail...coefficient of rt( b ) and power reflectivity of RT( B )=lrt( b )12 , viewed from the cavity. RB>RT is used in the design. Written in terms of the power...reflectivities, the total power reflectivity from the Fabry-Perot is given by: p lf-RT. R-f-• B exp(-.al)1 2 I ~ ~l .•RTRBeXp(._C.)j2 Assuming RB=0.97, Figure

Accuracy of the new ICD-9-CM code for "drip-and-ship" thrombolytic treatment in patients with ischemic stroke.

PubMed

Tonarelli, Silvina B; Tibbs, Michael; Vazquez, Gabriela; Lakshminarayan, Kamakshi; Rodriguez, Gustavo J; Qureshi, Adnan I

2012-02-01

A new International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) diagnosis code, V45.88, was approved by the Centers for Medicare and Medicaid Services (CMS) on October 1, 2008. This code identifies patients in whom intravenous (IV) recombinant tissue plasminogen activator (rt-PA) is initiated in one hospital's emergency department, followed by transfer within 24 hours to a comprehensive stroke center, a paradigm commonly referred to as "drip-and-ship." This study assessed the use and accuracy of the new V45.88 code for identifying ischemic stroke patients who meet the criteria for drip-and-ship at 2 advanced certified primary stroke centers. Consecutive patients over a 12-month period were identified by primary ICD-9-CM diagnosis codes related to ischemic stroke. The accuracy of V45.88 code utilization using administrative data provided by Health Information Management Services was assessed through a comparison with data collected in prospective stroke registries maintained at each hospital by a trained abstractor. Out of a total of 428 patients discharged from both hospitals with a diagnosis of ischemic stroke, 37 patients were given ICD-9-CM code V45.88. The internally validated data from the prospective stroke database demonstrated that a total of 40 patients met the criteria for drip-and-ship. A concurrent comparison found that 92% (sensitivity) of the patients treated with drip-and-ship were coded with V45.88. None of the non-drip-and-ship stroke cases received the V45.88 code (100% specificity). The new ICD-9-CM code for drip-and-ship appears to have high specificity and sensitivity, allowing effective data collection by the CMS. Copyright © 2012 National Stroke Association. Published by Elsevier Inc. All rights reserved.

Simulation, Theory, and Observations of the Spectrum of the Rayleigh-Taylor Instability due to Laser Imprint of Planar Targets

NASA Astrophysics Data System (ADS)

Keskinen, M. J.; Karasik, Max; Bates, J. W.; Schmitt, A. J.

2006-10-01

A limitation on the efficiency of high gain direct drive inertial confinement fusion is the extent of pellet disruption caused by the Rayleigh-Taylor (RT) instability. The RT instability can be seeded by pellet surface irregularities and/or laser imprint nonuniformities. It is important to characterize the evolution of the RT instability, e.g., the k-spectrum of areal mass. In this paper we study the time-dependent evolution of the spectrum of the Rayleigh-Taylor instability due to laser imprint in planar targets. This is achieved using the NRL FAST hydrodynamic simulation code together with analytical models. It is found that the optically smoothed laser imprint-driven RT spectrum develops into an inverse power law in k-space after several linear growth times. FAST simulation code results are compared with recent NRL Nike KrF laser experimental data. An analytical model, which is a function of Froude and Atwood numbers, is derived for the RT spectrum and favorably compared with both FAST simulation and Nike observations.

Room temperature deintercalation of alkali metal atoms from epitaxial graphene by formation of charge-transfer complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shin, H.-C.; Ahn, S. J.; Kim, H. W.

2016-08-22

Atom (or molecule) intercalations and deintercalations have been used to control the electronic properties of graphene. In general, finite energies above room temperature (RT) thermal energy are required for the intercalations and deintercalations. Here, we demonstrate that alkali metal atoms can be deintercalated from epitaxial graphene on a SiC substrate at RT, resulting in the reduction in density of states at the Fermi level. The change in density of states at the Fermi level at RT can be applied to a highly sensitive graphene sensor operating at RT. Na atoms, which were intercalated at a temperature of 80 °C, were deintercalatedmore » at a high temperature above 1000 °C when only a thermal treatment was used. In contrast to the thermal treatment, the intercalated Na atoms were deintercalated at RT when tetrafluorotetracyanoquinodimethane (F4-TCNQ) molecules were adsorbed on the surface. The RT deintercalation occurred via the formation of charge-transfer complexes between Na atoms and F4-TCNQ molecules.« less

A design tool for direct and non-stochastic calculations of near-field radiative transfer in complex structures: The NF-RT-FDTD algorithm

NASA Astrophysics Data System (ADS)

Didari, Azadeh; Pinar Mengüç, M.

2017-08-01

Advances in nanotechnology and nanophotonics are inextricably linked with the need for reliable computational algorithms to be adapted as design tools for the development of new concepts in energy harvesting, radiative cooling, nanolithography and nano-scale manufacturing, among others. In this paper, we provide an outline for such a computational tool, named NF-RT-FDTD, to determine the near-field radiative transfer between structured surfaces using Finite Difference Time Domain method. NF-RT-FDTD is a direct and non-stochastic algorithm, which accounts for the statistical nature of the thermal radiation and is easily applicable to any arbitrary geometry at thermal equilibrium. We present a review of the fundamental relations for far- and near-field radiative transfer between different geometries with nano-scale surface and volumetric features and gaps, and then we discuss the details of the NF-RT-FDTD formulation, its application to sample geometries and outline its future expansion to more complex geometries. In addition, we briefly discuss some of the recent numerical works for direct and indirect calculations of near-field thermal radiation transfer, including Scattering Matrix method, Finite Difference Time Domain method (FDTD), Wiener Chaos Expansion, Fluctuating Surface Current (FSC), Fluctuating Volume Current (FVC) and Thermal Discrete Dipole Approximations (TDDA).

Effects of distance to care and rural or urban residence on receipt of radiation therapy among North Carolina Medicare enrollees with breast cancer.

PubMed

Wheeler, Stephanie B; Kuo, Tzy-Mey; Durham, Danielle; Frizzelle, Brian; Reeder-Hayes, Katherine; Meyer, Anne-Marie

2014-01-01

Distance to oncology service providers and rurality may affect receipt of guideline-recommended radiation therapy (RT), but the extent to which these factors affect the care of Medicare-insured patients is unknown. Using cancer registry data linked to Medicare claims from the Integrated Cancer Information and Surveillance System (ICISS), we identified all women aged 65 years or older who were diagnosed with stage I, II, or III breast cancer from 2003 through 2005, who had Medicare claims through 2006, and who were clinically eligible for RT. We geocoded the address of each RT service provider's practice location and calculated the travel distance from each patient's residential address to the nearest RT provider. We used ZIP codes to classify each patient's residence as rural or urban according to rural- urban commuting area codes. We used generalized estimating equations models with county-level clustering and interaction terms between distance categories and rural-urban status to estimate the effect of distance to care and rural-urban status on receipt of RT. In urban areas, increasing distance to the nearest RT provider was associated with a lower likelihood of receiving RT (odds ratio [OR] = 0.54; 95% confidence interval [CI], 0.30-0.97) for those living more than 20 miles from the nearest RT provider compared with those living less than 10 miles away. In rural areas, those living within 10-20 miles of the nearest RT provider were more likely to receive RT than those living less than 10 miles away (OR = 1.73; 95% CI, 1.08-2.76). Results may not be generalizable to areas outside North Carolina or to non-Medicare populations. Coordinated outreach programs targeted differently to rural and urban patients may be necessary to improve the quality of oncology care.

Antiretroviral drug resistance and phylogenetic diversity of HIV-1 in Chile.

PubMed

Ríos, Maritza; Delgado, Elena; Pérez-Alvarez, Lucía; Fernández, Jorge; Gálvez, Paula; de Parga, Elena Vázquez; Yung, Verónica; Thomson, Michael M; Nájera, Rafael

2007-06-01

This study reports the analysis of human immunodeficiency virus type 1 (HIV-1) protease (PR) and reverse transcriptase (RT) coding sequences from 136 HIV-1-infected subjects from Chile, 66 (49%) of them under antiretroviral (ARV) treatment. The prevalence of mutations conferring high or intermediate resistance levels to ARVs was 77% among treated patients and 2.5% among drug-naïve subjects. The distribution of resistance prevalence in treated patients by drug class was 61% to nucleoside RT inhibitors, 84% to nonnucleoside RT inhibitors, and 46% to PR inhibitors. Phylogenetic analysis revealed that 115 (85%) subjects were infected with subtype B viruses, 1 with a subtype F1 virus, and 20 (15%) carried BF intersubtype recombinants. Most BF recombinants grouped into two clusters, one related to CRF12_BF, while the other could represent a new circulating recombinant form (CRF). In conclusion, this is the first report analysing the prevalence of ARV resistance which includes patients under HAART from Chile. Additionally, phylogenetic analysis of the PR-RT coding sequences reveals the presence of BF intersubtype recombinants. (c) 2007 Wiley-Liss, Inc.

Muddy Water? Variation in Reporting Receipt of Breast Cancer Radiation Therapy by Population-Based Tumor Registries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walker, Gary V.; Giordano, Sharon H.; Williams, Melanie

2013-07-15

Purpose: To evaluate, in the setting of breast cancer, the accuracy of registry radiation therapy (RT) coding compared with the gold standard of Medicare claims. Methods and Materials: Using Surveillance, Epidemiology, and End Results (SEER)–Medicare data, we identified 73,077 patients aged ≥66 years diagnosed with breast cancer in the period 2001-2007. Underascertainment (1 - sensitivity), sensitivity, specificity, κ, and χ{sup 2} were calculated for RT receipt determined by registry data versus claims. Multivariate logistic regression characterized patient, treatment, and geographic factors associated with underascertainment of RT. Findings in the SEER–Medicare registries were compared with three non-SEER registries (Florida, New York,more » and Texas). Results: In the SEER–Medicare registries, 41.6% (n=30,386) of patients received RT according to registry coding, versus 49.3% (n=36,047) according to Medicare claims (P<.001). Underascertainment of RT was more likely if patients resided in a newer SEER registry (odds ratio [OR] 1.70, 95% confidence interval [CI] 1.60-1.80; P<.001), rural county (OR 1.34, 95% CI 1.21-1.48; P<.001), or if RT was delayed (OR 1.006/day, 95% CI 1.006-1.007; P<.001). Underascertainment of RT receipt in SEER registries was 18.7% (95% CI 18.6-18.8%), compared with 44.3% (95% CI 44.0-44.5%) in non-SEER registries. Conclusions: Population-based tumor registries are highly variable in ascertainment of RT receipt and should be augmented with other data sources when evaluating quality of breast cancer care. Future work should identify opportunities for the radiation oncology community to partner with registries to improve accuracy of treatment data.« less

New techniques for modeling the reliability of reactor pressure vessels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, K.I.; Simonen, F.A.; Liebetrau, A.M.

1986-01-01

In recent years several probabilistic fracture mechanics codes, including the VISA code, have been developed to predict the reliability of reactor pressure vessels. This paper describes several new modeling techniques used in a second generation of the VISA code entitled VISA-II. Results are presented that show the sensitivity of vessel reliability predictions to such factors as inservice inspection to detect flaws, random positioning of flaws within the vessel wall thickness, and fluence distributions that vary throughout the vessel. The algorithms used to implement these modeling techniques are also described. Other new options in VISA-II are also described in this paper.more » The effect of vessel cladding has been included in the heat transfer, stress, and fracture mechanics solutions in VISA-II. The algorithms for simulating flaws has been changed to consider an entire vessel rather than a single flaw in a single weld. The flaw distribution was changed to include the distribution of both flaw depth and length. A menu of several alternate equations has been included to predict the shift in RT/sub NDT/. For flaws that arrest and later re-initiate, an option was also included to allow correlating the current arrest toughness with subsequent initiation toughnesses.« less

Modelling of underwater light fields in turbid and eutrophic waters: application and validation with experimental data

NASA Astrophysics Data System (ADS)

Sundarabalan, B.; Shanmugam, P.

2015-01-01

A reliable radiative transfer (RT) model is an essential and indispensable tool for understanding the radiative transfer processes in homogenous and layered waters, analyzing measurements made by radiance sensors and developing remote-sensing algorithms to derive meaningful physical quantities and biogeochemical variables in turbid and productive coastal waters. Existing radiative transfer models have been designed to be applicable to either homogenous waters or inhomogeneous waters. To overcome such constraints associated with these models, this study presents a radiative transfer model that treats a homogenous layer as a diffuse part and an inhomogeneous layer as a direct part in the water column and combines these two parts appropriately in order to generate more reliable underwater light-field data such as upwelling radiance (Lu), downwelling irradiance (Ed) and upwelling irradiance (Eu). The diffuse model assumes the inherent optical properties (IOPs) to be vertically continuous and the light fields to exponentially decrease with depth, whereas the direct part considers the water column to be vertically inhomogeneous (layer-by-layer phenomena) with the vertically varying phase function. The surface and bottom boundary conditions, source function due to chlorophyll and solar incident geometry are also included in the present RT model. The performance of this model is assessed in a variety of waters (clear, turbid and eutrophic) using the measured radiometric data. The present model shows an advantage in terms of producing accurate Lu, Ed and Eu profiles (in spatial domain) in different waters determined by both homogenous and inhomogeneous conditions. The feasibility of predicting these underwater light fields based on the remotely estimated IOP data is also examined using the present RT model. For this application, vertical profiles of the water constituents and IOPs are estimated by empirical models based on our in situ data. The present RT model generates Lu, Ed and Eu spectra closely consistent with the measured data. These results lead to a conclusion that the present RT model is a viable alternative to existing RT models and has an important implication for remote sensing of optically complex waters.

Using iRT, a normalized retention time for more targeted measurement of peptides

PubMed Central

Escher, Claudia; Reiter, Lukas; MacLean, Brendan; Ossola, Reto; Herzog, Franz; Chilton, John; MacCoss, Michael J.; Rinner, Oliver

2014-01-01

Multiple reaction monitoring (MRM) has recently become the method of choice for targeted quantitative measurement of proteins using mass spectrometry. The method, however, is limited in the number of peptides that can be measured in one run. This number can be markedly increased by scheduling the acquisition if the accurate retention time (RT) of each peptide is known. Here we present iRT, an empirically derived dimensionless peptide-specific value that allows for highly accurate RT prediction. The iRT of a peptide is a fixed number relative to a standard set of reference iRT-peptides that can be transferred across laboratories and chromatographic systems. We show that iRT facilitates the setup of multiplexed experiments with acquisition windows more than 4 times smaller compared to in silico RT predictions resulting in improved quantification accuracy. iRTs can be determined by any laboratory and shared transparently. The iRT concept has been implemented in Skyline, the most widely used software for MRM experiments. PMID:22577012

Nonlinear Transient Problems Using Structure Compatible Heat Transfer Code

NASA Technical Reports Server (NTRS)

Hou, Gene

2000-01-01

The report documents the recent effort to enhance a transient linear heat transfer code so as to solve nonlinear problems. The linear heat transfer code was originally developed by Dr. Kim Bey of NASA Largely and called the Structure-Compatible Heat Transfer (SCHT) code. The report includes four parts. The first part outlines the formulation of the heat transfer problem of concern. The second and the third parts give detailed procedures to construct the nonlinear finite element equations and the required Jacobian matrices for the nonlinear iterative method, Newton-Raphson method. The final part summarizes the results of the numerical experiments on the newly enhanced SCHT code.

RT11LIB: a library of subroutines for transferring data between a PDP-11 and CDC-6600

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, H.D.

1978-01-01

RT11LIB is a library of subroutines available to CDC 6600 users for the purpose of transferring data or program listings between a PDP-11 and a CDC 6600. These subroutines, operating on a CDC 6600 under the NOS/BE or SCOPE 3.4 operating systems, read or write magnetic tapes that are compatible with the PDP-11's RT11 operating system. Data written on the tape by the PDP-11 can be read by these subroutines and then translated into CDC 6600 format for subsequent data analysis. The translation process provides for many data formats, including byte, integer, floating point, and character string formats. Alternatively, datamore » from the CDC 6600 can be translated into PDP-11 format then written onto the tape for subsequent use on the PDP-11. This facility allows a program punched on a card deck by a keypunch operator to be transferred to the PDP-11, even though the PDP-11 is not itself equipped with a card reader.« less

Burner liner thermal/structural load modeling: TRANCITS program user's manual

NASA Technical Reports Server (NTRS)

Maffeo, R.

1985-01-01

Transfer Analysis Code to Interface Thermal/Structural Problems (TRANCITS) is discussed. The TRANCITS code satisfies all the objectives for transferring thermal data between heat transfer and structural models of combustor liners and it can be used as a generic thermal translator between heat transfer and stress models of any component, regardless of the geometry. The TRANCITS can accurately and efficiently convert the temperature distributions predicted by the heat transfer programs to those required by the stress codes. It can be used for both linear and nonlinear structural codes and can produce nodal temperatures, elemental centroid temperatures, or elemental Gauss point temperatures. The thermal output of both the MARC and SINDA heat transfer codes can be interfaced directly with TRANCITS, and it will automatically produce stress model codes formatted for NASTRAN and MARC. Any thermal program and structural program can be interfaced by using the neutral input and output forms supported by TRANCITS.

ARCHER{sub RT} – A GPU-based and photon-electron coupled Monte Carlo dose computing engine for radiation therapy: Software development and application to helical tomotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Su, Lin; Du, Xining; Liu, Tianyu

Purpose: Using the graphical processing units (GPU) hardware technology, an extremely fast Monte Carlo (MC) code ARCHER{sub RT} is developed for radiation dose calculations in radiation therapy. This paper describes the detailed software development and testing for three clinical TomoTherapy® cases: the prostate, lung, and head and neck. Methods: To obtain clinically relevant dose distributions, phase space files (PSFs) created from optimized radiation therapy treatment plan fluence maps were used as the input to ARCHER{sub RT}. Patient-specific phantoms were constructed from patient CT images. Batch simulations were employed to facilitate the time-consuming task of loading large PSFs, and to improvemore » the estimation of statistical uncertainty. Furthermore, two different Woodcock tracking algorithms were implemented and their relative performance was compared. The dose curves of an Elekta accelerator PSF incident on a homogeneous water phantom were benchmarked against DOSXYZnrc. For each of the treatment cases, dose volume histograms and isodose maps were produced from ARCHER{sub RT} and the general-purpose code, GEANT4. The gamma index analysis was performed to evaluate the similarity of voxel doses obtained from these two codes. The hardware accelerators used in this study are one NVIDIA K20 GPU, one NVIDIA K40 GPU, and six NVIDIA M2090 GPUs. In addition, to make a fairer comparison of the CPU and GPU performance, a multithreaded CPU code was developed using OpenMP and tested on an Intel E5-2620 CPU. Results: For the water phantom, the depth dose curve and dose profiles from ARCHER{sub RT} agree well with DOSXYZnrc. For clinical cases, results from ARCHER{sub RT} are compared with those from GEANT4 and good agreement is observed. Gamma index test is performed for voxels whose dose is greater than 10% of maximum dose. For 2%/2mm criteria, the passing rates for the prostate, lung case, and head and neck cases are 99.7%, 98.5%, and 97.2%, respectively. Due to specific architecture of GPU, modified Woodcock tracking algorithm performed inferior to the original one. ARCHER{sub RT} achieves a fast speed for PSF-based dose calculations. With a single M2090 card, the simulations cost about 60, 50, 80 s for three cases, respectively, with the 1% statistical error in the PTV. Using the latest K40 card, the simulations are 1.7–1.8 times faster. More impressively, six M2090 cards could finish the simulations in 8.9–13.4 s. For comparison, the same simulations on Intel E5-2620 (12 hyperthreading) cost about 500–800 s. Conclusions: ARCHER{sub RT} was developed successfully to perform fast and accurate MC dose calculation for radiotherapy using PSFs and patient CT phantoms.« less

NSTX-U Control System Upgrades

DOE PAGES

Erickson, K. G.; Gates, D. A.; Gerhardt, S. P.; ...

2014-06-01

The National Spherical Tokamak Experiment (NSTX) is undergoing a wealth of upgrades (NSTX-U). These upgrades, especially including an elongated pulse length, require broad changes to the control system that has served NSTX well. A new fiber serial Front Panel Data Port input and output (I/O) stream will supersede the aging copper parallel version. Driver support for the new I/O and cyber security concerns require updating the operating system from Redhat Enterprise Linux (RHEL) v4 to RedHawk (based on RHEL) v6. While the basic control system continues to use the General Atomics Plasma Control System (GA PCS), the effort to forwardmore » port the entire software package to run under 64-bit Linux instead of 32-bit Linux included PCS modifications subsequently shared with GA and other PCS users. Software updates focused on three key areas: (1) code modernization through coding standards (C99/C11), (2) code portability and maintainability through use of the GA PCS code generator, and (3) support of 64-bit platforms. Central to the control system upgrade is the use of a complete real time (RT) Linux platform provided by Concurrent Computer Corporation, consisting of a computer (iHawk), an operating system and drivers (RedHawk), and RT tools (NightStar). Strong vendor support coupled with an extensive RT toolset influenced this decision. The new real-time Linux platform, I/O, and software engineering will foster enhanced capability and performance for NSTX-U plasma control.« less

Optical and UV spectroscopy of the peculiar RS CVn system RT Lacertae

NASA Technical Reports Server (NTRS)

Huenemoerder, D. P.; Barden, S. C.

1986-01-01

H-alpha and H-beta spectra of the peculiar double-lined RS CVn binary RT Lacertae have been obtained using the IUE, together with a ground-based coude-feed telescope at KPNO. The ground-based spectra show an asymmetry related to the orbital phase in the H-alpha profile. H-beta profiles showed excess emission in one hemisphere and excess absorption in the other, with a broad Gaussian emission component superposed on the excess H-alpha line. A radial velocity curve was derived to estimate the mass ratio and geometry of the system. It is shown that the component of RT Lac fills 80-90 percent of the equilibrium Roche surface. Low-resolution ultraviolet data show that the supposed cooler component is bluer than its companion, suggesting evidence of a scattering shell or a cloud produced by the splash of a gas stream. The phase behavior of the low resolution ultraviolet data support the conclusion that RT Lac is a mass transfer system and that mass transfer is the primary cause of its activity.

A RT-based Technique for the Analysis and the Removal of Titan's Atmosphere by Cassini/VIMS-IR data

NASA Astrophysics Data System (ADS)

Sindoni, G.; Tosi, F.; Adriani, A.; Moriconi, M. L.; D'Aversa, E.; Grassi, D.; Oliva, F.; Dinelli, B. M.; Castelli, E.

2015-12-01

Since 2004, the Visual and Infrared Mapping Spectrometer (VIMS), together with the CIRS and UVIS spectrometers, aboard the Cassini spacecraft has provided insight on Saturn and Titan atmospheres through remote sensing observations. The presence of clouds and aerosols in Titan's dense atmosphere makes the analysis of the surface radiation a difficult task. For this purpose, an atmospheric radiative transfer (RT) model is required. The implementation of a RT code, which includes multiple scattering, in an inversion algorithm based on the Bayesian approach, can provide strong constraints about both the surface albedo and the atmospheric composition. The application of this retrieval procedure we have developed to VIMS-IR spectra acquired in nadir or slant geometries allows us to retrieve the equivalent opacity of Titan's atmosphere in terms of variable aerosols and gaseous content. Thus, the separation of the atmospheric and surface contributions in the observed spectrum is possible. The atmospheric removal procedure was tested on the spectral range 1-2.2μm of publicly available VIMS data covering the Ontario Lacus and Ligeia Mare regions. The retrieval of the accurate composition of Titan's atmosphere is a much more complex task. So far, the information about the vertical structure of the atmosphere by limb spectra was mostly derived under conditions where the scattering could be neglected [1,2]. Indeed, since the very high aerosol load in the middle-low atmosphere produces strong scattering effects on the measured spectra, the analysis requires a RT modeling taking into account multiple scattering in a spherical-shell geometry. Therefore the use of an innovative method we are developing based on the Monte-Carlo approach, can provide important information about the vertical distribution of the aerosols and the gases composing Titan's atmosphere.[1]Bellucci et al., (2009). Icarus, 201, Issue 1, p. 198-216.[2]de Kok et al., (2007). Icarus, 191, Issue 1, p. 223-235.

Primer development to obtain complete coding sequence of HA and NA genes of influenza A/H3N2 virus.

PubMed

Agustiningsih, Agustiningsih; Trimarsanto, Hidayat; Setiawaty, Vivi; Artika, I Made; Muljono, David Handojo

2016-08-30

Influenza is an acute respiratory illness and has become a serious public health problem worldwide. The need to study the HA and NA genes in influenza A virus is essential since these genes frequently undergo mutations. This study describes the development of primer sets for RT-PCR to obtain complete coding sequence of Hemagglutinin (HA) and Neuraminidase (NA) genes of influenza A/H3N2 virus from Indonesia. The primers were developed based on influenza A/H3N2 sequence worldwide from Global Initiative on Sharing All Influenza Data (GISAID) and further tested using Indonesian influenza A/H3N2 archived samples of influenza-like illness (ILI) surveillance from 2008 to 2009. An optimum RT-PCR condition was acquired for all HA and NA fragments designed to cover complete coding sequence of HA and NA genes. A total of 71 samples were successfully sequenced for complete coding sequence both of HA and NA genes out of 145 samples of influenza A/H3N2 tested. The developed primer sets were suitable for obtaining complete coding sequences of HA and NA genes of Indonesian samples from 2008 to 2009.

Comparison of models for predicting the changes in phytoplankton community composition in the receiving water system of an inter-basin water transfer project.

PubMed

Zeng, Qinghui; Liu, Yi; Zhao, Hongtao; Sun, Mingdong; Li, Xuyong

2017-04-01

Inter-basin water transfer projects might cause complex hydro-chemical and biological variation in the receiving aquatic ecosystems. Whether machine learning models can be used to predict changes in phytoplankton community composition caused by water transfer projects have rarely been studied. In the present study, we used machine learning models to predict the total algal cell densities and changes in phytoplankton community composition in Miyun reservoir caused by the middle route of the South-to-North Water Transfer Project (SNWTP). The model performances of four machine learning models, including regression trees (RT), random forest (RF), support vector machine (SVM), and artificial neural network (ANN) were evaluated and the best model was selected for further prediction. The results showed that the predictive accuracies (Pearson's correlation coefficient) of the models were RF (0.974), ANN (0.951), SVM (0.860), and RT (0.817) in the training step and RF (0.806), ANN (0.734), SVM (0.730), and RT (0.692) in the testing step. Therefore, the RF model was the best method for estimating total algal cell densities. Furthermore, the predicted accuracies of the RF model for dominant phytoplankton phyla (Cyanophyta, Chlorophyta, and Bacillariophyta) in Miyun reservoir ranged from 0.824 to 0.869 in the testing step. The predicted proportions with water transfer of the different phytoplankton phyla ranged from -8.88% to 9.93%, and the predicted dominant phyla with water transfer in each season remained unchanged compared to the phytoplankton succession without water transfer. The results of the present study provide a useful tool for predicting the changes in phytoplankton community caused by water transfer. The method is transferrable to other locations via establishment of models with relevant data to a particular area. Our findings help better understanding the possible changes in aquatic ecosystems influenced by inter-basin water transfer. Copyright © 2017 Elsevier Ltd. All rights reserved.

Using iRT, a normalized retention time for more targeted measurement of peptides.

PubMed

Escher, Claudia; Reiter, Lukas; MacLean, Brendan; Ossola, Reto; Herzog, Franz; Chilton, John; MacCoss, Michael J; Rinner, Oliver

2012-04-01

Multiple reaction monitoring (MRM) has recently become the method of choice for targeted quantitative measurement of proteins using mass spectrometry. The method, however, is limited in the number of peptides that can be measured in one run. This number can be markedly increased by scheduling the acquisition if the accurate retention time (RT) of each peptide is known. Here we present iRT, an empirically derived dimensionless peptide-specific value that allows for highly accurate RT prediction. The iRT of a peptide is a fixed number relative to a standard set of reference iRT-peptides that can be transferred across laboratories and chromatographic systems. We show that iRT facilitates the setup of multiplexed experiments with acquisition windows more than four times smaller compared to in silico RT predictions resulting in improved quantification accuracy. iRTs can be determined by any laboratory and shared transparently. The iRT concept has been implemented in Skyline, the most widely used software for MRM experiments. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Code for Multiblock CFD and Heat-Transfer Computations

NASA Technical Reports Server (NTRS)

Fabian, John C.; Heidmann, James D.; Lucci, Barbara L.; Ameri, Ali A.; Rigby, David L.; Steinthorsson, Erlendur

2006-01-01

The NASA Glenn Research Center General Multi-Block Navier-Stokes Convective Heat Transfer Code, Glenn-HT, has been used extensively to predict heat transfer and fluid flow for a variety of steady gas turbine engine problems. Recently, the Glenn-HT code has been completely rewritten in Fortran 90/95, a more object-oriented language that allows programmers to create code that is more modular and makes more efficient use of data structures. The new implementation takes full advantage of the capabilities of the Fortran 90/95 programming language. As a result, the Glenn-HT code now provides dynamic memory allocation, modular design, and unsteady flow capability. This allows for the heat-transfer analysis of a full turbine stage. The code has been demonstrated for an unsteady inflow condition, and gridding efforts have been initiated for a full turbine stage unsteady calculation. This analysis will be the first to simultaneously include the effects of rotation, blade interaction, film cooling, and tip clearance with recessed tip on turbine heat transfer and cooling performance. Future plans call for the application of the new Glenn-HT code to a range of gas turbine engine problems of current interest to the heat-transfer community. The new unsteady flow capability will allow researchers to predict the effect of unsteady flow phenomena upon the convective heat transfer of turbine blades and vanes. Work will also continue on the development of conjugate heat-transfer capability in the code, where simultaneous solution of convective and conductive heat-transfer domains is accomplished. Finally, advanced turbulence and fluid flow models and automatic gridding techniques are being developed that will be applied to the Glenn-HT code and solution process.

Multiple Scattering in Planetary Regoliths Using Incoherent Interactions

NASA Astrophysics Data System (ADS)

Muinonen, K.; Markkanen, J.; Vaisanen, T.; Penttilä, A.

2017-12-01

We consider scattering of light by a planetary regolith using novel numerical methods for discrete random media of particles. Understanding the scattering process is of key importance for spectroscopic, photometric, and polarimetric modeling of airless planetary objects, including radar studies. In our modeling, the size of the spherical random medium can range from microscopic to macroscopic sizes, whereas the particles are assumed to be of the order of the wavelength in size. We extend the radiative transfer and coherent backscattering method (RT-CB) to the case of dense packing of particles by adopting the ensemble-averaged first-order incoherent extinction, scattering, and absorption characteristics of a volume element of particles as input. In the radiative transfer part, at each absorption and scattering process, we account for absorption with the help of the single-scattering albedo and peel off the Stokes parameters of radiation emerging from the medium in predefined scattering angles. We then generate a new scattering direction using the joint probability density for the local polar and azimuthal scattering angles. In the coherent backscattering part, we utilize amplitude scattering matrices along the radiative-transfer path and the reciprocal path. Furthermore, we replace the far-field interactions of the RT-CB method with rigorous interactions facilitated by the Superposition T-matrix method (STMM). This gives rise to a new RT-RT method, radiative transfer with reciprocal interactions. For microscopic random media, we then compare the new results to asymptotically exact results computed using the STMM, succeeding in the numerical validation of the new methods.Acknowledgments. Research supported by European Research Council with Advanced Grant No. 320773 SAEMPL, Scattering and Absorption of ElectroMagnetic waves in ParticuLate media. Computational resources provided by CSC - IT Centre for Science Ltd, Finland.

Development and validation of a gene profile predicting benefit of postmastectomy radiotherapy in patients with high-risk breast cancer: a study of gene expression in the DBCG82bc cohort.

PubMed

Tramm, Trine; Mohammed, Hayat; Myhre, Simen; Kyndi, Marianne; Alsner, Jan; Børresen-Dale, Anne-Lise; Sørlie, Therese; Frigessi, Arnoldo; Overgaard, Jens

2014-10-15

To identify genes predicting benefit of radiotherapy in patients with high-risk breast cancer treated with systemic therapy and randomized to receive or not receive postmastectomy radiotherapy (PMRT). The study was based on the Danish Breast Cancer Cooperative Group (DBCG82bc) cohort. Gene-expression analysis was performed in a training set of frozen tumor tissue from 191 patients. Genes were identified through the Lasso method with the endpoint being locoregional recurrence (LRR). A weighted gene-expression index (DBCG-RT profile) was calculated and transferred to quantitative real-time PCR (qRT-PCR) in corresponding formalin-fixed, paraffin-embedded (FFPE) samples, before validation in FFPE from 112 additional patients. Seven genes were identified, and the derived DBCG-RT profile divided the 191 patients into "high LRR risk" and "low LRR risk" groups. PMRT significantly reduced risk of LRR in "high LRR risk" patients, whereas "low LRR risk" patients showed no additional reduction in LRR rate. Technical transfer of the DBCG-RT profile to FFPE/qRT-PCR was successful, and the predictive impact was successfully validated in another 112 patients. A DBCG-RT gene profile was identified and validated, identifying patients with very low risk of LRR and no benefit from PMRT. The profile may provide a method to individualize treatment with PMRT. ©2014 American Association for Cancer Research.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Qiang, E-mail: cq0405@126.com; Luoyang Electronic Equipment Testing Center, Luoyang 471000; Chen, Bin, E-mail: emcchen@163.com

The Rayleigh-Taylor (R-T) instabilities are important hydrodynamics and magnetohydrodynamics (MHD) phenomena that are found in systems in high energy density physics and normal fluids. The formation and evolution of the R-T instability at channel boundary during back-flow of the lightning return stroke are analyzed using the linear perturbation theory and normal mode analysis methods, and the linear growth rate of the R-T instability in typical condition for lightning return stroke channel is obtained. Then, the R-T instability phenomena of lightning return stroke are simulated using a two-dimensional Eulerian finite volumes resistive radiation MHD code. The numerical results show that themore » evolution characteristics of the R-T instability in the early stage of back-flow are consistent with theoretical predictions obtained by linear analysis. The simulation also yields more evolution characteristics for the R-T instability beyond the linear theory. The results of this work apply to some observed features of the return stroke channel and further advance previous theoretical and experimental work.« less

A New Model for Real-Time Regional Vertical Total Electron Content and Differential Code Bias Estimation Using IGS Real-Time Service (IGS-RTS) Products

NASA Astrophysics Data System (ADS)

Abdelazeem, Mohamed; Çelik, Rahmi N.; El-Rabbany, Ahmed

2016-04-01

The international global navigation satellite system (GNSS) real-time service (IGS-RTS) products have been used extensively for real-time precise point positioning and ionosphere modeling applications. In this study, we develop a regional model for real-time vertical total electron content (RT-VTEC) and differential code bias (RT-DCB) estimation over Europe using the IGS-RTS satellite orbit and clock products. The developed model has a spatial and temporal resolution of 1°×1° and 15 minutes, respectively. GPS observations from a regional network consisting of 60 IGS and EUREF reference stations are processed in the zero-difference mode using the Bernese-5.2 software package in order to extract the geometry-free linear combination of the smoothed code observations. The spherical harmonic expansion function is used to model the VTEC, the receiver and the satellite DCBs. To validate the proposed model, the RT-VTEC values are computed and compared with the final IGS-global ionospheric map (IGS-GIM) counterparts in three successive days under high solar activity including one of an extreme geomagnetic activity. The real-time satellite DCBs are also estimated and compared with the IGS-GIM counterparts. Moreover, the real-time receiver DCB for six IGS stations are obtained and compared with the IGS-GIM counterparts. The examined stations are located in different latitudes with different receiver types. The findings reveal that the estimated RT-VTEC values show agreement with the IGS-GIM counterparts with root mean-square-errors (RMSEs) values less than 2 TEC units. In addition, RMSEs of both the satellites and receivers DCBs are less than 0.85 ns and 0.65 ns, respectively in comparison with the IGS-GIM.

Modelling of underwater light fields in turbid and eutrophic waters: application and validation with experimental data

NASA Astrophysics Data System (ADS)

Sundarabalan, B.; Shanmugam, P.

2014-09-01

A reliable radiative transfer model is an essential and indispensable tool for understanding of the radiative transfer processes in homogenous and layered waters, analyzing measurements made by radiance sensors and developing remote sensing algorithms to derive meaningful physical quantities and biogeochemical variables in turbid and productive coastal waters. Existing radiative transfer models have been designed to be applicable to either homogenous waters or inhomogeneous waters. To overcome such constraints associated with these models, this study presents a radiative transfer model that treats a homogenous layer as a diffuse part and an inhomogeneous layer as a direct part in the water column and combines these two parts appropriately in order to generate more reliable underwater light field data such as upwelling radiance (Lu), downwelling irradiance (Ed) and upwelling irradiance (Eu). The diffuse model assumes the inherent optical properties (IOPs) to be vertically continuous and the light fields to exponentially decrease with the depth, whereas the direct part considers the water column to be vertically inhomogeneous (layer-by-layer phenomena) with the vertically varying phase function. The surface and bottom boundary conditions, source function due to chlorophyll and solar incident geometry are also included in the present RT model. The performance of this model is assessed in a variety of waters (clear, turbid and eutrophic) using the measured radiometric data. The present model shows an advantage in terms of producing accurate Lu, Ed and Eu profiles (in spatial domain) in different waters determined by both homogenous and inhomogeneous conditions. The feasibility of predicting these underwater light fields based on the remotely estimated IOP data is also examined using the present RT model. For this application, vertical profiles of the water constituents and IOPs are estimated by empirical models based on our in-situ data. The present RT model generates Lu, Ed and Eu spectra closely consistent with the measured data. These results lead to a conclusion that the present RT model is a viable alternative to existing RT models and has an important implication for remote sensing of optically complex waters.

Toxicity Screening of Hydrolyzed H, HD, and HT using the Bioluminescent Marine Bacterium, Vibrio Fischeri, by Means of Microtox Assay

DTIC Science & Technology

2006-01-01

PERFORMING ORGANIZATION REPORT DIR, ECBC, ATTN: AMSRD-ECB-RT- TE /AMSRD-ECB-RT-TV, NUMBER APG, MD 21010-5424 ECBC-TR-460 9. SPONSORING / MONITORING AGENCY...Johnson a. REPORT b. ABSTRACT c . THIS PAGE 19b. TELEPHONE NUMBER (include area code) U U U UL 13 (410) 436-2914 Standard Form 298 (Rev. 8-98) Prescribed...8 4. D ISC USSIO N

[Construction of transgenic tobacco expressing popW and analysis of its biological phenotype].

PubMed

Wang, Cui; Liu, Hongxia; Cao, Jing; Wang, Chao; Guo, Jianhua

2014-04-01

In a previous study, we cloned popW from Ralstonia solanacearum strain ZJ3721, coding PopW, a new harpin protein. The procaryotically expressed PopW can induce resistance to Tobacco mosaic virus (TMV), enhance growth and improve quality of tobacco, when sprayed onto tobacco leaves. Here, we constructed an expression vector pB- popW by cloning popW into the bionary vector pBI121 and transformed it into Agrobacterium tumefaciens strain EHA105 via freeze-thaw method. Tobacco (Nicotiana tobacum cv. Xanthi nc.) transformation was conducted by infection of tobacco leaf discs with recombinant A. tumefaciens. After screening on MS medium containing kanamycin, PCR and RT-PCR analysis, 21 T3 lines were identified as positive transgenic. Genomic intergration and expression of the transferred gene were determined by PCR and RT-PCR. And GUS staining analysis indicated that the protein expressed in transgenic tobacco was bioactive and exhibited different expression levels among lines. Disease bioassays showed that the transgenic tobacco had enhanced resistance to TMV with biocontrol efficiency up to 54.25%. Transgenic tobacco also exhibited enhanced plant growth, the root length of 15 d old seedlings was 1.7 times longer than that of wild type tobacco. 60 d after transplanting to pots, the height, fresh weight and dry weight of transgenic tobacco were 1.4, 1.7, 1.8 times larger than that of wild type tobacco, respectively.

Tests of Exoplanet Atmospheric Radiative Transfer Codes

NASA Astrophysics Data System (ADS)

Harrington, Joseph; Challener, Ryan; DeLarme, Emerson; Cubillos, Patricio; Blecic, Jasmina; Foster, Austin; Garland, Justin

2016-10-01

Atmospheric radiative transfer codes are used both to predict planetary spectra and in retrieval algorithms to interpret data. Observational plans, theoretical models, and scientific results thus depend on the correctness of these calculations. Yet, the calculations are complex and the codes implementing them are often written without modern software-verification techniques. In the process of writing our own code, we became aware of several others with artifacts of unknown origin and even outright errors in their spectra. We present a series of tests to verify atmospheric radiative-transfer codes. These include: simple, single-line line lists that, when combined with delta-function abundance profiles, should produce a broadened line that can be verified easily; isothermal atmospheres that should produce analytically-verifiable blackbody spectra at the input temperatures; and model atmospheres with a range of complexities that can be compared to the output of other codes. We apply the tests to our own code, Bayesian Atmospheric Radiative Transfer (BART) and to several other codes. The test suite is open-source software. We propose this test suite as a standard for verifying current and future radiative transfer codes, analogous to the Held-Suarez test for general circulation models. This work was supported by NASA Planetary Atmospheres grant NX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G.

Propensity-Weighted Comparison of Long-Term Risk of Urinary Adverse Events in Elderly Women Treated For Cervical Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elliott, Sean P., E-mail: selliott@umn.edu; Fan, Yunhua; Jarosek, Stephanie

Purpose: Cervical cancer treatment is associated with a risk of urinary adverse events (UAEs) such as ureteral stricture and vesicovaginal fistula. We sought to measure the long-term UAE risk after surgery and radiation therapy (RT), with confounding controlled through propensity-weighted models. Methods and Materials: From the Surveillance, Epidemiology, and End Results (SEER)-Medicare database, we identified women ≥66 years old with nonmetastatic cervical cancer treated with simple surgery (SS), radical hysterectomy (RH), external beam RT plus brachytherapy (EBRT+BT), or RT+surgery. We matched them to noncancer controls 1:3. Differences in demographic and cancer characteristics were balanced by propensity weighting. Grade 3 tomore » 4 UAEs were identified by diagnosis codes plus treatment codes. Cumulative incidence was measured using Kaplan-Meier methods. The hazard associated with different cancer treatments was compared using Cox models. Results: UAEs occurred in 272 of 1808 cases (17%) and 222 of 5424 (4%) controls; most (62%) were ureteral strictures. The raw cumulative incidence of UAEs was highest in advanced cancers. UAEs occurred in 31% of patients after EBRT+BT, 25% of patients after RT+surgery, and 15% of patients after RH; however, after propensity weighting, the incidence was similar. In adjusted Cox models (reference = controls), the UAE risk was highest after RT+surgery (hazard ratio [HR], 5.07; 95% confidence interval [CI], 2.32-11.07), followed by EBRT+BT (HR, 3.33; 95% CI, 1.45-7.65), RH (HR, 3.65; 95% CI, 1.41-9.46) and SS (HR, 0.99; 95% CI, 0.32-3.01). The higher risk after RT+surgery versus EBRT+BT was statistically significant, whereas, EBRT+BT and RH were not significantly different from each other. Conclusions: UAEs are common after cervical cancer treatment, particularly in patients with advanced cancers. UAEs are more common after RT, but these women tend to have the advanced cancers. After propensity weighting, the risk after RT was similar to that after surgery.« less

Numerical Simulation of Doped Targets for ICF

NASA Astrophysics Data System (ADS)

Phillips, Lee; Gardner, John H.; Bodner, Stephen E.; Colombant, Denis; Klapisch, Marcel; Bar-Shalom, Avraham

1997-11-01

The ablative Rayleigh-Taylor (RT) instability can be reduced by preheating the ablator, thereby reducing the peak density and increasing the mass ablation velocity. The ablator can be preheated with radiation from higher Z dopants.(Gardner, J.H., Bodner, S.E., Dahlburg, J.P., Phys. Fluids 3), 1070 (1991) Dopants also reduce the density gradient at the ablator, which provides a second mechanism to reduce the RT growth rate. We have recently developed a more sophisticated and detailed radiation package that uses opacities generated by an STA code, with non-LTE radiation transport based on the Busquet method. This radiation package has been incorporated into NRL's FAST2D radiation hydrodynamics code, which has been used to evaluate and optimize the use of various dopants that can provide interesting levels of preheat for an ICF target.

Two Perspectives on the Origin of the Standard Genetic Code

NASA Astrophysics Data System (ADS)

Sengupta, Supratim; Aggarwal, Neha; Bandhu, Ashutosh Vishwa

2014-12-01

The origin of a genetic code made it possible to create ordered sequences of amino acids. In this article we provide two perspectives on code origin by carrying out simulations of code-sequence coevolution in finite populations with the aim of examining how the standard genetic code may have evolved from more primitive code(s) encoding a small number of amino acids. We determine the efficacy of the physico-chemical hypothesis of code origin in the absence and presence of horizontal gene transfer (HGT) by allowing a diverse collection of code-sequence sets to compete with each other. We find that in the absence of horizontal gene transfer, natural selection between competing codes distinguished by differences in the degree of physico-chemical optimization is unable to explain the structure of the standard genetic code. However, for certain probabilities of the horizontal transfer events, a universal code emerges having a structure that is consistent with the standard genetic code.

Using RxNorm and NDF-RT to classify medication data extracted from electronic health records: experiences from the Rochester Epidemiology Project.

PubMed

Pathak, Jyotishman; Murphy, Sean P; Willaert, Brian N; Kremers, Hilal M; Yawn, Barbara P; Rocca, Walter A; Chute, Christopher G

2011-01-01

RxNorm and NDF-RT published by the National Library of Medicine (NLM) and Veterans Affairs (VA), respectively, are two publicly available federal medication terminologies. In this study, we evaluate the applicability of RxNorm and National Drug File-Reference Terminology (NDF-RT) for extraction and classification of medication data retrieved using structured querying and natural language processing techniques from electronic health records at two different medical centers within the Rochester Epidemiology Project (REP). Specifically, we explore how mappings between RxNorm concept codes and NDF-RT drug classes can be leveraged for hierarchical organization and grouping of REP medication data, identify gaps and coverage issues, and analyze the recently released NLM's NDF-RT Web service API. Our study concludes that RxNorm and NDF-RT can be applied together for classification of medication extracted from multiple EHR systems, although several issues and challenges remain to be addressed. We further conclude that the Web service APIs developed by the NLM provide useful functionalities for such activities.

Rotational and vibrotational transfer in H*-CO2 collisions: The influence of stereokinematic restrictions

NASA Astrophysics Data System (ADS)

Clare, Suzanne; Marks, Alison J.; McCaffery, Anthony J.

1999-11-01

We describe a quantitative angular momentum (AM) model for predicting rotational transfer (RT) and vibrotational transfer (VRT) in collisions between CO2 and hot H atoms. This molecule is important in several contexts, not least as a bridge between the relative simplicity of diatomic molecules and the complexities of polyatomic RT and VRT. We show that for pure RT, an AM constraint dominates but that this changes to a dominant energetic constraint in the case of VRT. The requirement that the (001) vibrational channel be opened simultaneously with the generation of AM imposes special restrictions which effectively limit the trajectories that lead to VRT. The origin of this is a constraint-induced restriction on the effective impact parameter (bnmax) for individual Δj channels and the effect is manifest as reduced probability for populating low Δj channels. In CO2-H* this leads to a shift in the peak of (VRT) Δj probabilities away from zero as found experimentally for the (001) vibrational mode. We report a Monte Carlo trajectory calculation similar to that of Kreutz and Flynn [J. Chem. Phys. 93, 452 (1990)] but predict an exponential-like dependence of pure RT on Δj. For VRT to (001) the constraint-induced restrictions on bnmax are incorporated quantitatively and the vibrational channel-opening velocity is treated as a vector quantity. The results of these calculations are in good agreement with experiment. The underlying mechanism, likely to be general in VRT, is clearly revealed in plots of relative velocity versus rotational AM change.

Single-pair fluorescence resonance energy transfer analysis of mRNA transcripts for highly sensitive gene expression profiling in near real time.

PubMed

Peng, Zhiyong; Young, Brandon; Baird, Alison E; Soper, Steven A

2013-08-20

Expression analysis of mRNAs transcribed from certain genes can be used as important sources of biomarkers for in vitro diagnostics. While the use of reverse transcription quantitative PCR (RT-qPCR) can provide excellent analytical sensitivity for monitoring transcript numbers, more sensitive approaches for expression analysis that can report results in near real-time are needed for many critical applications. We report a novel assay that can provide exquisite limits-of-quantitation and consists of reverse transcription (RT) followed by a ligase detection reaction (LDR) with single-pair fluorescence resonance energy transfer (spFRET) to provide digital readout through molecular counting. For this assay, no PCR was employed, which enabled short assay turnaround times. To facilitate implementation of the assay, a cyclic olefin copolymer (COC) microchip, which was fabricated using hot embossing, was employed to carry out the LDR in a continuous flow format with online single-molecule detection following the LDR. As demonstrators of the assay's utility, MMP-7 mRNA was expression profiled from several colorectal cancer cell lines. It was found that the RT-LDR/spFRET assay produced highly linear calibration plots even in the low copy number regime. Comparison to RT-qPCR indicated a better linearity over the low copy number range investigated (10-10,000 copies) with an R(2) = 0.9995 for RT-LDR/spFRET and R(2) = 0.98 for RT-qPCR. In addition, differentiating between copy numbers of 10 and 50 could be performed with higher confidence using RT-LDR/spFRET. To demonstrate the short assay turnaround times obtainable using the RT-LDR/spFRET assay, a two thermal cycle LDR was carried out on amphiphysin gene transcripts that can serve as important diagnostic markers for ischemic stroke. The ability to supply diagnostic information on possible stroke events in short turnaround times using RT-LDR/spFRET will enable clinicians to treat patients effectively with appropriate time-sensitive therapeutics.

Racial Disparities in Intravenous Recombinant Tissue Plasminogen Activator Use Persist at Primary Stroke Centers.

PubMed

Aparicio, Hugo J; Carr, Brendan G; Kasner, Scott E; Kallan, Michael J; Albright, Karen C; Kleindorfer, Dawn O; Mullen, Michael T

2015-10-14

Primary stroke centers (PSCs) utilize more recombinant tissue plasminogen activator (rt-PA) than non-PSCs. The impact of PSCs on racial disparities in rt-PA use is unknown. We used data from the Nationwide Inpatient Sample from 2004 to 2010, limited to states that publicly reported hospital identity and race. Hospitals certified as PSCs by The Joint Commission were identified. Adults with a diagnosis of ischemic stroke were analyzed. Rt-PA use was defined by the International Classification of Diseases, 9th Revision procedure code 99.10. Discharges (304 152 patients) from 26 states met eligibility criteria, and of these 71.5% were white, 15.0% black, 7.9% Hispanic, and 5.6% other. Overall, 24.7% of white, 27.4% of black, 16.2% of Hispanic, and 29.8% of other patients presented to PSCs. A higher proportion received rt-PA at PSCs than non-PSCs in all race/ethnic groups (white 7.6% versus 2.6%, black 4.8% versus 2.0%, Hispanic 7.1% versus 2.4%, other 7.2% versus 2.5%, all P<0.001). In a multivariable model adjusting for year, age, sex, insurance, medical comorbidities, a diagnosis-related group-based mortality risk indicator, ZIP code median income, and hospital characteristics, blacks were less likely to receive rt-PA than whites at non-PSCs (odds ratio=0.58, 95% CI 0.50 to 0.67) and PSCs (odds ratio=0.63, 95% CI 0.54 to 0.74) and Hispanics were less likely than whites to receive rt-PA at PSCs (odds ratio=0.77, 95% CI: 0.63 to 0.95). In the fully adjusted model, interaction between race and presentation to a PSC for likelihood of receiving rt-PA did not reach significance (P=0.98). Racial disparities in intravenous rt-PA use were not reduced by presentation to PSCs. Black patients were less likely to receive thrombolytic treatment than white patients at both non-PSCs and PSCs. Hispanic patients were less likely to be seen at PSCs relative to white patients and were less likely to receive intravenous rt-PA in the fully adjusted model. © 2015 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

Burner liner thermal-structural load modeling

NASA Technical Reports Server (NTRS)

Maffeo, R.

1986-01-01

The software package Transfer Analysis Code to Interface Thermal/Structural Problems (TRANCITS) was developed. The TRANCITS code is used to interface temperature data between thermal and structural analytical models. The use of this transfer module allows the heat transfer analyst to select the thermal mesh density and thermal analysis code best suited to solve the thermal problem and gives the same freedoms to the stress analyst, without the efficiency penalties associated with common meshes and the accuracy penalties associated with the manual transfer of thermal data.

Aberrant expression of long noncoding RNAs in cumulus cells isolated from PCOS patients.

PubMed

Huang, Xin; Hao, Cuifang; Bao, Hongchu; Wang, Meimei; Dai, Huangguan

2016-01-01

To describe the long noncoding RNA (lncRNA) profiles in cumulus cells isolated from polycystic ovary syndrome (PCOS) patients by employing a microarray and in-depth bioinformatics analysis. This information will help us understand the occurrence and development of PCOS. In this study, we used a microarray to describe lncRNA profiles in cumulus cells isolated from ten patients (five PCOS and five normal women). Several differentially expressed lncRNAs were chosen to validate the microarray results by quantitative RT-PCR (qRT-PCR). Then, the differentially expressed lncRNAs were classified into three subgroups (HOX loci lncRNA, enhancer-like lncRNA, and lincRNA) to deduce their potential features. Furthermore, a lncRNA/mRNA co-expression network was constructed by using the Cytoscape software (V2.8.3, http://www.cytoscape.org/ ). We observed that 623 lncRNAs and 260 messenger RNAs (mRNAs) were significantly up- or down-regulated (≥2-fold change), and these differences could be used to discriminate cumulus cells of PCOS from those of normal patients. Five differentially expressed lncRNAs (XLOC_011402, ENST00000454271, ENST00000433673, ENST00000450294, and ENST00000432431) were selected to validate the microarray results using quantitative RT-PCR (qRT-PCR). The qRT-PCR results were consistent with the microarray data. Further analysis indicated that many differentially expressed lncRNAs were transcribed from chromosome 2 and may act as enhancers to regulate their neighboring protein-coding genes. Forty-three lncRNAs and 29 mRNAs were used to construct the coding-non-coding gene co-expression network. Most pairs positively correlated, and one mRNA correlated with one or more lncRNAs. Our study is the first to determine genome-wide lncRNA expression patterns in cumulus cells isolated from PCOS patients by microarray. The results show that clusters of lncRNAs were aberrantly expressed in cumulus cells of PCOS patients compared with those of normal women, which revealed that lncRNAs differentially expressed in PCOS and normal women may contribute to the occurrence of PCOS and affect oocyte development.

LeRC-HT: NASA Lewis Research Center General Multiblock Navier-Stokes Heat Transfer Code Developed

NASA Technical Reports Server (NTRS)

Heidmann, James D.; Gaugler, Raymond E.

1999-01-01

For the last several years, LeRC-HT, a three-dimensional computational fluid dynamics (CFD) computer code for analyzing gas turbine flow and convective heat transfer, has been evolving at the NASA Lewis Research Center. The code is unique in its ability to give a highly detailed representation of the flow field very close to solid surfaces. This is necessary for an accurate representation of fluid heat transfer and viscous shear stresses. The code has been used extensively for both internal cooling passage flows and hot gas path flows--including detailed film cooling calculations, complex tip-clearance gap flows, and heat transfer. In its current form, this code has a multiblock grid capability and has been validated for a number of turbine configurations. The code has been developed and used primarily as a research tool (at least 35 technical papers have been published relative to the code and its application), but it should be useful for detailed design analysis. We now plan to make this code available to selected users for further evaluation.

Coherent Backscattering by Particulate Planetary Media of Nonspherical Particles

NASA Astrophysics Data System (ADS)

Muinonen, Karri; Penttila, Antti; Wilkman, Olli; Videen, Gorden

2014-11-01

The so-called radiative-transfer coherent-backscattering method (RT-CB) has been put forward as a practical Monte Carlo method to compute multiple scattering in discrete random media mimicking planetary regoliths (K. Muinonen, Waves in Random Media 14, p. 365, 2004). In RT-CB, the interaction between the discrete scatterers takes place in the far-field approximation and the wave propagation faces exponential extinction. There is a significant constraint in the RT-CB method: it has to be assumed that the form of the scattering matrix is that of the spherical particle. We aim to extend the RT-CB method to nonspherical single particles showing significant depolarization characteristics. First, ensemble-averaged single-scattering albedos and phase matrices of nonspherical particles are matched using a phenomenological radiative-transfer model within a microscopic volume element. Second, the phenomenologial single-particle model is incorporated into the Monte Carlo RT-CB method. In the ray tracing, the electromagnetic phases within the microscopic volume elements are omitted as having negligible lengths, whereas the phases are duly accounted for in the paths between two or more microscopic volume elements. We assess the computational feasibility of the extended RT-CB method and show preliminary results for particulate media mimicking planetary regoliths. The present work can be utilized in the interpretation of astronomical observations of asteroids and other planetary objects. In particular, the work sheds light on the depolarization characteristics of planetary regoliths at small phase angles near opposition. The research has been partially funded by the ERC Advanced Grant No 320773 entitled “Scattering and Absorption of Electromagnetic Waves in Particulate Media” (SAEMPL), by the Academy of Finland (contract 257966), NASA Outer Planets Research Program (contract NNX10AP93G), and NASA Lunar Advanced Science and Exploration Research Program (contract NNX11AB25G).

Bio-Optics of the Chesapeake Bay from Measurements and Radiative Transfer Calculations

NASA Technical Reports Server (NTRS)

Tzortziou, Maria; Herman, Jay R.; Gallegos, Charles L.; Neale, Patrick J.; Subramaniam, Ajit; Harding, Lawrence W., Jr.; Ahmad, Ziauddin

2005-01-01

We combined detailed bio-optical measurements and radiative transfer (RT) modeling to perform an optical closure experiment for optically complex and biologically productive Chesapeake Bay waters. We used this experiment to evaluate certain assumptions commonly used when modeling bio-optical processes, and to investigate the relative importance of several optical characteristics needed to accurately model and interpret remote sensing ocean-color observations in these Case 2 waters. Direct measurements were made of the magnitude, variability, and spectral characteristics of backscattering and absorption that are critical for accurate parameterizations in satellite bio-optical algorithms and underwater RT simulations. We found that the ratio of backscattering to total scattering in the mid-mesohaline Chesapeake Bay varied considerably depending on particulate loading, distance from land, and mixing processes, and had an average value of 0.0128 at 530 nm. Incorporating information on the magnitude, variability, and spectral characteristics of particulate backscattering into the RT model, rather than using a volume scattering function commonly assumed for turbid waters, was critical to obtaining agreement between RT calculations and measured radiometric quantities. In situ measurements of absorption coefficients need to be corrected for systematic overestimation due to scattering errors, and this correction commonly employs the assumption that absorption by particulate matter at near infrared wavelengths is zero.

Structure and expression of MHC class Ib genes of the central M region in rat and mouse: M4, M5, and M6.

PubMed

Lambracht-Washington, Doris; Moore, Yuki F; Wonigeit, Kurt; Lindahl, Kirsten Fischer

2008-04-01

The M region at the telomeric end of the murine major histocompatibility complex (MHC) contains class I genes that are highly conserved in rat and mouse. We have sequenced a cosmid clone of the LEW rat strain (RT1 haplotype) containing three class I genes, RT1.M6-1, RT1.M4, and RT1.M5. The sequences of allelic genes of the BN strain (RT1n haplotype) were obtained either from cDNAs or genomic clones. For the coding parts of the genes few differences were found between the two RT1 haplotypes. In LEW, however, only RT1.M5 and RT1.M6 have open reading frames; whereas in BN all three genes were intact. In line with the findings in BN, transcription was found for all three rat genes in several tissues from strain Sprague Dawley. Protein expression in transfectants could be demonstrated for RT1.M6-1 using the monoclonal antibody OX18. By sequencing of transcripts obtained by RT-PCR, a second, transcribed M6 gene, RT1.M6-2, was discovered, which maps next to RT1.M6-1 outside of the region covered by the cosmid. In addition, alternatively spliced forms for RT1.M5 and RT1.M6 were detected. Of the orthologous mouse genes, H2-M4, H2-M5, and H2-M6, only H2-M5 has an open reading frame. Other important differences between the corresponding parts of the M region of the two species are insertion of long LINE repeats, duplication of RT1.M6, and the inversion of RT1.M5 in the rat. This demonstrates substantial evolutionary dynamics in this region despite conservation of the class I gene sequences themselves.

Novel Codon Insert in HIV Type 1 Clade B Reverse Transcriptase Associated with Low-Level Viremia During Antiretroviral Therapy

PubMed Central

Gianella, Sara; Vazquez, Homero; Ignacio, Caroline; Zweig, Adam C.; Richman, Douglas D.; Smith, Davey M.

2014-01-01

Abstract We investigated the pol genotype in two phylogenetically and epidemiologically linked partners, who were both experiencing persistent low-level viremia during antiretroviral therapy. In one partner we identified a new residue insertion between codon 248 and 249 of the HIV-1 RNA reverse transcriptase (RT) coding region (HXB2 numbering). We then investigated the potential impact of identified mutations in RT and antiretroviral binding affinity using a novel computational approach. PMID:24020934

A generalized one-dimensional computer code for turbomachinery cooling passage flow calculations

NASA Technical Reports Server (NTRS)

Kumar, Ganesh N.; Roelke, Richard J.; Meitner, Peter L.

1989-01-01

A generalized one-dimensional computer code for analyzing the flow and heat transfer in the turbomachinery cooling passages was developed. This code is capable of handling rotating cooling passages with turbulators, 180 degree turns, pin fins, finned passages, by-pass flows, tip cap impingement flows, and flow branching. The code is an extension of a one-dimensional code developed by P. Meitner. In the subject code, correlations for both heat transfer coefficient and pressure loss computations were developed to model each of the above mentioned type of coolant passages. The code has the capability of independently computing the friction factor and heat transfer coefficient on each side of a rectangular passage. Either the mass flow at the inlet to the channel or the exit plane pressure can be specified. For a specified inlet total temperature, inlet total pressure, and exit static pressure, the code computers the flow rates through the main branch and the subbranches, flow through tip cap for impingement cooling, in addition to computing the coolant pressure, temperature, and heat transfer coefficient distribution in each coolant flow branch. Predictions from the subject code for both nonrotating and rotating passages agree well with experimental data. The code was used to analyze the cooling passage of a research cooled radial rotor.

Retrieval of land parameters by multi-sensor information using the Earth Observation Land Data Assimilation System

NASA Astrophysics Data System (ADS)

Chernetskiy, Maxim; Gobron, Nadine; Gomez-Dans, Jose; Disney, Mathias

2016-07-01

Upcoming satellite constellations will substantially increase the amount of Earth Observation (EO) data, and presents us with the challenge of consistently using all these available information to infer the state of the land surface, parameterised through Essential Climate Variables (ECVs). A promising approach to this problem is the use of physically based models that describe the processes that generate the images, using e.g. radiative transfer (RT) theory. However, these models need to be inverted to infer the land surface parameters from the observations, and there is often not enough information in the EO data to satisfactorily achieve this. Data assimilation (DA) approaches supplement the EO data with prior information in the form of models or prior parameter distributions, and have the potential for solving the inversion problem. These methods however are computationally expensive. In this study, we show the use of fast surrogate models of the RT codes (emulators) based on Gaussian Processes (Gomez-Dans et al, 2016) embedded with the Earth Observation Land Data Assimilation System (EO-LDAS) framework (Lewis et al 2012) in order to estimate the surface of the land surface from a heterogeneous set of optical observations. The study uses time series of moderate spatial resolution observations from MODIS (250 m), MERIS (300 m) and MISR (275 m) over one site to infer the temporal evolution of a number of land surface parameters (and associated uncertainties) related to vegetation: leaf area index (LAI), leaf chlorophyll content, etc. These parameter estimates are then used as input to an RT model (semidiscrete or PROSAIL, for example) to calculate fluxes such as broad band albedo or fAPAR. The study demonstrates that blending different sensors in a consistent way using physical models results in a rich and coherent set of land surface parameters retrieved, with quantified uncertainties. The use of RT models also allows for the consistent prediction of fluxes, with a simple mechanism for propagating the uncertainty in the land surface parameters to the flux estimates.

Transfer Function Bounds for Partial-unit-memory Convolutional Codes Based on Reduced State Diagram

NASA Technical Reports Server (NTRS)

Lee, P. J.

1984-01-01

The performance of a coding system consisting of a convolutional encoder and a Viterbi decoder is analytically found by the well-known transfer function bounding technique. For the partial-unit-memory byte-oriented convolutional encoder with m sub 0 binary memory cells and (k sub 0 m sub 0) inputs, a state diagram of 2(K) (sub 0) was for the transfer function bound. A reduced state diagram of (2 (m sub 0) +1) is used for easy evaluation of transfer function bounds for partial-unit-memory codes.

Development and evaluation of tailored specific real-time RT-PCR assays for detection of foot-and-mouth disease virus serotypes circulating in East Africa.

PubMed

Bachanek-Bankowska, Katarzyna; Mero, Herieth R; Wadsworth, Jemma; Mioulet, Valerie; Sallu, Raphael; Belsham, Graham J; Kasanga, Christopher J; Knowles, Nick J; King, Donald P

2016-11-01

Rapid, reliable and accurate diagnostic methods provide essential support to programmes that monitor and control foot-and-mouth disease (FMD). While pan-specific molecular tests for FMD virus (FMDV) detection are well established and widely used in endemic and FMD-free countries, current serotyping methods mainly rely either on antigen detection ELISAs or nucleotide sequencing approaches. This report describes the development of a panel of serotype-specific real-time RT-PCR assays (rRT-PCR) tailored to detect FMDV lineages currently circulating in East Africa. These assays target sequences within the VP1-coding region that share high intra-lineage identity, but do not cross-react with FMD viruses from other serotypes that circulate in the region. These serotype-specific assays operate with the same thermal profile as the pan-diagnostic tests making it possible to run them in parallel to produce C T values comparable to the pan-diagnostic test detecting the 3D-coding region. These assays were evaluated alongside the established pan-specific molecular test using field samples and virus isolates collected from Tanzania, Kenya and Ethiopia that had been previously characterised by nucleotide sequencing. Samples (n=71) representing serotype A (topotype AFRICA, lineage G-I), serotype O (topotypes EA-2 and EA-4), serotype SAT 1 (topotype I (NWZ)) and serotype SAT2 (topotype IV) were correctly identified with these rRT-PCR assays. Furthermore, FMDV RNA from samples that did not contain infectious virus could still be serotyped using these assays. These serotype-specific real-time RT-PCR assays can detect and characterise FMDVs currently circulating in East Africa and hence improve disease control in this region. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Task-set inertia and memory-consolidation bottleneck in dual tasks.

PubMed

Koch, Iring; Rumiati, Raffaella I

2006-11-01

Three dual-task experiments examined the influence of processing a briefly presented visual object for deferred verbal report on performance in an unrelated auditory-manual reaction time (RT) task. RT was increased at short stimulus-onset asynchronies (SOAs) relative to long SOAs, showing that memory consolidation processes can produce a functional processing bottleneck in dual-task performance. In addition, the experiments manipulated the spatial compatibility of the orientation of the visual object and the side of the speeded manual response. This cross-task compatibility produced relative RT benefits only when the instruction for the visual task emphasized overlap at the level of response codes across the task sets (Experiment 1). However, once the effective task set was in place, it continued to produce cross-task compatibility effects even in single-task situations ("ignore" trials in Experiment 2) and when instructions for the visual task did not explicitly require spatial coding of object orientation (Experiment 3). Taken together, the data suggest a considerable degree of task-set inertia in dual-task performance, which is also reinforced by finding costs of switching task sequences (e.g., AC --> BC vs. BC --> BC) in Experiment 3.

Lessons Learned from Numerical Simulations of Interfacial Instabilities

NASA Astrophysics Data System (ADS)

Cook, Andrew

2015-11-01

Rayleigh-Taylor (RT), Richtmyer-Meshkov (RM) and Kelvin-Helmholtz (KH) instabilities serve as efficient mixing mechanisms in a wide variety of flows, from supernovae to jet engines. Over the past decade, we have used the Miranda code to temporally integrate the multi-component Navier-Stokes equations at spatial resolutions up to 29 billion grid points. The code employs 10th-order compact schemes for spatial derivatives, combined with 4th-order Runge-Kutta time advancement. Some of our major findings are as follows: The rate of growth of a mixing layer is equivalent to the net mass flux through the equi-molar plane. RT growth rates can be significantly reduced by adding shear. RT instability can produce shock waves. The growth rate of RM instability can be predicted from known interfacial perturbations. RM vortex projectiles can far outrun the mixing region. Thermal fluctuations in molecular dynamics simulations can seed instabilities along the braids in KH instability. And finally, enthalpy diffusion is essential in preserving the second law of thermodynamics. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Antimicrobial peptide gene expression in periodontitis patients: A pilot study.

PubMed

Jourdain, Marie-Laure; Pierrard, Loïc; Kanagaratnam, Lukshe; Velard, Frédéric; Sergheraert, Johan; Lefèvre, Benoît; Gangloff, Sophie C; Braux, Julien

2018-05-01

Antimicrobial peptides (AMPs) are one of the most active components of innate immunity and have characteristics that could place them at the heart of the pathogenesis of periodontal disease. This study investigated differences in the expression of AMP coding genes obtained using a simple harvesting technique, gingival smear, between two groups of patients: chronic periodontitis subjects versus healthy ones. Twenty-three patients were enrolled in two groups: 12 were diagnosed with moderate or severe generalized chronic periodontitis, and 11 were diagnosed as clinically healthy. Gingival smears were retrieved and studied using reverse transcription-quantitative PCR (RT-qPCR) after mRNA purification. Fifteen gene expressions were obtained using real-time RT-qPCR. Three AMP genes, histatin 3 (HTN3), α-defensin 4 (DEFA4) and lysozyme C (LYZ), presented different expression levels in periodontitis patients compared with healthy subjects. The relative expression level of DEFA4 appeared to be a protective factor against periodontitis. Gingival smears studied by RT-qPCR may be used to assess the expression of AMPs coding genes. A lack of expression of DEFA4 could be a potential indicator of periodontitis status. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Glenn-HT: The NASA Glenn Research Center General Multi-Block Navier-Stokes Heat Transfer Code

NASA Technical Reports Server (NTRS)

Gaugler, Raymond E.; Lee, Chi-Miag (Technical Monitor)

2001-01-01

For the last several years, Glenn-HT, a three-dimensional (3D) Computational Fluid Dynamics (CFD) computer code for the analysis of gas turbine flow and convective heat transfer has been evolving at the NASA Glenn Research Center. The code is unique in the ability to give a highly detailed representation of the flow field very close to solid surfaces in order to get accurate representation of fluid heat transfer and viscous shear stresses. The code has been validated and used extensively for both internal cooling passage flow and for hot gas path flows, including detailed film cooling calculations and complex tip clearance gap flow and heat transfer. In its current form, this code has a multiblock grid capability and has been validated for a number of turbine configurations. The code has been developed and used primarily as a research tool, but it can be useful for detailed design analysis. In this paper, the code is described and examples of its validation and use for complex flow calculations are presented, emphasizing the applicability to turbomachinery for space launch vehicle propulsion systems.

Glenn-HT: The NASA Glenn Research Center General Multi-Block Navier-Stokes Heat Transfer Code

NASA Technical Reports Server (NTRS)

Gaugfer, Raymond E.

2002-01-01

For the last several years, Glenn-HT, a three-dimensional (3D) Computational Fluid Dynamics (CFD) computer code for the analysis of gas turbine flow and convective heat transfer has been evolving at the NASA Glenn Research Center. The code is unique in the ability to give a highly detailed representation of the flow field very close to solid surfaces in order to get accurate representation of fluid heat transfer and viscous shear stresses. The code has been validated and used extensively for both internal cooling passage flow and for hot gas path flows, including detailed film cooling calculations and complex tip clearance gap flow and heat transfer. In its current form, this code has a multiblock grid capability and has been validated for a number of turbine configurations. The code has been developed and used primarily as a research tool, but it can be useful for detailed design analysis. In this presentation, the code is described and examples of its validation and use for complex flow calculations are presented, emphasizing the applicability to turbomachinery.

Glenn-HT: The NASA Glenn Research Center General Multi-Block Navier Stokes Heat Transfer Code

NASA Technical Reports Server (NTRS)

Gaugler, Raymond E.

2002-01-01

For the last several years, Glenn-HT, a three-dimensional (3D) Computational Fluid Dynamics (CFD) computer code for the analysis of gas turbine flow and convective heat transfer has been evolving at the NASA Glenn Research Center. The code is unique in the ability to give a highly detailed representation of the flow field very close to solid surfaces in order to get accurate representation of fluid beat transfer and viscous shear stresses. The code has been validated and used extensively for both internal cooling passage flow and for hot gas path flows, including detailed film cooling calculations and complex tip clearance gap flow and heat transfer. In its current form, this code has a multiblock grid capability and has been validated for a number of turbine configurations. The code has been developed and used primarily as a research tool, but it can be useful for detailed design analysis. In this presentation, the code is described and examples of its validation and use for complex flow calculations are presented, emphasizing the applicability to turbomachinery.

Mass transfer effects in a gasification riser

DOE Office of Scientific and Technical Information (OSTI.GOV)

Breault, Ronald W.; Li, Tingwen; Nicoletti, Phillip

2013-07-01

In the development of multiphase reacting computational fluid dynamics (CFD) codes, a number of simplifications were incorporated into the codes and models. One of these simplifications was the use of a simplistic mass transfer correlation for the faster reactions and omission of mass transfer effects completely on the moderate speed and slow speed reactions such as those in a fluidized bed gasifier. Another problem that has propagated is that the mass transfer correlation used in the codes is not universal and is being used far from its developed bubbling fluidized bed regime when applied to circulating fluidized bed (CFB) risermore » reactors. These problems are true for the major CFD codes. To alleviate this problem, a mechanistic based mass transfer coefficient algorithm has been developed based upon an earlier work by Breault et al. This fundamental approach uses the local hydrodynamics to predict a local, time varying mass transfer coefficient. The predicted mass transfer coefficients and the corresponding Sherwood numbers agree well with literature data and are typically about an order of magnitude lower than the correlation noted above. The incorporation of the new mass transfer model gives the expected behavior for all the gasification reactions evaluated in the paper. At the expected and typical design values for the solid flow rate in a CFB riser gasifier an ANOVA analysis has shown the predictions from the new code to be significantly different from the original code predictions. The new algorithm should be used such that the conversions are not over predicted. Additionally, its behaviors with changes in solid flow rate are consistent with the changes in the hydrodynamics.« less

FILM-30: A Heat Transfer Properties Code for Water Coolant

DOE Office of Scientific and Technical Information (OSTI.GOV)

MARSHALL, THERON D.

2001-02-01

A FORTRAN computer code has been written to calculate the heat transfer properties at the wetted perimeter of a coolant channel when provided the bulk water conditions. This computer code is titled FILM-30 and the code calculates its heat transfer properties by using the following correlations: (1) Sieder-Tate: forced convection, (2) Bergles-Rohsenow: onset to nucleate boiling, (3) Bergles-Rohsenow: partially developed nucleate boiling, (4) Araki: fully developed nucleate boiling, (5) Tong-75: critical heat flux (CHF), and (6) Marshall-98: transition boiling. FILM-30 produces output files that provide the heat flux and heat transfer coefficient at the wetted perimeter as a function ofmore » temperature. To validate FILM-30, the calculated heat transfer properties were used in finite element analyses to predict internal temperatures for a water-cooled copper mockup under one-sided heating from a rastered electron beam. These predicted temperatures were compared with the measured temperatures from the author's 1994 and 1998 heat transfer experiments. There was excellent agreement between the predicted and experimentally measured temperatures, which confirmed the accuracy of FILM-30 within the experimental range of the tests. FILM-30 can accurately predict the CHF and transition boiling regimes, which is an important advantage over current heat transfer codes. Consequently, FILM-30 is ideal for predicting heat transfer properties for applications that feature high heat fluxes produced by one-sided heating.« less

Validated reverse transcription droplet digital PCR serves as a higher order method for absolute quantification of Potato virus Y strains.

PubMed

Mehle, Nataša; Dobnik, David; Ravnikar, Maja; Pompe Novak, Maruša

2018-05-03

RNA viruses have a great potential for high genetic variability and rapid evolution that is generated by mutation and recombination under selection pressure. This is also the case of Potato virus Y (PVY), which comprises a high diversity of different recombinant and non-recombinant strains. Consequently, it is hard to develop reverse transcription real-time quantitative PCR (RT-qPCR) with the same amplification efficiencies for all PVY strains which would enable their equilibrate quantification; this is specially needed in mixed infections and other studies of pathogenesis. To achieve this, we initially transferred the PVY universal RT-qPCR assay to a reverse transcription droplet digital PCR (RT-ddPCR) format. RT-ddPCR is an absolute quantification method, where a calibration curve is not needed, and it is less prone to inhibitors. The RT-ddPCR developed and validated in this study achieved a dynamic range of quantification over five orders of magnitude, and in terms of its sensitivity, it was comparable to, or even better than, RT-qPCR. RT-ddPCR showed lower measurement variability. We have shown that RT-ddPCR can be used as a reference tool for the evaluation of different RT-qPCR assays. In addition, it can be used for quantification of RNA based on in-house reference materials that can then be used as calibrators in diagnostic laboratories.

The natural emergence of the correlation between H2 and star formation rate surface densities in galaxy simulations

NASA Astrophysics Data System (ADS)

Lupi, Alessandro; Bovino, Stefano; Capelo, Pedro R.; Volonteri, Marta; Silk, Joseph

2018-03-01

In this study, we present a suite of high-resolution numerical simulations of an isolated galaxy to test a sub-grid framework to consistently follow the formation and dissociation of H2 with non-equilibrium chemistry. The latter is solved via the package KROME, coupled to the mesh-less hydrodynamic code GIZMO. We include the effect of star formation (SF), modelled with a physically motivated prescription independent of H2, supernova feedback and mass-losses from low-mass stars, extragalactic and local stellar radiation, and dust and H2 shielding, to investigate the emergence of the observed correlation between H2 and SF rate surface densities. We present two different sub-grid models and compare them with on-the-fly radiative transfer (RT) calculations, to assess the main differences and limits of the different approaches. We also discuss a sub-grid clumping factor model to enhance the H2 formation, consistent with our SF prescription, which is crucial, at the achieved resolution, to reproduce the correlation with H2. We find that both sub-grid models perform very well relative to the RT simulation, giving comparable results, with moderate differences, but at much lower computational cost. We also find that, while the Kennicutt-Schmidt relation for the total gas is not strongly affected by the different ingredients included in the simulations, the H2-based counterpart is much more sensitive, because of the crucial role played by the dissociating radiative flux and the gas shielding.

Utilizing Low-Volume Aqueous Acoustic Transfer with the Echo 525 to Enable Miniaturization of qRT-PCR Assay.

PubMed

Agrawal, Sony; Cifelli, Steven; Johnstone, Richard; Pechter, David; Barbey, Deborah A; Lin, Karen; Allison, Tim; Agrawal, Shree; Rivera-Gines, Aida; Milligan, James A; Schneeweis, Jonathan; Houle, Kevin; Struck, Alice J; Visconti, Richard; Sills, Matthew; Wildey, Mary Jo

2016-02-01

Quantitative reverse transcription PCR (qRT-PCR) is a valuable tool for characterizing the effects of inhibitors on viral replication. The amplification of target viral genes through the use of specifically designed fluorescent probes and primers provides a reliable method for quantifying RNA. Due to reagent costs, use of these assays for compound evaluation is limited. Until recently, the inability to accurately dispense low volumes of qRT-PCR assay reagents precluded the routine use of this PCR assay for compound evaluation in drug discovery. Acoustic dispensing has become an integral part of drug discovery during the past decade; however, acoustic transfer of microliter volumes of aqueous reagents was time consuming. The Labcyte Echo 525 liquid handler was designed to enable rapid aqueous transfers. We compared the accuracy and precision of a qPCR assay using the Labcyte Echo 525 to those of the BioMek FX, a traditional liquid handler, with the goal of reducing the volume and cost of the assay. The data show that the Echo 525 provides higher accuracy and precision compared to the current process using a traditional liquid handler. Comparable data for assay volumes from 500 nL to 12 µL allowed the miniaturization of the assay, resulting in significant cost savings of drug discovery and process streamlining. © 2015 Society for Laboratory Automation and Screening.

Modelling the light-scattering properties of a planetary-regolith analog sample

NASA Astrophysics Data System (ADS)

Vaisanen, T.; Markkanen, J.; Hadamcik, E.; Levasseur-Regourd, A. C.; Lasue, J.; Blum, J.; Penttila, A.; Muinonen, K.

2017-12-01

Solving the scattering properties of asteroid surfaces can be made cheaper, faster, and more accurate with reliable physics-based electromagnetic scattering programs for large and dense random media. Existing exact methods fail to produce solutions for such large systems and it is essential to develop approximate methods. Radiative transfer (RT) is an approximate method which works for sparse random media such as atmospheres fails when applied to dense media. In order to make the method applicable to dense media, we have developed a radiative-transfer coherent-backscattering method (RT-CB) with incoherent interactions. To show the current progress with the RT-CB, we have modeled a planetary-regolith analog sample. The analog sample is a low-density agglomerate produced by random ballistic deposition of almost equisized silicate spheres studied using the PROGRA2-surf experiment. The scattering properties were then computed with the RT-CB assuming that the silicate spheres were equisized and that there were a Gaussian particle size distribution. The results were then compared to the measured data and the intensity plot is shown below. The phase functions are normalized to unity at the 40-deg phase angle. The tentative intensity modeling shows good match with the measured data, whereas the polarization modeling shows discrepancies. In summary, the current RT-CB modeling is promising, but more work needs to be carried out, in particular, for modeling the polarization. Acknowledgments. Research supported by European Research Council with Advanced Grant No. 320773 SAEMPL, Scattering and Absorption of ElectroMagnetic waves in ParticuLate media. Computational resources provided by CSC - IT Centre for Science Ltd, Finland.

Towards Improved Radiative Transfer Simulations of Hyperspectral Measurements for Cloudy Atmospheres

NASA Astrophysics Data System (ADS)

Natraj, V.; Li, C.; Aumann, H. H.; Yung, Y. L.

2016-12-01

Usage of hyperspectral measurements in the infrared for weather forecasting requires radiative transfer (RT) models that can accurately compute radiances given the atmospheric state. On the other hand, it is necessary for the RT models to be fast enough to meet operational processing processing requirements. Until recently, this has proven to be a very hard challenge. In the last decade, however, significant progress has been made in this regard, due to computer speed increases, and improved and optimized RT models. This presentation will introduce a new technique, based on principal component analysis (PCA) of the inherent optical properties (such as profiles of trace gas absorption and single scattering albedo), to perform fast and accurate hyperspectral RT calculations in clear or cloudy atmospheres. PCA is a technique to compress data while capturing most of the variability in the data. By performing PCA on the optical properties, we limit the number of computationally expensive multiple scattering RT calculations to the PCA-reduced data set, and develop a series of PC-based correction factors to obtain the hyperspectral radiances. This technique has been showed to deliver accuracies of 0.1% of better with respect to brute force, line-by-line (LBL) models such as LBLRTM and DISORT, but is orders of magnitude faster than the LBL models. We will compare the performance of this method against other models on a large atmospheric state data set (7377 profiles) that includes a wide range of thermodynamic and cloud profiles, along with viewing geometry and surface emissivity information. 2016. All rights reserved.

Direct Linearization and Adjoint Approaches to Evaluation of Atmospheric Weighting Functions and Surface Partial Derivatives: General Principles, Synergy and Areas of Application

NASA Technical Reports Server (NTRS)

Ustino, Eugene A.

2006-01-01

This slide presentation reviews the observable radiances as functions of atmospheric parameters and of surface parameters; the mathematics of atmospheric weighting functions (WFs) and surface partial derivatives (PDs) are presented; and the equation of the forward radiative transfer (RT) problem is presented. For non-scattering atmospheres this can be done analytically, and all WFs and PDs can be computed analytically using the direct linearization approach. For scattering atmospheres, in general case, the solution of the forward RT problem can be obtained only numerically, but we need only two numerical solutions: one of the forward RT problem and one of the adjoint RT problem to compute all WFs and PDs we can think of. In this presentation we discuss applications of both the linearization and adjoint approaches

Assessment of 3D cloud radiative transfer effects applied to collocated A-Train data

NASA Astrophysics Data System (ADS)

Okata, M.; Nakajima, T.; Suzuki, K.; Toshiro, I.; Nakajima, T. Y.; Okamoto, H.

2017-12-01

This study investigates broadband radiative fluxes in the 3D cloud-laden atmospheres using a 3D radiative transfer (RT) model, MCstar, and the collocated A-Train cloud data. The 3D extinction coefficients are constructed by a newly devised Minimum cloud Information Deviation Profiling Method (MIDPM) that extrapolates CPR radar profiles at nadir into off-nadir regions within MODIS swath based on collocated information of MODIS-derived cloud properties and radar reflectivity profiles. The method is applied to low level maritime water clouds, for which the 3D-RT simulations are performed. The radiative fluxes thus simulated are compared to those obtained from CERES as a way to validate the MIDPM-constructed clouds and our 3D-RT simulations. The results show that the simulated SW flux agrees with CERES values within 8 - 50 Wm-2. One of the large biases occurred by cyclic boundary condition that was required to pose into our computational domain limited to 20km by 20km with 1km resolution. Another source of the bias also arises from the 1D assumption for cloud property retrievals particularly for thin clouds, which tend to be affected by spatial heterogeneity leading to overestimate of the cloud optical thickness. These 3D-RT simulations also serve to address another objective of this study, i.e. to characterize the "observed" specific 3D-RT effects by the cloud morphology. We extend the computational domain to 100km by 100km for this purpose. The 3D-RT effects are characterized by errors of existing 1D approximations to 3D radiation field. The errors are investigated in terms of their dependence on solar zenith angle (SZA) for the satellite-constructed real cloud cases, and we define two indices from the error tendencies. According to the indices, the 3D-RT effects are classified into three types which correspond to different simple three morphologies types, i.e. isolated cloud type, upper cloud-roughened type and lower cloud-roughened type. These 3D-RT effects linked to cloud morphologies are also visualized in the form of the RGB composite maps constructed from MODIS/Aqua three channels, which show cloud optical thickness and cloud height information. Such a classification offers a novel insight into 3D-RT effect in a manner that directly relates to cloud morphology.

Earth Sciences Push Radiative Transfer Theory

NASA Astrophysics Data System (ADS)

Davis, Anthony; Mishchenko, Michael

2009-12-01

2009 International Conference on Advances in Mathematics, Computational Methods, and Reactor Physics; Saratoga Springs, New York, 4-7 May 2009; The theories of radiative transfer and particle—particularly neutron—transport are grounded in distinctive microscale physics that deals with either optics or particle dynamics. However, it is not practical to track every wave or particle in macroscopic systems, nor do all of these details matter. That is why Newton's laws, which describe individual particles, are replaced by those of Euler, Navier-Stokes, Maxwell, Boltzmann, Gibbs, and others, which describe the collective behavior of vast numbers of particles. And that is why the radiative transfer (RT) equation is used to describe the flow of radiation through geophysical-scale systems, leaving to Maxwell's wave equations only the task of providing the optical properties of the medium, be it air, water, snow, ice, or biomass. Interestingly, particle transport is determined by the linear transport equation, which is mathematically identical to the RT equation, so geophysicists and nuclear scientists are interested in the same mathematics and computational techniques.

Tools for Management of Chlorinated Solvent - Contaminated Sites

DTIC Science & Technology

2009-12-03

Equations coded into  RT3D reaction module   Spreadsheet as series of  CSTRs ● Model assumes No NAPL present   ( , , , )ij i I S i j i M MD v M F C...ER‐0623 ● Mechanics  MnO4 transport and consumption  Based on series of  CSTRs  NOD kinetics  identical to RT3D  Includes cost estimating tool to

Terrestrial solar spectral modeling. [SOLTRAN, BRITE, and FLASH codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bird, R.E.

The utility of accurate computer codes for calculating the solar spectral irradiance under various atmospheric conditions was recognized. New absorption and extraterrestrial spectral data are introduced. Progress is made in radiative transfer modeling outside of the solar community, especially for space and military applications. Three rigorous radiative transfer codes SOLTRAN, BRITE, and FLASH are employed. The SOLTRAN and BRITE codes are described and results from their use are presented.

TIME-DEPENDENT MULTI-GROUP MULTI-DIMENSIONAL RELATIVISTIC RADIATIVE TRANSFER CODE BASED ON SPHERICAL HARMONIC DISCRETE ORDINATE METHOD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tominaga, Nozomu; Shibata, Sanshiro; Blinnikov, Sergei I., E-mail: tominaga@konan-u.ac.jp, E-mail: sshibata@post.kek.jp, E-mail: Sergei.Blinnikov@itep.ru

We develop a time-dependent, multi-group, multi-dimensional relativistic radiative transfer code, which is required to numerically investigate radiation from relativistic fluids that are involved in, e.g., gamma-ray bursts and active galactic nuclei. The code is based on the spherical harmonic discrete ordinate method (SHDOM) which evaluates a source function including anisotropic scattering in spherical harmonics and implicitly solves the static radiative transfer equation with ray tracing in discrete ordinates. We implement treatments of time dependence, multi-frequency bins, Lorentz transformation, and elastic Thomson and inelastic Compton scattering to the publicly available SHDOM code. Our code adopts a mixed-frame approach; the source functionmore » is evaluated in the comoving frame, whereas the radiative transfer equation is solved in the laboratory frame. This implementation is validated using various test problems and comparisons with the results from a relativistic Monte Carlo code. These validations confirm that the code correctly calculates the intensity and its evolution in the computational domain. The code enables us to obtain an Eddington tensor that relates the first and third moments of intensity (energy density and radiation pressure) and is frequently used as a closure relation in radiation hydrodynamics calculations.« less

Geographic Disparity in the Use of Hypofractionated Radiation Therapy Among Elderly Women Undergoing Breast Conservation for Invasive Breast Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gillespie, Erin F.; Matsuno, Rayna K.; Xu, Beibei

Purpose: To evaluate geographic heterogeneity in the delivery of hypofractionated radiation therapy (RT) for breast cancer among Medicare beneficiaries across the United States. Methods and Materials: We identified 190,193 patients from the Centers for Medicare and Medicaid Services Chronic Conditions Warehouse. The study included patients aged >65 years diagnosed with invasive breast cancer treated with breast conservation surgery followed by radiation diagnosed between 2000 and 2012. We analyzed data by hospital referral region based on patient residency ZIP code. The proportion of women who received hypofractionated RT within each region was analyzed over the study period. Multivariable logistic regression models identified predictors ofmore » hypofractionated RT. Results: Over the entire study period we found substantial geographic heterogeneity in the use of hypofractionated RT. The proportion of women receiving hypofractionated breast RT in individual hospital referral regions varied from 0% to 61%. We found no correlation between the use of hypofractionated RT and urban/rural setting or general geographic region. The proportion of hypofractionated RT increased in regions with higher density of radiation oncologists, as well as lower total Medicare reimbursements. Conclusions: This study demonstrates substantial geographic heterogeneity in the use of hypofractionated RT among elderly women with invasive breast cancer treated with lumpectomy in the United States. This heterogeneity persists despite clinical data from multiple randomized trials proving efficacy and safety compared with standard fractionation, and highlights possible inefficiency in health care delivery.« less

Numerical calculations of non-inductive current driven by microwaves in JET

NASA Astrophysics Data System (ADS)

Kirov, K. K.; Baranov, Yu; Mailloux, J.; Nave, M. F. F.; Contributors, JET

2016-12-01

Recent studies at JET focus on analysis of the lower hybrid (LH) wave power absorption and current drive (CD) calculations by means of a new ray tracing (RT)/Fokker-Planck (FP) package. The RT code works in real 2D geometry accounting for the plasma boundary and the launcher shape. LH waves with different parallel refractive index, {{N}\\parallel} , spectra in poloidal direction can be launched thus simulating authentic antenna spectrum with rows fed by different combinations of klystrons. Various FP solvers were tested most advanced of which is a relativistic bounce averaged FP code. LH wave power deposition profiles from the new RT/FP code were compared to the experimental results from electron cyclotron emission (ECE) analysis of pulses at 3.4 T low and high density. This kind of direct comparison between power deposition profiles from experimental ECE data and numerical model were carried out for the first time for waves in the LH range of frequencies. The results were in a reasonable agreement with experimental data at lower density, line averaged values of {{n}\\text{e}}≈ 2.4× {{10}19} {{\\text{m}}-3} . At higher density, {{n}\\text{e}}≈ 3× {{10}19} {{\\text{m}}-3} , the code predicted larger on-axis LH power deposition, which is inconsistent with the experimental observations. Both calculations were unable to produce LH wave absorption at the plasma periphery, which contradicts to the analysis of the ECE data and possible sources of these discrepancies have been briefly discussed in the paper. The code was also used to calculate the LH power deposition and CD profiles for the low-density preheat phase of JET’s advanced tokamak (AT) scenario. It was found that as the density evolves from hollow to flat and then to a more peaked profile the LH power and driven current move inward i.e. towards the plasma axis. A total driven current of about 70 kA for 1 MW of launched LH power was predicted in these conditions.

WetLab-2: Providing Quantitative PCR Capabilities on ISS

NASA Technical Reports Server (NTRS)

Parra, Macarena; Jung, Jimmy Kar Chuen; Almeida, Eduardo; Boone, Travis David; Schonfeld, Julie; Tran, Luan Hoang

2015-01-01

The objective of NASA Ames Research Centers WetLab-2 Project is to place on the ISS a system capable of conducting gene expression analysis via quantitative real-time PCR (qRT-PCR) of biological specimens sampled or cultured on orbit. The WetLab-2 system is capable of processing sample types ranging from microbial cultures to animal tissues dissected on-orbit. The project has developed a RNA preparation module that can lyse cells and extract RNA of sufficient quality and quantity for use as templates in qRT-PCR reactions. Our protocol has the advantage that it uses non-toxic chemicals, alcohols or other organics. The resulting RNA is transferred into a pipette and then dispensed into reaction tubes that contain all lyophilized reagents needed to perform qRT-PCR reactions. These reaction tubes are mounted on rotors to centrifuge the liquid to the reaction window of the tube using a cordless drill. System operations require simple and limited crew actions including syringe pushes, valve turns and pipette dispenses. The resulting process takes less than 30 min to have tubes ready for loading into the qRT-PCR unit.The project has selected a Commercial-Off-The-Shelf (COTS) qRT-PCR unit, the Cepheid SmartCycler, that will fly in its COTS configuration. The SmartCycler has a number of advantages including modular design (16 independent PCR modules), low power consumption, rapid thermal ramp times and four-color detection. The ability to detect up to four fluorescent channels will enable multiplex assays that can be used to normalize for RNA concentration and integrity, and to study multiple genes of interest in each module. The WetLab-2 system will have the capability to downlink data from the ISS to the ground after a completed run and to uplink new programs. The ability to conduct qRT-PCR on-orbit eliminates the confounding effects on gene expression of reentry stresses and shock acting on live cells and organisms or the concern of RNA degradation of fixed samples. The system can be used to validate terrestrial analyses of samples returned from ISS by providing on-orbit gene expression benchmarking prior to sample return. The ability to get on-orbit data will provide investigators with the opportunity to adjust experimental parameters in real time for subsequent trials, without the need for sample return and re-flight to sample multigenerational changes. The system can also be used for analysis of air, surface, water, and clinical samples to monitor environmental contaminants and crew health. The verification flight of the instrument is scheduled to launch on SpaceX-7 in June 2015. The WetLab-2 Project is supported by NASAs ISS Program at JSC, Code OZ.

TORUS: Radiation transport and hydrodynamics code

NASA Astrophysics Data System (ADS)

Harries, Tim

2014-04-01

TORUS is a flexible radiation transfer and radiation-hydrodynamics code. The code has a basic infrastructure that includes the AMR mesh scheme that is used by several physics modules including atomic line transfer in a moving medium, molecular line transfer, photoionization, radiation hydrodynamics and radiative equilibrium. TORUS is useful for a variety of problems, including magnetospheric accretion onto T Tauri stars, spiral nebulae around Wolf-Rayet stars, discs around Herbig AeBe stars, structured winds of O supergiants and Raman-scattered line formation in symbiotic binaries, and dust emission and molecular line formation in star forming clusters. The code is written in Fortran 2003 and is compiled using a standard Gnu makefile. The code is parallelized using both MPI and OMP, and can use these parallel sections either separately or in a hybrid mode.

The power of integration: radiotherapy and global palliative care.

PubMed

Rodin, Danielle; Grover, Surbhi; Elmore, Shekinah N; Knaul, Felicia M; Atun, Rifat; Caulley, Lisa; Herrera, Cristian A; Jones, Joshua A; Price, Aryeh J; Munshi, Anusheel; Gandhi, Ajeet K; Shah, Chiman; Gospodarowicz, Mary

2016-07-01

Radiotherapy (RT) is a powerful tool for the palliation of the symptoms of advanced cancer, although access to it is limited or absent in many low- and middle-income countries (LMICs). There are multiple factors contributing to this, including assumptions about the economic feasibility of RT in LMICs, the logical challenges of building capacity to deliver it in those regions, and the lack of political support to drive change of this kind. It is encouraging that the problem of RT access has begun to be included in the global discourse on cancer control and that palliative care and RT have been incorporated into national cancer control plans in some LMICs. Further, RT twinning programs involving high- and low-resource settings have been established to improve knowledge transfer and exchange. However, without large-scale action, the consequences of limited access to RT in LMICs will become dire. The number of new cancer cases around the world is expected to double by 2030, with twice as many deaths occurring in LMICs as in high-income countries (HICs). A sustained and coordinated effort involving research, education, and advocacy is required to engage global institutions, universities, health care providers, policymakers, and private industry in the urgent need to build RT capacity and delivery in LMICs.

Cross-domain expression recognition based on sparse coding and transfer learning

NASA Astrophysics Data System (ADS)

Yang, Yong; Zhang, Weiyi; Huang, Yong

2017-05-01

Traditional facial expression recognition methods usually assume that the training set and the test set are independent and identically distributed. However, in actual expression recognition applications, the conditions of independent and identical distribution are hardly satisfied for the training set and test set because of the difference of light, shade, race and so on. In order to solve this problem and improve the performance of expression recognition in the actual applications, a novel method based on transfer learning and sparse coding is applied to facial expression recognition. First of all, a common primitive model, that is, the dictionary is learnt. Then, based on the idea of transfer learning, the learned primitive pattern is transferred to facial expression and the corresponding feature representation is obtained by sparse coding. The experimental results in CK +, JAFFE and NVIE database shows that the transfer learning based on sparse coding method can effectively improve the expression recognition rate in the cross-domain expression recognition task and is suitable for the practical facial expression recognition applications.

Generic detection of poleroviruses using an RT-PCR assay targeting the RdRp coding sequence.

PubMed

Lotos, Leonidas; Efthimiou, Konstantinos; Maliogka, Varvara I; Katis, Nikolaos I

2014-03-01

In this study a two-step RT-PCR assay was developed for the generic detection of poleroviruses. The RdRp coding region was selected as the primers' target, since it differs significantly from that of other members in the family Luteoviridae and its sequence can be more informative than other regions in the viral genome. Species specific RT-PCR assays targeting the same region were also developed for the detection of the six most widespread poleroviral species (Beet mild yellowing virus, Beet western yellows virus, Cucurbit aphid-borne virus, Carrot red leaf virus, Potato leafroll virus and Turnip yellows virus) in Greece and the collection of isolates. These isolates along with other characterized ones were used for the evaluation of the generic PCR's detection range. The developed assay efficiently amplified a 593bp RdRp fragment from 46 isolates of 10 different Polerovirus species. Phylogenetic analysis using the generic PCR's amplicon sequence showed that although it cannot accurately infer evolutionary relationships within the genus it can differentiate poleroviruses at the species level. Overall, the described generic assay could be applied for the reliable detection of Polerovirus infections and, in combination with the specific PCRs, for the identification of new and uncharacterized species in the genus. Copyright © 2013 Elsevier B.V. All rights reserved.

Radiative transfer code SHARM for atmospheric and terrestrial applications

NASA Astrophysics Data System (ADS)

Lyapustin, A. I.

2005-12-01

An overview of the publicly available radiative transfer Spherical Harmonics code (SHARM) is presented. SHARM is a rigorous code, as accurate as the Discrete Ordinate Radiative Transfer (DISORT) code, yet faster. It performs simultaneous calculations for different solar zenith angles, view zenith angles, and view azimuths and allows the user to make multiwavelength calculations in one run. The Δ-M method is implemented for calculations with highly anisotropic phase functions. Rayleigh scattering is automatically included as a function of wavelength, surface elevation, and the selected vertical profile of one of the standard atmospheric models. The current version of the SHARM code does not explicitly include atmospheric gaseous absorption, which should be provided by the user. The SHARM code has several built-in models of the bidirectional reflectance of land and wind-ruffled water surfaces that are most widely used in research and satellite data processing. A modification of the SHARM code with the built-in Mie algorithm designed for calculations with spherical aerosols is also described.

Radiative transfer code SHARM for atmospheric and terrestrial applications.

PubMed

Lyapustin, A I

2005-12-20

An overview of the publicly available radiative transfer Spherical Harmonics code (SHARM) is presented. SHARM is a rigorous code, as accurate as the Discrete Ordinate Radiative Transfer (DISORT) code, yet faster. It performs simultaneous calculations for different solar zenith angles, view zenith angles, and view azimuths and allows the user to make multiwavelength calculations in one run. The Delta-M method is implemented for calculations with highly anisotropic phase functions. Rayleigh scattering is automatically included as a function of wavelength, surface elevation, and the selected vertical profile of one of the standard atmospheric models. The current version of the SHARM code does not explicitly include atmospheric gaseous absorption, which should be provided by the user. The SHARM code has several built-in models of the bidirectional reflectance of land and wind-ruffled water surfaces that are most widely used in research and satellite data processing. A modification of the SHARM code with the built-in Mie algorithm designed for calculations with spherical aerosols is also described.

Cognitive and Neural Sciences Division 1990 Programs

DTIC Science & Technology

1990-08-01

operator skill acquisition for advanced manufacturing environments. In (W. Karawowski and M. Rahimi, Eds.) Ergonomics of Advanced Manufacturing and...PRINCIPAL INVESTIGATOR: John H. Maunsell University of Rochester Strong School of Medicine and Dentistry (716) 275-2076 R&T PROJECT CODE: 4424242 CONTRACT

Radiative transfer model of snow for bare ice regions

NASA Astrophysics Data System (ADS)

Tanikawa, T.; Aoki, T.; Niwano, M.; Hosaka, M.; Shimada, R.; Hori, M.; Yamaguchi, S.

2016-12-01

Modeling a radiative transfer (RT) for coupled atmosphere-snow-bare ice systems is of fundamental importance for remote sensing applications to monitor snow and bare ice regions in the Greenland ice sheet and for accurate climate change predictions by regional and global climate models. Recently, the RT model for atmosphere-snow system was implemented for our regional and global climate models. However, the bare ice region where recently it has been expanded on the Greenland ice sheet due to the global warming, has not been implemented for these models, implying that this region leads miscalculations in these climate models. Thus, the RT model of snow for bare ice regions is needed for accurate climate change predictions. We developed the RT model for coupled atmosphere-snow-bare ice systems, and conducted a sensitivity analysis of the RT model to know the effect of snow, bare ice and geometry parameters on the spectral radiant quantities. The RT model considers snow and bare-ice inherent optical properties (IOPs), including snow grain size, air bubble size and its concentration and bare ice thickness. The conventional light scattering theory, Mie theory, was used for IOP calculations. Monte Carlo method was used for the multiple scattering. The sensitivity analyses showed that spectral albedo for the bare ice increased with increasing the concentration of the air bubble in the bare ice for visible wavelengths because the air bubble is scatterer with no absorption. For near infrared wavelengths, spectral albedo has no dependence on the air bubble due to the strong light absorption by ice. When increasing solar zenith angle, the spectral albedo were increased for all wavelengths. This is the similar trend with spectral snow albedo. Cloud cover influenced the bare ice spectral albedo by covering direct radiation into diffuse radiation. The purely diffuse radiation has an effective solar zenith angle near 50°. Converting direct into diffuse radiation reduces the effective solar zenith angle, resulting in reducing the spectral albedo. This is also the similar trend with spectral snow albedo. Further work should focus on the validation of the RT model using in situ measurement data through field and laboratory experiments.

Interfacility Transfers to General Pediatric Floors: A Qualitative Study Exploring the Role of Communication.

PubMed

Rosenthal, Jennifer L; Okumura, Megumi J; Hernandez, Lenore; Li, Su-Ting T; Rehm, Roberta S

2016-01-01

Children with special health care needs often require health services that are only provided at subspecialty centers. Such children who present to nonspecialty hospitals might require a hospital-to-hospital transfer. When transitioning between medical settings, communication is an integral aspect that can affect the quality of patient care. The objectives of the study were to identify barriers and facilitators to effective interfacility pediatric transfer communication to general pediatric floors from the perspectives of referring and accepting physicians, and then develop a conceptual model for effective interfacility transfer communication. This was a single-center qualitative study using grounded theory methodology. Referring and accepting physicians of children with special health care needs were interviewed. Four researchers coded the data using ATLAS.ti (version 7, Scientific Software Development GMBH, Berlin, Germany), using a 2-step process of open coding, followed by focused coding until no new codes emerged. The research team reached consensus on the final major categories and subsequently developed a conceptual model. Eight referring and 9 accepting physicians were interviewed. Theoretical coding resulted in 3 major categories: streamlined transfer process, quality handoff and 2-way communication, and positive relationships between physicians across facilities. The conceptual model unites these categories and shows how these categories contribute to effective interfacility transfer communication. Proposed interventions involved standardizing the communication process and incorporating technology such as telemedicine during transfers. Communication is perceived to be an integral component of interfacility transfers. We recommend that transfer systems be re-engineered to make the process more streamlined, to improve the quality of the handoff and 2-way communication, and to facilitate positive relationships between physicians across facilities. Copyright © 2016 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.

Incorporation of Condensation Heat Transfer in a Flow Network Code

NASA Technical Reports Server (NTRS)

Anthony, Miranda; Majumdar, Alok; McConnaughey, Paul K. (Technical Monitor)

2001-01-01

In this paper we have investigated the condensation of water vapor in a short tube. A numerical model of condensation heat transfer was incorporated in a flow network code. The flow network code that we have used in this paper is Generalized Fluid System Simulation Program (GFSSP). GFSSP is a finite volume based flow network code. Four different condensation models were presented in the paper. Soliman's correlation has been found to be the most stable in low flow rates which is of particular interest in this application. Another highlight of this investigation is conjugate or coupled heat transfer between solid or fluid. This work was done in support of NASA's International Space Station program.

A Pan-Lyssavirus Taqman Real-Time RT-PCR Assay for the Detection of Highly Variable Rabies virus and Other Lyssaviruses

PubMed Central

Wadhwa, Ashutosh; Wilkins, Kimberly; Gao, Jinxin; Condori Condori, Rene Edgar; Gigante, Crystal M.; Zhao, Hui; Ma, Xiaoyue; Ellison, James A.; Greenberg, Lauren; Velasco-Villa, Andres; Orciari, Lillian

2017-01-01

Rabies, resulting from infection by Rabies virus (RABV) and related lyssaviruses, is one of the most deadly zoonotic diseases and is responsible for up to 70,000 estimated human deaths worldwide each year. Rapid and accurate laboratory diagnosis of rabies is essential for timely administration of post-exposure prophylaxis in humans and control of the disease in animals. Currently, only the direct fluorescent antibody (DFA) test is recommended for routine rabies diagnosis. Reverse-transcription polymerase chain reaction (RT-PCR) based diagnostic methods have been widely adapted for the diagnosis of other viral pathogens, but there is currently no widely accepted rapid real-time RT-PCR assay for the detection of all lyssaviruses. In this study, we demonstrate the validation of a newly developed multiplex real-time RT-PCR assay named LN34, which uses a combination of degenerate primers and probes along with probe modifications to achieve superior coverage of the Lyssavirus genus while maintaining sensitivity and specificity. The primers and probes of the LN34 assay target the highly conserved non-coding leader region and part of the nucleoprotein (N) coding sequence of the Lyssavirus genome to maintain assay robustness. The probes were further modified by locked nucleotides to increase their melting temperature to meet the requirements for an optimal real-time RT-PCR assay. The LN34 assay was able to detect all RABV variants and other lyssaviruses in a validation panel that included representative RABV isolates from most regions of the world as well as representatives of 13 additional Lyssavirus species. The LN34 assay was successfully used for both ante-mortem and post-mortem diagnosis of over 200 clinical samples as well as field derived surveillance samples. This assay represents a major improvement over previously published rabies specific RT-PCR and real-time RT-PCR assays because of its ability to universally detect RABV and other lyssaviruses, its high throughput capability and its simplicity of use, which can be quickly adapted in a laboratory to enhance the capacity of rabies molecular diagnostics. The LN34 assay provides an alternative approach for rabies diagnostics, especially in rural areas and rabies endemic regions that lack the conditions and broad experience required to run the standard DFA assay. PMID:28081126

A Pan-Lyssavirus Taqman Real-Time RT-PCR Assay for the Detection of Highly Variable Rabies virus and Other Lyssaviruses.

PubMed

Wadhwa, Ashutosh; Wilkins, Kimberly; Gao, Jinxin; Condori Condori, Rene Edgar; Gigante, Crystal M; Zhao, Hui; Ma, Xiaoyue; Ellison, James A; Greenberg, Lauren; Velasco-Villa, Andres; Orciari, Lillian; Li, Yu

2017-01-01

Rabies, resulting from infection by Rabies virus (RABV) and related lyssaviruses, is one of the most deadly zoonotic diseases and is responsible for up to 70,000 estimated human deaths worldwide each year. Rapid and accurate laboratory diagnosis of rabies is essential for timely administration of post-exposure prophylaxis in humans and control of the disease in animals. Currently, only the direct fluorescent antibody (DFA) test is recommended for routine rabies diagnosis. Reverse-transcription polymerase chain reaction (RT-PCR) based diagnostic methods have been widely adapted for the diagnosis of other viral pathogens, but there is currently no widely accepted rapid real-time RT-PCR assay for the detection of all lyssaviruses. In this study, we demonstrate the validation of a newly developed multiplex real-time RT-PCR assay named LN34, which uses a combination of degenerate primers and probes along with probe modifications to achieve superior coverage of the Lyssavirus genus while maintaining sensitivity and specificity. The primers and probes of the LN34 assay target the highly conserved non-coding leader region and part of the nucleoprotein (N) coding sequence of the Lyssavirus genome to maintain assay robustness. The probes were further modified by locked nucleotides to increase their melting temperature to meet the requirements for an optimal real-time RT-PCR assay. The LN34 assay was able to detect all RABV variants and other lyssaviruses in a validation panel that included representative RABV isolates from most regions of the world as well as representatives of 13 additional Lyssavirus species. The LN34 assay was successfully used for both ante-mortem and post-mortem diagnosis of over 200 clinical samples as well as field derived surveillance samples. This assay represents a major improvement over previously published rabies specific RT-PCR and real-time RT-PCR assays because of its ability to universally detect RABV and other lyssaviruses, its high throughput capability and its simplicity of use, which can be quickly adapted in a laboratory to enhance the capacity of rabies molecular diagnostics. The LN34 assay provides an alternative approach for rabies diagnostics, especially in rural areas and rabies endemic regions that lack the conditions and broad experience required to run the standard DFA assay.

New Radiative Transfer Capability in the EPIC Atmospheric Model with Application to Saturn and Uranus

NASA Astrophysics Data System (ADS)

Dowling, Timothy Edward; Greathouse, T. K.; Sussman, M. G.; Chanover, N. J.

2010-10-01

We have adapted radiative transfer (RT) schemes from the gas-giant seasonal models of Greathouse et al. (EGU 2010) and Sussman et al. (AGU 2009) into the EPIC atmospheric model, and applied them to Saturn and Uranus. These additions give EPIC a hierarchy of RT options to account for solar heating via CH4 absorption from 5 microns to the UV, and radiative cooling due to thermal emission of CH4, C2H2, C2H6, and collision-induced opacity between 0 and 1600 cm-1. We have written an IDL tool to calculate radiative-equilibrium T(p) profiles for model initialization. We have ported the versatile DISORT RT model (Stamnes et al. 1988) from Fortran to C, and are incorporating it into an IDL post-processing tool to allow us to create synthetic spectra from EPIC output that accounts for thermal emission, reflected solar light, and aerosol and Rayleigh scattering. We give an update of applications to simulations of middle-atmosphere temperatures for Saturn and zonal-wind spin-up experiments for Uranus. This research is supported by NASA Planetary Atmospheres grant NNX08AE64G and NSF Planetary Astronomy grant AST-0807989.

Launching nurse-initiated HIV rapid testing in Veterans Affairs primary care: a comprehensive overview of a self-sustaining implementation.

PubMed

Knapp, H; Anaya, H D; Feld, J E; Hoang, T; Goetz, M B

2011-12-01

Our objectives were to use foundational pilot findings to guide the implementation of an HIV rapid testing (RT) intervention at one Veterans Affairs outpatient clinic and to evaluate the success and sustainability of this intervention over the course of one year. Policy modifications were drafted and adopted to enable nurses to order, administer, interpret and document HIV RTs. Staff enrolled in a two-part training sessions designed to teach pre- and post-test counselling techniques and the mechanics of administering, interpreting and coding test results in the patients' medical records. They were subsequently evaluated on their efforts at: (1) increasing HIV RT, (2) sustaining this effort one year post-launch. Enabling nurses to carry out HIV RT resulted in a significant increase in not only HIV RT, but also HIV testing rates overall at this facility, measured over the first year of this implementation. Our findings indicate that targeted strategies, aimed at increasing HIV RT rates, worked to increase testing rates overall, and also, that our initial testing strategies were independently sustainable, which is in contrast to findings in the literature on implementation science.

A tumor-promoting mechanism mediated by retrotransposon-encoded reverse transcriptase is active in human transformed cell lines

PubMed Central

Sciamanna, Ilaria; Gualtieri, Alberto; Cossetti, Cristina; Osimo, Emanuele Felice; Ferracin, Manuela; Macchia, Gianfranco; Aricò, Eleonora; Prosseda, Gianni; Vitullo, Patrizia; Misteli, Tom; Spadafora, Corrado

2013-01-01

LINE-1 elements make up the most abundant retrotransposon family in the human genome. Full-length LINE-1 elements encode a reverse transcriptase (RT) activity required for their own retrotranpsosition as well as that of non-autonomous Alu elements. LINE-1 are poorly expressed in normal cells and abundantly in cancer cells. Decreasing RT activity in cancer cells, by either LINE-1-specific RNA interference, or by RT inhibitory drugs, was previously found to reduce proliferation and promote differentiation and to antagonize tumor growth in animal models. Here we have investigated how RT exerts these global regulatory functions. We report that the RT inhibitor efavirenz (EFV) selectively downregulates proliferation of transformed cell lines, while exerting only mild effects on non-transformed cells; this differential sensitivity matches a differential RT abundance, which is high in the former and undetectable in the latter. Using CsCl density gradients, we selectively identify Alu and LINE-1 containing DNA:RNA hybrid molecules in cancer but not in normal cells. Remarkably, hybrid molecules fail to form in tumor cells treated with EFV under the same conditions that repress proliferation and induce the reprogramming of expression profiles of coding genes, microRNAs (miRNAs) and ultraconserved regions (UCRs). The RT-sensitive miRNAs and UCRs are significantly associated with Alu sequences. The results suggest that LINE-1-encoded RT governs the balance between single-stranded and double-stranded RNA production. In cancer cells the abundant RT reverse-transcribes retroelement-derived mRNAs forming RNA:DNA hybrids. We propose that this impairs the formation of double-stranded RNAs and the ensuing production of small regulatory RNAs, with a direct impact on gene expression. RT inhibition restores the ‘normal’ small RNA profile and the regulatory networks that depend on them. Thus, the retrotransposon-encoded RT drives a previously unrecognized mechanism crucial to the transformed state in tumor cells. PMID:24345856

Experimental Products Development Team (EPDT) Supporting New AWIPS . Part 2; Capabilities

NASA Technical Reports Server (NTRS)

Burks, Jason E.

2015-01-01

In 2012, the Experimental Products Development Team (EPDT) was formed within NASA's Short-term Prediction Research and Transition (SPoRT) Center to create training for development of plug-ins to extend the National Weather Service (NWS) Advanced Weather Interactive Processing System (AWIPS) version 2. The broader atmospheric science community had a need for AWIPS II development training being created at SPoRT and EPDT was expanded to include other groups who were looking for training. Since the expansion of the group occurred, EPDT has provided AWIPS II development training to over thirty participants spanning a wide variety of groups such as NWS Systems Engineering Center, NWS Meteorological Development Laboratory, and several NOAA Cooperative Institutes. Participants within EPDT solidify their learning experience through hands-on learning and by participating in a "code-sprint" in which they troubleshoot existing and develop plug-ins. The hands-on learning workshop is instructor lead with participants completing exercises within the AWIPS II Development Environment. During the code sprints EPDT groups work on projects important to the community and have worked on various plug-ins such as an RGB image recipe creation tool, and an mPing (crowd sourced precipitation type reporting system) ingest and display. EPDT has developed a well-defined training regime which prepares participants to fully develop plug-ins for the extendible AWIPS II architecture from ingest to the display of new data. SPoRT has hosted 2 learning workshops and 1 code sprint over the last two years, and continues to build and shape the EPDT group based on feedback from previous workshops. The presentation will provide an overview of EPDT current and future activities, and best practices developed within EPDT.

Multiple scattering in planetary regoliths using first-order incoherent interactions

NASA Astrophysics Data System (ADS)

Muinonen, Karri; Markkanen, Johannes; Väisänen, Timo; Penttilä, Antti

2017-10-01

We consider scattering of light by a planetary regolith modeled using discrete random media of spherical particles. The size of the random medium can range from microscopic sizes of a few wavelengths to macroscopic sizes approaching infinity. The size of the particles is assumed to be of the order of the wavelength. We extend the numerical Monte Carlo method of radiative transfer and coherent backscattering (RT-CB) to the case of dense packing of particles. We adopt the ensemble-averaged first-order incoherent extinction, scattering, and absorption characteristics of a volume element of particles as input for the RT-CB. The volume element must be larger than the wavelength but smaller than the mean free path length of incoherent extinction. In the radiative transfer part, at each absorption and scattering process, we account for absorption with the help of the single-scattering albedo and peel off the Stokes parameters of radiation emerging from the medium in predefined scattering angles. We then generate a new scattering direction using the joint probability density for the local polar and azimuthal scattering angles. In the coherent backscattering part, we utilize amplitude scattering matrices along the radiative-transfer path and the reciprocal path, and utilize the reciprocity of electromagnetic waves to verify the computation. We illustrate the incoherent volume-element scattering characteristics and compare the dense-medium RT-CB to asymptotically exact results computed using the Superposition T-matrix method (STMM). We show that the dense-medium RT-CB compares favorably to the STMM results for the current cases of sparse and dense discrete random media studied. The novel method can be applied in modeling light scattering by the surfaces of asteroids and other airless solar system objects, including UV-Vis-NIR spectroscopy, photometry, polarimetry, and radar scattering problems.Acknowledgments. Research supported by European Research Council with Advanced Grant No. 320773 SAEMPL, Scattering and Absorption of ElectroMagnetic waves in ParticuLate media. Computational resources provided by CSC - IT Centre for Science Ltd, Finland.

XCO2 Retrieval Errors from a PCA-based Approach to Fast Radiative Transfer

NASA Astrophysics Data System (ADS)

Somkuti, Peter; Boesch, Hartmut; Natraj, Vijay; Kopparla, Pushkar

2017-04-01

Multiple-scattering radiative transfer (RT) calculations are an integral part of forward models used to infer greenhouse gas concentrations in the shortwave-infrared spectral range from satellite missions such as GOSAT or OCO-2. Such calculations are, however, computationally expensive and, combined with the recent growth in data volume, necessitate the use of acceleration methods in order to make retrievals feasible on an operational level. The principle component analysis (PCA)-based approach to fast radiative transfer introduced by Natraj et al. 2005 is a spectral binning method, in which the many line-by-line monochromatic calculations are replaced by a small set of representative ones. From the PCA performed on the optical layer properties for a scene-dependent atmosphere, the results of the representative calculations are mapped onto all spectral points in the given band. Since this RT scheme is an approximation, the computed top-of-atmosphere radiances exhibit errors compared to the "full" line-by-line calculation. These errors ultimately propagate into the final retrieved greenhouse gas concentrations, and their magnitude depends on scene-dependent parameters such as aerosol loadings or viewing geometry. An advantage of this method is the ability to choose the degree of accuracy by increasing or decreasing the number of empirical orthogonal functions used for the reconstruction of the radiances. We have performed a large set of global simulations based on real GOSAT scenes and assess the retrieval errors induced by the fast RT approximation through linear error analysis. We find that across a wide range of geophysical parameters, the errors are for the most part smaller than ± 0.2 ppm and ± 0.06 ppm (out of roughly 400 ppm) for ocean and land scenes respectively. A fast RT scheme that produces low errors is important, since regional biases in XCO2 even in the low sub-ppm range can cause significant changes in carbon fluxes obtained from inversions (Chevallier et al. 2007).

Ultraviolet resources over Northern Eurasia.

PubMed

Chubarova, Natalia; Zhdanova, Yekaterina

2013-10-05

We propose a new climatology of UV resources over Northern Eurasia, which includes the assessments of both detrimental (erythema) and positive (vitamin D synthesis) effects of ultraviolet radiation on human health. The UV resources are defined by using several classes and subclasses - UV deficiency, UV optimum, and UV excess - for 6 different skin types. To better quantifying the vitamin D irradiance threshold we accounted for an open body fraction S as a function of effective air temperature. The spatial and temporal distribution of UV resources was estimated by radiative transfer (RT) modeling (8 stream DISORT RT code) with 1×1° grid and monthly resolution. For this purpose special datasets of main input geophysical parameters (total ozone content, aerosol characteristics, surface UV albedo, UV cloud modification factor) have been created over the territory of Northern Eurasia. The new approaches were used to retrieve aerosol parameters and cloud modification factor in the UV spectral region. As a result, the UV resources were obtained for clear-sky and mean cloudy conditions for different skin types. We show that the distribution of UV deficiency, UV optimum and UV excess is regulated by various geophysical parameters (mainly, total ozone, cloudiness and open body fraction) and can significantly deviate from latitudinal dependence. We also show that the UV optimum conditions can be simultaneously observed for people with different skin types (for example, for 4-5 skin types at the same time in spring over Western Europe). These UV optimum conditions for different skin types occupy a much larger territory over Europe than that over Asia. Copyright © 2013 Elsevier B.V. All rights reserved.

Novel microscopy-based screening method reveals regulators of contact-dependent intercellular transfer

PubMed Central

Michael Frei, Dominik; Hodneland, Erlend; Rios-Mondragon, Ivan; Burtey, Anne; Neumann, Beate; Bulkescher, Jutta; Schölermann, Julia; Pepperkok, Rainer; Gerdes, Hans-Hermann; Kögel, Tanja

2015-01-01

Contact-dependent intercellular transfer (codeIT) of cellular constituents can have functional consequences for recipient cells, such as enhanced survival and drug resistance. Pathogenic viruses, prions and bacteria can also utilize this mechanism to spread to adjacent cells and potentially evade immune detection. However, little is known about the molecular mechanism underlying this intercellular transfer process. Here, we present a novel microscopy-based screening method to identify regulators and cargo of codeIT. Single donor cells, carrying fluorescently labelled endocytic organelles or proteins, are co-cultured with excess acceptor cells. CodeIT is quantified by confocal microscopy and image analysis in 3D, preserving spatial information. An siRNA-based screening using this method revealed the involvement of several myosins and small GTPases as codeIT regulators. Our data indicates that cellular protrusions and tubular recycling endosomes are important for codeIT. We automated image acquisition and analysis to facilitate large-scale chemical and genetic screening efforts to identify key regulators of codeIT. PMID:26271723

Response Times to Stimuli of Increasing Complexity as a Function of Aging

ERIC Educational Resources Information Center

Jordan, T. C.; Rabbitt, P. M. A.

1977-01-01

These experiments consider the effects of aging on response times to stimuli of increasing complexity in serial choice RT tasks, whether age differences were reduced or abolished on such tasks, and examines repetition effects of a particular coding rule. (Author/RK)

Plume Tracker: A New Toolkit for the Mapping of Volcanic Plumes with Multispectral Thermal Infrared Remote Sensing

NASA Astrophysics Data System (ADS)

Realmuto, V. J.; Baxter, S.; Webley, P. W.

2011-12-01

Plume Tracker is the next generation of interactive plume mapping tools pioneered by MAP_SO2. First developed in 1995, MAP_SO2 has been used to study plumes at a number of volcanoes worldwide with data acquired by both airborne and space-borne instruments. The foundation of these tools is a radiative transfer (RT) model, based on MODTRAN, which we use as the forward model for our estimation of ground temperature and sulfur dioxide concentration. Plume Tracker retains the main functions of MAP_SO2, providing interactive tools to input radiance measurements and ancillary data, such as profiles of atmospheric temperature and humidity, to the retrieval procedure, generating the retrievals, and visualizing the resulting retrievals. Plume Tracker improves upon MAP_SO2 in the following areas: (1) an RT model based on an updated version of MODTRAN, (2) a retrieval procedure based on maximizing the vector projection of model spectra onto observed spectra, rather than minimizing the least-squares misfit between the model and observed spectra, (3) an ability to input ozone profiles to the RT model, (4) increased control over the vertical distribution of the atmospheric gas species used in the model, (5) a standard programmatic interface to the RT model code, based on the Component Object Model (COM) interface, which will provide access to any programming language that conforms to the COM standard, and (6) a new binning algorithm that decreases running time by exploiting spatial redundancy in the radiance data. Based on our initial testing, the binning algorithm can reduce running time by an order of magnitude. The Plume Tracker project is a collaborative effort between the Jet Propulsion Laboratory and Geophysical Institute (GI) of the University of Alaska-Fairbanks. Plume Tracker is integrated into the GI's operational plume dispersion modeling system and will ingest temperature and humidity profiles generated by the Weather Research and Forecasting model, together with plume height estimates from the Puff model. The access to timely forecasts of atmospheric conditions, together with the reductions in running time, will increase the utility of Plume Tracker in the Alaska Volcano Observatory's mission to mitigate volcanic hazards in Alaska and the Northern Pacific region.

[Applying the clustering technique for characterising maintenance outsourcing].

PubMed

Cruz, Antonio M; Usaquén-Perilla, Sandra P; Vanegas-Pabón, Nidia N; Lopera, Carolina

2010-06-01

Using clustering techniques for characterising companies providing health institutions with maintenance services. The study analysed seven pilot areas' equipment inventory (264 medical devices). Clustering techniques were applied using 26 variables. Response time (RT), operation duration (OD), availability and turnaround time (TAT) were amongst the most significant ones. Average biomedical equipment obsolescence value was 0.78. Four service provider clusters were identified: clusters 1 and 3 had better performance, lower TAT, RT and DR values (56 % of the providers coded O, L, C, B, I, S, H, F and G, had 1 to 4 day TAT values:

Radiative Transfer in Protoplanetary Disks

NASA Astrophysics Data System (ADS)

Graziani, L.; Aiello, S.; Belleni-Morante, A.; Cecchi-Pestellini, C.

2008-09-01

Abstract Protoplanetary disks are the precursors of planetary systems. All building materials needed to assembly the planetary systems are supplied by these reservoirs, including many organic molecules [1,2]. Thus, the physical and chemical properties in Protoplanetary disks set the boundary conditions for the formation and evolution of planets and other solar system bodies. In standard radiative scenario structure and chemistry of protoplanetary disks depend strongly on the nature of central star around which they formed. The dust temperature is manly set by the stellar luminosity, while the chemistry of the whole disk depends on the UV and X ray fluxes [3,4,6,8]. Therefore, a knowledge as accurate as possible of the radiative transfer (RT) inside disks is a prerequisite for their modelling. Actually, real disks are complex, stratified and inhomogeneous environments requiring a detailed dust mixture modelling and the ability to follow the radiation transfer across radial and vertical gradients. Different energetic processes as the mass accretion processes onto the star surface, the viscous dissipative heating dominating the midplane region, and the flared atmospheres radiation reprocessing, have a significant role in the disk structuring [4,5,8]. During the last 10 years many authors suggested various numerical and analytical techniques to resolve the disk temperature structure providing vertical temperature profiles and disk SED databases [4,6]. In this work we present the results of our semi analytical and numerical model solving the radiative transfer problem in two separate interesting disk regions: 1) Disk atmospheres at large radius, r > 10 AU. 2) Vertical disk structure over 1 < r < 10 AU and 10 < r < 100 AU. A simplified analytical approach based on P-N approximation [7] for a rectified disk surface (suitable for limited range of r) is compared and contrasted with a more accurate Monte Carlo integration [5]. Our code can handle arbitrary dust inhomogeneities, vertical and radial, in terms of mineralogical and density changes. Different dust mixture models from Pollack [9], Gail [10] and Henning [11] are implemented and tested. The code solves the RT in the 4 Stokes radiation field formalism providing an accurate radiation flux description and the polarization configuration for UV and X-Ray stellar fluxes in various disk regions (disk surface, disk midplane etc..). The complete model is developed within the context of a classical TTauri protostar and for different dust compositions and different ranges of star luminosity in UV and X -Ray are. The effects on some prebiotic molecules are estimated. References [1]Ehrenfreund, P. & Charnley, S.B. (2000), Ann.Rev.Astr.Astrophys, 38, 427-483. [2]Markwick, A.J. & Charnley, S.B. (2004). in P. Eherenfreund et alt. (eds) "Astrobiology: Future Perspectives", Kluwer, 33-66. [3] Chiang, E. I. & Goldreich, P. (1997), ApJ, 490, 368 [4] D'Alessio, P., Canto, J., Calvet, N., & Lizano, S. (1998), ApJ, 500, 411. [5] Bjorkman, J. E. & Wood, K. 2001, ApJ, 554, 615. [6] Dullemond C. P. & A.Natta 2003, A&A 405, 597-605. [7] B. Davison & J. B. Sykes: Neutron Transport theory, Oxford Press 1958. [8] D'Alessio P. et al (2007), Chondrites and the Protoplanetary Disk, ASPConference Series,Vol.341. [9] J.B.Pollack et al. (1994), ApJ,421:615-639. [10] H.P.Gail, (2001), A&A, v.378 [11] T.Henning & R.Stognienko.(1996), ApJ, 311.

Geocoronal Balmer α line profile observations and forward-model analysis

NASA Astrophysics Data System (ADS)

Mierkiewicz, E. J.; Bishop, J.; Roesler, F. L.; Nossal, S. M.

2006-05-01

High spectral resolution geocoronal Balmer α line profile observations from Pine Bluff Observatory (PBO) are presented in the context of forward-model analysis. Because Balmer series column emissions depend significantly on multiple scattering, retrieval of hydrogen parameters of general aeronomic interest from these observations (e.g., the hydrogen column abundance) currently requires a forward modeling approach. This capability is provided by the resonance radiative transfer code LYAO_RT. We have recently developed a parametric data-model comparison search procedure employing an extensive grid of radiative transport model input parameters (defining a 6-dimensional parameter space) to map-out bounds for feasible forward model retrieved atomic hydrogen density distributions. We applied this technique to same-night (March, 2000) ground-based Balmer α data from PBO and geocoronal Lyman β measurements from the Espectrógrafo Ultravioleta extremo para la Radiación Difusa (EURD) instrument on the Spanish satellite MINISAT-1 (provided by J.F. Gómez and C. Morales of the Laboratorio de Astrofisica Espacial y Física Fundamental, INTA, Madrid, Spain) in order to investigate the modeling constraints imposed by two sets of independent geocoronal intensity measurements, both of which rely on astronomical calibration methods. In this poster we explore extending this analysis to the line profile information also contained in the March 2000 PBO Balmer α data set. In general, a decrease in the Doppler width of the Balmer α emission with shadow altitude is a persistent feature in every night of PBO observations in which a wide range of shadow altitudes are observed. Preliminary applications of the LYAO_RT code, which includes the ability to output Doppler line profiles for both the singly and multiply scattered contributions to the Balmer α emission line, displays good qualitative agreement with regard to geocoronal Doppler width trends observed from PBO. Model-data Balmer α Doppler width comparisons, using the best-fit model parameters obtained during the March 2000 PBO/EURD forward-model study, will be presented and discussed, including the feasibility of using Balmer α observed Doppler widths as an additional model constraint in our forward-model search procedure.

Effect of Radiotherapy Planning Complexity on Survival of Elderly Patients With Unresected Localized Lung Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Chang H.; Bonomi, Marcelo; Cesaretti, Jamie

2011-11-01

Purpose: To evaluate whether complex radiotherapy (RT) planning was associated with improved outcomes in a cohort of elderly patients with unresected Stage I-II non-small-cell lung cancer (NSCLC). Methods and Materials: Using the Surveillance, Epidemiology, and End Results registry linked to Medicare claims, we identified 1998 patients aged >65 years with histologically confirmed, unresected stage I-II NSCLC. Patients were classified into an intermediate or complex RT planning group using Medicare physician codes. To address potential selection bias, we used propensity score modeling. Survival of patients who received intermediate and complex simulation was compared using Cox regression models adjusting for propensity scoresmore » and in a stratified and matched analysis according to propensity scores. Results: Overall, 25% of patients received complex RT planning. Complex RT planning was associated with better overall (hazard ratio 0.84; 95% confidence interval, 0.75-0.95) and lung cancer-specific (hazard ratio 0.81; 95% confidence interval, 0.71-0.93) survival after controlling for propensity scores. Similarly, stratified and matched analyses showed better overall and lung cancer-specific survival of patients treated with complex RT planning. Conclusions: The use of complex RT planning is associated with improved survival among elderly patients with unresected Stage I-II NSCLC. These findings should be validated in prospective randomized controlled trials.« less

Decision to adopt medical technology: case study of breast cancer radiotherapy techniques.

PubMed

Gold, Heather Taffet; Pitrelli, Kimberly; Hayes, Mary Katherine; Murphy, Madhuvanti Mahadeo

2014-11-01

To understand decision making concerning adoption and nonadoption of accelerated partial breast radiotherapy (RT) prior to long-term randomized trial evidence. A total of 36 radiation oncologists and surgeons were recruited through purposive and snowball sampling strategies from September 2010 through January 2013. Semistructured phone interviews were conducted and audio-recorded and lasted 20-45 minutes. Qualitative analysis was conducted using a framework approach, iteratively exploring key concepts and emerging issues raised by subjects. Interviews were transcribed and imported into Atlas.ti v6. Transcripts were independently coded by 3 researchers shortly after each interview, followed by consensus development on each coded transcript. Barriers and facilitators of adoption, practice patterns, and informational/educational sources concerning accelerated partial breast RT were all assessed to determine major themes. Nearly half of physicians were surgeons (47%), and half were radiation oncologists (53%), with 61% overall in urban settings. Twenty-nine of the 36 physicians interviewed used brachytherapy-based partial breast RT. Five major factors were involved in physicians' decisions to adopt accelerated partial breast RT: facilitators encouraging adoption (e.g., enthusiastic colleagues and patient convenience), financial and prestige incentives, pressures to adopt (e.g., potential declines in referrals), judgment concerning acceptable level of scientific evidence, and barriers (e.g., not having appropriate machinery or referral mechanism in place). If technology was adopted, clinical guideline adherence varied. Technology adoption is based on financial and social pressures, along with often-limited scientific evidence and what seems "best" for patients. For technology adoption and diffusion to be rational and evidence-based, we must encourage appropriate financial payment models to curb use outside of research studies and promote development of additional treatment registries until sufficient evidence is gathered. © The Author(s) 2014.

[Detection of gene mutation in glucose-6-phosphate dehydrogenase deficiency by RT-PCR sequencing].

PubMed

Lyu, Rong-Yu; Chen, Xiao-Wen; Zhang, Min; Chen, Yun-Sheng; Yu, Jie; Wen, Fei-Qiu

2016-07-01

Since glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common hereditary hemolytic erythrocyte enzyme deficiency, most cases have single nucleotide mutations in the coding region, and current test methods for gene mutation have some missed detections, this study aimed to investigate the feasibility of RT-PCR sequencing in the detection of gene mutation in G6PD deficiency. According to the G6PD/6GPD ratio, 195 children with anemia of unknown cause or who underwent physical examination between August 2013 and July 2014 were classified into G6PD-deficiency group with 130 children (G6PD/6GPD ratio <1.00) and control group with 65 children (G6PD/6GPD ratio≥1.00). The primer design and PCR amplification conditions were optimized, and RT-PCR sequencing was used to analyze the complete coding sequence and verify the genomic DNA sequence in the two groups. In the G6PD-deficiency group, the detection rate of gene mutation was 100% and 13 missense mutations were detected, including one new mutation. In the control group, no missense mutation was detected in 28 boys; 13 heterozygous missense mutations, 1 homozygous same-sense mutation (C1191T) which had not been reported in China and abroad, and 14 single nucleotide polymorphisms of C1311T were detected in 37 girls. The control group showed a high rate of missed detection of G6PD deficiency (carriers) in the specimens from girls (35%, 13/37). RT-PCR sequencing has a high detection rate of G6PD gene mutation and a certain value in clinical diagnosis of G6PD deficiency.

A reverse transcriptase-dependent mechanism plays central roles in fundamental biological processes.

PubMed

Spadafora, Corrado

2008-01-01

This review summarizes emerging evidence that LINE-1 (Long Interspersed Nuclear Elements) -encoded reverse transcriptase (RT) regulates fundamental biological processes. Earlier studies showed that sperm cells can be used as vectors of both exogenous DNA and RNA molecules in sperm-mediated gene transfer assays. During these studies, a sperm endogenous RT activity was identified, which can reverse-transcribe exogenous RNA directly, or DNA molecules through sequential transcription and reverse transcription. Resulting cDNA copies generated in sperm cells can be delivered to embryos at fertilization, further propagated in tissues as low-copy extrachromosomal structures and transmitted to the progeny in a non-mendelian fashion. Being transcriptionally competent, they can induce phenotypic variations in positive tissues. An RT activity is also present in preimplantation embryos, and its inhibition causes developmental arrest in early preimplantation stages, paralleled by an extensive reprogramming of gene expression. In analogy with this, drug-mediated inhibition of RT activity, or RNA interference-mediated silencing of human LINE-1, reduce cell proliferation and induce differentiation in a variety of cancer cell lines. Furthermore, RT inhibition in vivo antagonizes the growth of human tumors in animal models. As a whole, these data implicate a RT-dependent machinery in the genesis of new genetic information in spermatozoa and in normal and pathological developmental processes.

The identification of unfolding facial expressions.

PubMed

Fiorentini, Chiara; Schmidt, Susanna; Viviani, Paolo

2012-01-01

We asked whether the identification of emotional facial expressions (FEs) involves the simultaneous perception of the facial configuration or the detection of emotion-specific diagnostic cues. We recorded at high speed (500 frames s-1) the unfolding of the FE in five actors, each expressing six emotions (anger, surprise, happiness, disgust, fear, sadness). Recordings were coded every 10 frames (20 ms of real time) with the Facial Action Coding System (FACS, Ekman et al 2002, Salt Lake City, UT: Research Nexus eBook) to identify the facial actions contributing to each expression, and their intensity changes over time. Recordings were shown in slow motion (1/20 of recording speed) to one hundred observers in a forced-choice identification task. Participants were asked to identify the emotion during the presentation as soon as they felt confident to do so. Responses were recorded along with the associated response times (RTs). The RT probability density functions for both correct and incorrect responses were correlated with the facial activity during the presentation. There were systematic correlations between facial activities, response probabilities, and RT peaks, and significant differences in RT distributions for correct and incorrect answers. The results show that a reliable response is possible long before the full FE configuration is reached. This suggests that identification is reached by integrating in time individual diagnostic facial actions, and does not require perceiving the full apex configuration.

Conformational States of the Rapana thomasiana Hemocyanin and Its Substructures Studied by Dynamic Light Scattering and Time-Resolved Fluorescence Spectroscopy

PubMed Central

Georgieva, Dessislava; Schwark, Daniel; Nikolov, Peter; Idakieva, Krassimira; Parvanova, Katja; Dierks, Karsten; Genov, Nicolay; Betzel, Christian

2005-01-01

Hemocyanins are dioxygen-transporting proteins freely dissolved in the hemolymph of mollusks and arthropods. Dynamic light scattering and time-resolved fluorescence measurements show that the oxygenated and apo-forms of the Rapana thomasiana hemocyanin, its structural subunits RtH1 and RtH2, and those of the functional unit RtH2e, exist in different conformations. The oxygenated respiratory proteins are less compact and more asymmetric than the respective apo-forms. Different conformational states were also observed for the R. thomasiana hemocyanin in the absence and presence of an allosteric regulator. The results are in agreement with a molecular mechanism for cooperative dioxygen binding in molluscan hemocyanins including transfer of conformational changes from one functional unit to another. PMID:15533921

Validation of Small RNAs In Xylella fastidiosa by qRT-PCR

USDA-ARS?s Scientific Manuscript database

Xylella fastidiosa causes many economically important crop diseases including almond leaf scorch disease and Pierce’ disease of grapevine. Although non-coding small RNAs (sRNAs) are regarded as ubiquitous regulatory elements in bacteria, research attention to sRNAs in X. fastidiosa has been limited...

Neoadjuvant Radiotherapy: A Risk Factor for Short-Term Wound Complications after Radical Resection for Rectal Cancer?

PubMed

Holubar, Stefan D; Brickman, Rachel K; Greaves, Spencer W; Ivatury, S Joga

2016-08-01

Neoadjuvant radiotherapy (RT) for rectal cancer may increase wound complications after oncologic proctectomy. We aimed to assess the relationship between neoadjuvant RT and 30-day wound complications after radical surgery for rectal cancer. We identified rectal cancer patients (International Classification of Diseases, revision-9 [ICD-9] code 154.1) who underwent radical resection, using NSQIP from 2005 to 2010. Patients were stratified into preoperative radiation vs no radiation groups. Our primary outcome was any wound complication. The association between preoperative RT and postoperative wound complication rate was assessed by univariate, multivariable, and propensity score analyses. Of 242,670 colorectal cases, 6,297 patients were included. Of these, 2,476 (39%) received RT within 90 days preoperatively. The RT group, compared with the no RT group, received more chemotherapy within 30 days preoperatively (15.0% vs 2.5%, p < 0.0001), and had less laparoscopic (18.9% vs 25.1%, p < 0.0001) or sphincter-preserving surgery (61.8% vs 67.1%, p < 0.0001). In the univariate analyses, there was no difference in wound complications (19.6% vs 18.7%, p = 0.42) between groups. Similarly, there was no difference in overall complications (29.6% vs 29.8%, p = 0.89), return to operating room (6.7% vs 6.7%, p = 0.96), or length of stay (8.4 vs 8.4 days, p = 0.72) between the RT and no RT groups, respectively. The mortality rate in the RT group was lower on univariate analysis (0.7% vs 1.4%, p = 0.008), but was not significantly different in the multivariable analyses. Multivariable and propensity score analyses were consistent with the lack of association between preoperative RT and postoperative wound complications. Neoadjuvant radiotherapy does not appear to be an independent risk factor for wound complications after radical surgery for rectal cancer. Copyright © 2016 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

Decomposition of the optical transfer function: wavefront coding imaging systems

NASA Astrophysics Data System (ADS)

Muyo, Gonzalo; Harvey, Andy R.

2005-10-01

We describe the mapping of the optical transfer function (OTF) of an incoherent imaging system into a geometrical representation. We show that for defocused traditional and wavefront-coded systems the OTF can be represented as a generalized Cornu spiral. This representation provides a physical insight into the way in which wavefront coding can increase the depth of field of an imaging system and permits analytical quantification of salient OTF parameters, such as the depth of focus, the location of nulls, and amplitude and phase modulation of the wavefront-coding OTF.

SKIRT: The design of a suite of input models for Monte Carlo radiative transfer simulations

NASA Astrophysics Data System (ADS)

Baes, M.; Camps, P.

2015-09-01

The Monte Carlo method is the most popular technique to perform radiative transfer simulations in a general 3D geometry. The algorithms behind and acceleration techniques for Monte Carlo radiative transfer are discussed extensively in the literature, and many different Monte Carlo codes are publicly available. On the contrary, the design of a suite of components that can be used for the distribution of sources and sinks in radiative transfer codes has received very little attention. The availability of such models, with different degrees of complexity, has many benefits. For example, they can serve as toy models to test new physical ingredients, or as parameterised models for inverse radiative transfer fitting. For 3D Monte Carlo codes, this requires algorithms to efficiently generate random positions from 3D density distributions. We describe the design of a flexible suite of components for the Monte Carlo radiative transfer code SKIRT. The design is based on a combination of basic building blocks (which can be either analytical toy models or numerical models defined on grids or a set of particles) and the extensive use of decorators that combine and alter these building blocks to more complex structures. For a number of decorators, e.g. those that add spiral structure or clumpiness, we provide a detailed description of the algorithms that can be used to generate random positions. Advantages of this decorator-based design include code transparency, the avoidance of code duplication, and an increase in code maintainability. Moreover, since decorators can be chained without problems, very complex models can easily be constructed out of simple building blocks. Finally, based on a number of test simulations, we demonstrate that our design using customised random position generators is superior to a simpler design based on a generic black-box random position generator.

An investigation of tritium transfer in reactor loops

NASA Astrophysics Data System (ADS)

Ilyasova, O. H.; Mosunova, N. A.

2017-09-01

The work is devoted to the important task of the numerical simulation and analysis of the tritium behaviour in the reactor loops. The simulation was carried out by HYDRA-IBRAE/LM code, which is being developed in Nuclear safety institute of the Russian Academy of Sciences. The code is intended for modeling of the liquid metal flow (sodium, lead and lead-bismuth) on the base of non-homogeneous and non-equilibrium two-fluid model. In order to simulate tritium transfer in the code, the special module has been developed. Module includes the models describing the main phenomena of tritium behaviour in reactor loops: transfer, permeation, leakage, etc. Because of shortage of the experimental data, a lot of analytical tests and comparative calculations were considered. Some of them are presented in this work. The comparison of estimation results and experimental and analytical data demonstrate not only qualitative but also good quantitative agreement. It is possible to confirm that HYDRA-IBRAE/LM code allows modeling tritium transfer in reactor loops.

The fourth radiation transfer model intercomparison (RAMI-IV): Proficiency testing of canopy reflectance models with ISO-13528

NASA Astrophysics Data System (ADS)

Widlowski, J.-L.; Pinty, B.; Lopatka, M.; Atzberger, C.; Buzica, D.; Chelle, M.; Disney, M.; Gastellu-Etchegorry, J.-P.; Gerboles, M.; Gobron, N.; Grau, E.; Huang, H.; Kallel, A.; Kobayashi, H.; Lewis, P. E.; Qin, W.; Schlerf, M.; Stuckens, J.; Xie, D.

2013-07-01

The radiation transfer model intercomparison (RAMI) activity aims at assessing the reliability of physics-based radiative transfer (RT) models under controlled experimental conditions. RAMI focuses on computer simulation models that mimic the interactions of radiation with plant canopies. These models are increasingly used in the development of satellite retrieval algorithms for terrestrial essential climate variables (ECVs). Rather than applying ad hoc performance metrics, RAMI-IV makes use of existing ISO standards to enhance the rigor of its protocols evaluating the quality of RT models. ISO-13528 was developed "to determine the performance of individual laboratories for specific tests or measurements." More specifically, it aims to guarantee that measurement results fall within specified tolerance criteria from a known reference. Of particular interest to RAMI is that ISO-13528 provides guidelines for comparisons where the true value of the target quantity is unknown. In those cases, "truth" must be replaced by a reliable "conventional reference value" to enable absolute performance tests. This contribution will show, for the first time, how the ISO-13528 standard developed by the chemical and physical measurement communities can be applied to proficiency testing of computer simulation models. Step by step, the pre-screening of data, the identification of reference solutions, and the choice of proficiency statistics will be discussed and illustrated with simulation results from the RAMI-IV "abstract canopy" scenarios. Detailed performance statistics of the participating RT models will be provided and the role of the accuracy of the reference solutions as well as the choice of the tolerance criteria will be highlighted.

Fast simulation tool for ultraviolet radiation at the earth's surface

NASA Astrophysics Data System (ADS)

Engelsen, Ola; Kylling, Arve

2005-04-01

FastRT is a fast, yet accurate, UV simulation tool that computes downward surface UV doses, UV indices, and irradiances in the spectral range 290 to 400 nm with a resolution as small as 0.05 nm. It computes a full UV spectrum within a few milliseconds on a standard PC, and enables the user to convolve the spectrum with user-defined and built-in spectral response functions including the International Commission on Illumination (CIE) erythemal response function used for UV index calculations. The program accounts for the main radiative input parameters, i.e., instrumental characteristics, solar zenith angle, ozone column, aerosol loading, clouds, surface albedo, and surface altitude. FastRT is based on look-up tables of carefully selected entries of atmospheric transmittances and spherical albedos, and exploits the smoothness of these quantities with respect to atmospheric, surface, geometrical, and spectral parameters. An interactive site, http://nadir.nilu.no/~olaeng/fastrt/fastrt.html, enables the public to run the FastRT program with most input options. This page also contains updated information about FastRT and links to freely downloadable source codes and binaries.

Experiences of the Breast Cancer Patients Undergoing Radiotherapy at a Public Hospital Peshawar Pakistan

PubMed Central

Habibullah, Gulzar; Gul, Raisa; Cassum, Shanaz; Elahi, Rehana

2018-01-01

Objective: This study aimed to explore the experiences of female breast cancer patients undergoing radiotherapy (RT) in a public hospital in Peshawar, Pakistan. Methods: This study employed a descriptive exploratory method. A purposive sample of 14 breast cancer women undergoing RT was selected for this study. Data were collected over the period of 5 months, using a semi-structured interview guide and conducting in-depth face-to-face interviews. These interviews were audio taped and transcribed by a bilingual transcriber. The translated version of the interview was coded, and the analysis was done manually. Results: Four main categories emerged from data analysis, which were: feelings and perceptions of the patients, their challenges, coping strategies, and teaching and informational needs. Conclusions: Women undergoing RT in this culture experience more intense psychological effects, as compared to the physical effects. Keeping in mind, the magnitude of the emotional stress experienced by the participants, recommendations for policy reforms, and training for female RT staff are suggested based on findings of this research. PMID:29607379

HBOI Underwater Imaging and Communication Research - Phase 1

DTIC Science & Technology

2012-04-19

validation of one-way pulse stretching radiative transfer code The objective was to develop and validate time-resolved radiative transfer models that...and validation of one-way pulse stretching radiative transfer code The models were subjected to a series of validation experiments over 12.5 meter...about the theoretical basis of the model together with validation results can be found in Dalgleish et al., (20 1 0). Forward scattering Mueller

Consistency evaluation between EGSnrc and Geant4 charged particle transport in an equilibrium magnetic field.

PubMed

Yang, Y M; Bednarz, B

2013-02-21

Following the proposal by several groups to integrate magnetic resonance imaging (MRI) with radiation therapy, much attention has been afforded to examining the impact of strong (on the order of a Tesla) transverse magnetic fields on photon dose distributions. The effect of the magnetic field on dose distributions must be considered in order to take full advantage of the benefits of real-time intra-fraction imaging. In this investigation, we compared the handling of particle transport in magnetic fields between two Monte Carlo codes, EGSnrc and Geant4, to analyze various aspects of their electromagnetic transport algorithms; both codes are well-benchmarked for medical physics applications in the absence of magnetic fields. A water-air-water slab phantom and a water-lung-water slab phantom were used to highlight dose perturbations near high- and low-density interfaces. We have implemented a method of calculating the Lorentz force in EGSnrc based on theoretical models in literature, and show very good consistency between the two Monte Carlo codes. This investigation further demonstrates the importance of accurate dosimetry for MRI-guided radiation therapy (MRIgRT), and facilitates the integration of a ViewRay MRIgRT system in the University of Wisconsin-Madison's Radiation Oncology Department.

Consistency evaluation between EGSnrc and Geant4 charged particle transport in an equilibrium magnetic field

NASA Astrophysics Data System (ADS)

Yang, Y. M.; Bednarz, B.

2013-02-01

Following the proposal by several groups to integrate magnetic resonance imaging (MRI) with radiation therapy, much attention has been afforded to examining the impact of strong (on the order of a Tesla) transverse magnetic fields on photon dose distributions. The effect of the magnetic field on dose distributions must be considered in order to take full advantage of the benefits of real-time intra-fraction imaging. In this investigation, we compared the handling of particle transport in magnetic fields between two Monte Carlo codes, EGSnrc and Geant4, to analyze various aspects of their electromagnetic transport algorithms; both codes are well-benchmarked for medical physics applications in the absence of magnetic fields. A water-air-water slab phantom and a water-lung-water slab phantom were used to highlight dose perturbations near high- and low-density interfaces. We have implemented a method of calculating the Lorentz force in EGSnrc based on theoretical models in literature, and show very good consistency between the two Monte Carlo codes. This investigation further demonstrates the importance of accurate dosimetry for MRI-guided radiation therapy (MRIgRT), and facilitates the integration of a ViewRay MRIgRT system in the University of Wisconsin-Madison's Radiation Oncology Department.

Heat transfer in rocket engine combustion chambers and regeneratively cooled nozzles

NASA Technical Reports Server (NTRS)

1993-01-01

A conjugate heat transfer computational fluid dynamics (CFD) model to describe regenerative cooling in the main combustion chamber and nozzle and in the injector faceplate region for a launch vehicle class liquid rocket engine was developed. An injector model for sprays which treats the fluid as a variable density, single-phase media was formulated, incorporated into a version of the FDNS code, and used to simulate the injector flow typical of that in the Space Shuttle Main Engine (SSME). Various chamber related heat transfer analyses were made to verify the predictive capability of the conjugate heat transfer analysis provided by the FDNS code. The density based version of the FDNS code with the real fluid property models developed was successful in predicting the streamtube combustion of individual injector elements.

Two way time transfer results at NRL and USNO

NASA Technical Reports Server (NTRS)

Galysh, Ivan J.; Landis, G. Paul

1993-01-01

The Naval Research Laboratory (NRL) has developed a two way time transfer modem system for the United States Naval Observatory (USNO). Two modems in conjunction with a pair of Very Small Aperture Terminal (VSAT) and a communication satellite can achieve sub nanosecond time transfer. This performance is demonstrated by the results of testing at and between NRL and USNO. The modems use Code Division Multiple Access (CDMA) methods to separate their signals through a single path in the satellite. Each modem transmitted a different Pseudo Random Noise (PRN) code and received the others PRN code. High precision time transfer is possible with two way methods because of reciprocity of many of the terms of the path and hardware delay between the two modems. The hardware description was given in a previous paper.

Molecular diagnosis of lyssaviruses and sequence comparison of Australian bat lyssavirus samples.

PubMed

Foord, A J; Heine, H G; Pritchard, L I; Lunt, R A; Newberry, K M; Rootes, C L; Boyle, D B

2006-07-01

To evaluate and implement molecular diagnostic tests for the detection of lyssaviruses in Australia. A published hemi-nested reverse transcriptase polymerase chain reaction (RT-PCR) for the detection of all lyssavirus genotypes was modified to a fully nested RT-PCR format and compared with the original assay. TaqMan assays for the detection of Australian bat lyssavirus (ABLV) were compared with both the nested and hemi-nested RT-PCR assays. The sequences of RT-PCR products were determined to assess sequence variations of the target region (nucleocapsid gene) in samples of ABLV originating from different regions. The nested RT-PCR assay was highly analytically specific, and at least as analytically sensitive as the hemi-nested assay. The TaqMan assays were highly analytically specific and more analytically sensitive than either RT-PCR assay, with a detection level of approximately 10 genome equivalents per microl. Sequence of the first 544 nucleotides of the nucleocapsid protein coding sequence was obtained from all samples of ABLV received at Australian Animal Health Laboratory during the study period. The nested RT-PCR provided a means for molecular diagnosis of all tested genotypes of lyssavirus including classical rabies virus and Australian bat lyssavirus. The published TaqMan assay proved to be superior to the RT-PCR assays for the detection of ABLV in terms of analytical sensitivity. The TaqMan assay would also be faster and cross contamination is less likely. Nucleotide sequence analyses of samples of ABLV from a wide geographical range in Australia demonstrated the conserved nature of this region of the genome and therefore the suitability of this region for molecular diagnosis.

Enhancements to the SSME transfer function modeling code

NASA Technical Reports Server (NTRS)

Irwin, R. Dennis; Mitchell, Jerrel R.; Bartholomew, David L.; Glenn, Russell D.

1995-01-01

This report details the results of a one year effort by Ohio University to apply the transfer function modeling and analysis tools developed under NASA Grant NAG8-167 (Irwin, 1992), (Bartholomew, 1992) to attempt the generation of Space Shuttle Main Engine High Pressure Turbopump transfer functions from time domain data. In addition, new enhancements to the transfer function modeling codes which enhance the code functionality are presented, along with some ideas for improved modeling methods and future work. Section 2 contains a review of the analytical background used to generate transfer functions with the SSME transfer function modeling software. Section 2.1 presents the 'ratio method' developed for obtaining models of systems that are subject to single unmeasured excitation sources and have two or more measured output signals. Since most of the models developed during the investigation use the Eigensystem Realization Algorithm (ERA) for model generation, Section 2.2 presents an introduction of ERA, and Section 2.3 describes how it can be used to model spectral quantities. Section 2.4 details the Residue Identification Algorithm (RID) including the use of Constrained Least Squares (CLS) and Total Least Squares (TLS). Most of this information can be found in the report (and is repeated for convenience). Section 3 chronicles the effort of applying the SSME transfer function modeling codes to the a51p394.dat and a51p1294.dat time data files to generate transfer functions from the unmeasured input to the 129.4 degree sensor output. Included are transfer function modeling attempts using five methods. The first method is a direct application of the SSME codes to the data files and the second method uses the underlying trends in the spectral density estimates to form transfer function models with less clustering of poles and zeros than the models obtained by the direct method. In the third approach, the time data is low pass filtered prior to the modeling process in an effort to filter out high frequency characteristics. The fourth method removes the presumed system excitation and its harmonics in order to investigate the effects of the excitation on the modeling process. The fifth method is an attempt to apply constrained RID to obtain better transfer functions through more accurate modeling over certain frequency ranges. Section 4 presents some new C main files which were created to round out the functionality of the existing SSME transfer function modeling code. It is now possible to go from time data to transfer function models using only the C codes; it is not necessary to rely on external software. The new C main files and instructions for their use are included. Section 5 presents current and future enhancements to the XPLOT graphics program which was delivered with the initial software. Several new features which have been added to the program are detailed in the first part of this section. The remainder of Section 5 then lists some possible features which may be added in the future. Section 6 contains the conclusion section of this report. Section 6.1 is an overview of the work including a summary and observations relating to finding transfer functions with the SSME code. Section 6.2 contains information relating to future work on the project.

Further Development of the PCRTM Model and RT Model Inter Comparison

NASA Technical Reports Server (NTRS)

Yang, Qiguang; Liu, Xu; Wu, Wan; Kizer, Susan

2015-01-01

New results for the development of the PCRTM model will be presented. The new results were used for IASI retrieval validation inter comparison and better results were obtained compare to other fast radiative transfer models.

Medical Applications of the PHITS Code (3): User Assistance Program for Medical Physics Computation.

PubMed

Furuta, Takuya; Hashimoto, Shintaro; Sato, Tatsuhiko

2016-01-01

DICOM2PHITS and PSFC4PHITS are user assistance programs for medical physics PHITS applications. DICOM2PHITS is a program to construct the voxel PHITS simulation geometry from patient CT DICOM image data by using a conversion table from CT number to material composition. PSFC4PHITS is a program to convert the IAEA phase-space file data to PHITS format to be used as a simulation source of PHITS. Both of the programs are useful for users who want to apply PHITS simulation to verification of the treatment planning of radiation therapy. We are now developing a program to convert dose distribution obtained by PHITS to DICOM RT-dose format. We also want to develop a program which is able to implement treatment information included in other DICOM files (RT-plan and RT-structure) as a future plan.

Experimental demonstration of laser imprint reduction using underdense foams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Delorme, B.; Casner, A.; CELIA, University of Bordeaux-CNRS-CEA, F-33400 Talence

2016-04-15

Reducing the detrimental effect of the Rayleigh-Taylor (RT) instability on the target performance is a critical challenge. In this purpose, the use of targets coated with low density foams is a promising approach to reduce the laser imprint. This article presents results of ablative RT instability growth measurements, performed on the OMEGA laser facility in direct-drive for plastic foils coated with underdense foams. The laser beam smoothing is explained by the parametric instabilities developing in the foam and reducing the laser imprint on the plastic (CH) foil. The initial perturbation pre-imposed by the means of a specific phase plate wasmore » shown to be smoothed using different foam characteristics. Numerical simulations of the laser beam smoothing in the foam and of the RT growth are performed with a suite of paraxial electromagnetic and radiation hydrodynamic codes. They confirmed the foam smoothing effect in the experimental conditions.« less

Application of modern radiative transfer tools to model laboratory quartz emissivity

NASA Astrophysics Data System (ADS)

Pitman, Karly M.; Wolff, Michael J.; Clayton, Geoffrey C.

2005-08-01

Planetary remote sensing of regolith surfaces requires use of theoretical models for interpretation of constituent grain physical properties. In this work, we review and critically evaluate past efforts to strengthen numerical radiative transfer (RT) models with comparison to a trusted set of nadir incidence laboratory quartz emissivity spectra. By first establishing a baseline statistical metric to rate successful model-laboratory emissivity spectral fits, we assess the efficacy of hybrid computational solutions (Mie theory + numerically exact RT algorithm) to calculate theoretical emissivity values for micron-sized α-quartz particles in the thermal infrared (2000-200 cm-1) wave number range. We show that Mie theory, a widely used but poor approximation to irregular grain shape, fails to produce the single scattering albedo and asymmetry parameter needed to arrive at the desired laboratory emissivity values. Through simple numerical experiments, we show that corrections to single scattering albedo and asymmetry parameter values generated via Mie theory become more necessary with increasing grain size. We directly compare the performance of diffraction subtraction and static structure factor corrections to the single scattering albedo, asymmetry parameter, and emissivity for dense packing of grains. Through these sensitivity studies, we provide evidence that, assuming RT methods work well given sufficiently well-quantified inputs, assumptions about the scatterer itself constitute the most crucial aspect of modeling emissivity values.

A Method of Data Aggregation for Wearable Sensor Systems

PubMed Central

Shen, Bo; Fu, Jun-Song

2016-01-01

Data aggregation has been considered as an effective way to decrease the data to be transferred in sensor networks. Particularly for wearable sensor systems, smaller battery has less energy, which makes energy conservation in data transmission more important. Nevertheless, wearable sensor systems usually have features like frequently dynamic changes of topologies and data over a large range, of which current aggregating methods can’t adapt to the demand. In this paper, we study the system composed of many wearable devices with sensors, such as the network of a tactical unit, and introduce an energy consumption-balanced method of data aggregation, named LDA-RT. In the proposed method, we develop a query algorithm based on the idea of ‘happened-before’ to construct a dynamic and energy-balancing routing tree. We also present a distributed data aggregating and sorting algorithm to execute top-k query and decrease the data that must be transferred among wearable devices. Combining these algorithms, LDA-RT tries to balance the energy consumptions for prolonging the lifetime of wearable sensor systems. Results of evaluation indicate that LDA-RT performs well in constructing routing trees and energy balances. It also outperforms the filter-based top-k monitoring approach in energy consumption, load balance, and the network’s lifetime, especially for highly dynamic data sources. PMID:27347953

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strauss, Jonathan B.; Chen, Sea S.; Shah, Anand P.

Purpose: Heterotopic ossification (HO), or abnormal bone formation, is a common sequela of total hip arthroplasty. This abnormal bone can impair joint function and must be surgically removed to restore mobility. HO can be prevented by postoperative nonsteroidal anti-inflammatory drug (NSAID) use or radiotherapy (RT). NSAIDs are associated with multiple toxicities, including gastrointestinal bleeding. Although RT has been shown to be more efficacious than NSAIDs at preventing HO, its cost-effectiveness has been questioned. Methods and Materials: We performed an analysis of the cost of postoperative RT to the hip compared with NSAID administration, taking into account the costs of surgerymore » for HO formation, treatment-induced morbidity, and productivity loss from missed work. The costs of RT, surgical revision, and treatment of gastrointestinal bleeding were estimated using the 2007 Medicare Fee Schedule and inpatient diagnosis-related group codes. The cost of lost wages was estimated using the 2006 median salary data from the U.S. Census Bureau. Results: The cost of administering RT was estimated at $899 vs. $20 for NSAID use. After accounting for the additional costs associated with revision total hip arthroplasty and gastrointestinal bleeding, the corresponding estimated costs were $1,208 vs. $930. Conclusion: If the costs associated with treatment failure and treatment-induced morbidity are considered, the cost of NSAIDs approaches that of RT. Other NSAID morbidities and quality-of-life differences that are difficult to quantify add to the cost of NSAIDs. These considerations have led us to recommend RT as the preferred modality for use in prophylaxis against HO after total hip arthroplasty, even when the cost is considered.« less

Turbomachinery Heat Transfer and Loss Modeling for 3D Navier-Stokes Codes

NASA Technical Reports Server (NTRS)

DeWitt, Kenneth; Ameri, Ali

2005-01-01

This report's contents focus on making use of NASA Glenn on-site computational facilities,to develop, validate, and apply models for use in advanced 3D Navier-Stokes Computational Fluid Dynamics (CFD) codes to enhance the capability to compute heat transfer and losses in turbomachiney.

40 CFR 80.171 - Product transfer documents (PTDs).

Code of Federal Regulations, 2010 CFR

2010-07-01

... being transferred is exempt base gasoline to be used for research, development, or test purposes only, the following warning must also be stated on the PTD: “For use in research, development, and test... codes and other non-regulatory language. (1) Product codes and other non-regulatory language may not be...

The neurobiology of emotion regulation in posttraumatic stress disorder: Amygdala downregulation via real-time fMRI neurofeedback.

PubMed

Nicholson, Andrew A; Rabellino, Daniela; Densmore, Maria; Frewen, Paul A; Paret, Christian; Kluetsch, Rosemarie; Schmahl, Christian; Théberge, Jean; Neufeld, Richard W J; McKinnon, Margaret C; Reiss, Jim; Jetly, Rakesh; Lanius, Ruth A

2017-01-01

Amygdala dysregulation has been shown to be central to the pathophysiology of posttraumatic stress disorder (PTSD) representing a critical treatment target. Here, amygdala downregulation was targeted using real-time fMRI neurofeedback (rt-fMRI-nf) in patients with PTSD, allowing us to examine further the regulation of emotional states during symptom provocation. Patients (n = 10) completed three sessions of rt-fMRI-nf with the instruction to downregulate activation in the amygdala, while viewing personalized trauma words. Amygdala downregulation was assessed by contrasting (a) regulate trials, with (b) viewing trauma words and not attempting to regulate. Training was followed by one transfer run not involving neurofeedback. Generalized psychophysiological interaction (gPPI) and dynamic causal modeling (DCM) analyses were also computed to explore task-based functional connectivity and causal structure, respectively. It was found that PTSD patients were able to successfully downregulate both right and left amygdala activation, showing sustained effects within the transfer run. Increased activation in the dorsolateral and ventrolateral prefrontal cortex (PFC), regions related to emotion regulation, was observed during regulate as compared with view conditions. Importantly, activation in the PFC, rostral anterior cingulate cortex, and the insula, were negatively correlated to PTSD dissociative symptoms in the transfer run. Increased functional connectivity between the amygdala- and both the dorsolateral and dorsomedial PFC was found during regulate, as compared with view conditions during neurofeedback training. Finally, our DCM analysis exploring directional structure suggested that amygdala downregulation involves both top-down and bottom-up information flow with regard to observed PFC-amygdala connectivity. This is the first demonstration of successful downregulation of the amygdala using rt-fMRI-nf in PTSD, which was critically sustained in a subsequent transfer run without neurofeedback, and corresponded to increased connectivity with prefrontal regions involved in emotion regulation during the intervention. Hum Brain Mapp 38:541-560, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Transferability and within- and between-laboratory reproducibilities of EpiSensA for predicting skin sensitization potential in vitro: A ring study in three laboratories.

PubMed

Mizumachi, Hideyuki; Sakuma, Megumi; Ikezumi, Mayu; Saito, Kazutoshi; Takeyoshi, Midori; Imai, Noriyasu; Okutomi, Hiroko; Umetsu, Asami; Motohashi, Hiroko; Watanabe, Mika; Miyazawa, Masaaki

2018-05-03

The epidermal sensitization assay (EpiSensA) is an in vitro skin sensitization test method based on gene expression of four markers related to the induction of skin sensitization; the assay uses commercially available reconstructed human epidermis. EpiSensA has exhibited an accuracy of 90% for 72 chemicals, including lipophilic chemicals and pre-/pro-haptens, when compared with the results of the murine local lymph node assay. In this work, a ring study was performed by one lead and two naive laboratories to evaluate the transferability, as well as within- and between-laboratory reproducibilities, of EpiSensA. Three non-coded chemicals (two lipophilic sensitizers and one non-sensitizer) were tested for the assessment of transferability and 10 coded chemicals (seven sensitizers and three non-sensitizers, including four lipophilic chemicals) were tested for the assessment of reproducibility. In the transferability phase, the non-coded chemicals (two sensitizers and one non-sensitizer) were correctly classified at the two naive laboratories, indicating that the EpiSensA protocol was transferred successfully. For the within-laboratory reproducibility, the data generated with three coded chemicals tested in three independent experiments in each laboratory gave consistent predictions within laboratories. For the between-laboratory reproducibility, 9 of the 10 coded chemicals tested once in each laboratory provided consistent predictions among the three laboratories. These results suggested that EpiSensA has good transferability, as well as within- and between-laboratory reproducibility. Copyright © 2018 John Wiley & Sons, Ltd.

Design and Evaluation of a Chamber Capable of Containing the Detonation Effects of 40 Pounds of TNT

DTIC Science & Technology

1975-11-01

Boiler and Pressure Vessel Code , 197A. For the girth welds, short lengths of 26-in.-dia. pipe were tacked to the vessel around the...and tensile tests meet the requirements of Section IX, ASHE Boiler and Pressure Vessel Code , 1974. Weld made by W. H. Stefanov ■.^^ w-^iiMaLwärt...Macro Results Kos, No Remarl.s The results of the bond and it^nsile tests met the requirements of Section IX, ASME Boiler and Pressure

Predicting radiative heat transfer in thermochemical nonequilibrium flow fields. Theory and user's manual for the LORAN code

NASA Technical Reports Server (NTRS)

Chambers, Lin Hartung

1994-01-01

The theory for radiation emission, absorption, and transfer in a thermochemical nonequilibrium flow is presented. The expressions developed reduce correctly to the limit at equilibrium. To implement the theory in a practical computer code, some approximations are used, particularly the smearing of molecular radiation. Details of these approximations are presented and helpful information is included concerning the use of the computer code. This user's manual should benefit both occasional users of the Langley Optimized Radiative Nonequilibrium (LORAN) code and those who wish to use it to experiment with improved models or properties.

DRA/NASA/ONERA Collaboration on Icing Research. Part 2; Prediction of Airfoil Ice Accretion

NASA Technical Reports Server (NTRS)

Wright, William B.; Gent, R. W.; Guffond, Didier

1997-01-01

This report presents results from a joint study by DRA, NASA, and ONERA for the purpose of comparing, improving, and validating the aircraft icing computer codes developed by each agency. These codes are of three kinds: (1) water droplet trajectory prediction, (2) ice accretion modeling, and (3) transient electrothermal deicer analysis. In this joint study, the agencies compared their code predictions with each other and with experimental results. These comparison exercises were published in three technical reports, each with joint authorship. DRA published and had first authorship of Part 1 - Droplet Trajectory Calculations, NASA of Part 2 - Ice Accretion Prediction, and ONERA of Part 3 - Electrothermal Deicer Analysis. The results cover work done during the period from August 1986 to late 1991. As a result, all of the information in this report is dated. Where necessary, current information is provided to show the direction of current research. In this present report on ice accretion, each agency predicted ice shapes on two dimensional airfoils under icing conditions for which experimental ice shapes were available. In general, all three codes did a reasonable job of predicting the measured ice shapes. For any given experimental condition, one of the three codes predicted the general ice features (i.e., shape, impingement limits, mass of ice) somewhat better than did the other two. However, no single code consistently did better than the other two over the full range of conditions examined, which included rime, mixed, and glaze ice conditions. In several of the cases, DRA showed that the user's knowledge of icing can significantly improve the accuracy of the code prediction. Rime ice predictions were reasonably accurate and consistent among the codes, because droplets freeze on impact and the freezing model is simple. Glaze ice predictions were less accurate and less consistent among the codes, because the freezing model is more complex and is critically dependent upon unsubstantiated heat transfer and surface roughness models. Thus, heat transfer prediction methods used in the codes became the subject for a separate study in this report to compare predicted heat transfer coefficients with a limited experimental database of heat transfer coefficients for cylinders with simulated glaze and rime ice shapes. The codes did a good job of predicting heat transfer coefficients near the stagnation region of the ice shapes. But in the region of the ice horns, all three codes predicted heat transfer coefficients considerably higher than the measured values. An important conclusion of this study is that further research is needed to understand the finer detail of of the glaze ice accretion process and to develop improved glaze ice accretion models.

Fast and Accurate Hybrid Stream PCRTMSOLAR Radiative Transfer Model for Reflected Solar Spectrum Simulation in the Cloudy Atmosphere

NASA Technical Reports Server (NTRS)

Yang, Qiguang; Liu, Xu; Wu, Wan; Kizer, Susan; Baize, Rosemary R.

2016-01-01

A hybrid stream PCRTM-SOLAR model has been proposed for fast and accurate radiative transfer simulation. It calculates the reflected solar (RS) radiances with a fast coarse way and then, with the help of a pre-saved matrix, transforms the results to obtain the desired high accurate RS spectrum. The methodology has been demonstrated with the hybrid stream discrete ordinate (HSDO) radiative transfer (RT) model. The HSDO method calculates the monochromatic radiances using a 4-stream discrete ordinate method, where only a small number of monochromatic radiances are simulated with both 4-stream and a larger N-stream (N = 16) discrete ordinate RT algorithm. The accuracy of the obtained channel radiance is comparable to the result from N-stream moderate resolution atmospheric transmission version 5 (MODTRAN5). The root-mean-square errors are usually less than 5x10(exp -4) mW/sq cm/sr/cm. The computational speed is three to four-orders of magnitude faster than the medium speed correlated-k option MODTRAN5. This method is very efficient to simulate thousands of RS spectra under multi-layer clouds/aerosols and solar radiation conditions for climate change study and numerical weather prediction applications.

Probing the communication of deoxythymidine triphosphate in HIV-1 reverse transcriptase by communication maps and interaction energy studies.

PubMed

Gnanasekaran, Ramachandran

2017-11-08

We calculate communication maps for HIV-1 Reverse Transcriptase (RT) to elucidate energy transfer pathways between deoxythymidine triphosphate (dTTP) and other parts of the protein. This approach locates energy transport channels from the dTTP to remote regions of the protein via residues and water molecules. We examine the water dynamics near the catalytic site of HIV-1 RT by molecular dynamics (MD) simulations. We find that, within the catalytic site, the relaxation of water molecules is similar to that of the hydration water molecules present in other proteins and the relaxation time scale is fast enough to transport energy and helps in communication between dTTP and other residues in the system. To quantify energy transfer, we also calculate the interaction energies of dTTP, 2Mg 2+ , doxy-guanosine nucleotide (DG22) with their surrounding residues by using the B3LYP-D3 method. The results, from classical vibrational energy diffusivity and QM interaction energy, are complementary to identify the important residues involved in the process of polymerization. The positive and negative interactions by dTTP with different types of residues in the catalytic region make the residues transfer energy through vibrational communication.

SEURAT: SPH scheme extended with ultraviolet line radiative transfer

NASA Astrophysics Data System (ADS)

Abe, Makito; Suzuki, Hiroyuki; Hasegawa, Kenji; Semelin, Benoit; Yajima, Hidenobu; Umemura, Masayuki

2018-05-01

We present a novel Lyman alpha (Ly α) radiative transfer code, SEURAT (SPH scheme Extended with Ultraviolet line RAdiative Transfer), where line scatterings are solved adaptively with the resolution of the smoothed particle hydrodynamics (SPH). The radiative transfer method implemented in SEURAT is based on a Monte Carlo algorithm in which the scattering and absorption by dust are also incorporated. We perform standard test calculations to verify the validity of the code; (i) emergent spectra from a static uniform sphere, (ii) emergent spectra from an expanding uniform sphere, and (iii) escape fraction from a dusty slab. Thereby, we demonstrate that our code solves the {Ly} α radiative transfer with sufficient accuracy. We emphasize that SEURAT can treat the transfer of {Ly} α photons even in highly complex systems that have significantly inhomogeneous density fields. The high adaptivity of SEURAT is desirable to solve the propagation of {Ly} α photons in the interstellar medium of young star-forming galaxies like {Ly} α emitters (LAEs). Thus, SEURAT provides a powerful tool to model the emergent spectra of {Ly} α emission, which can be compared to the observations of LAEs.

Expression of nitric oxide synthase-2 in the lungs decreases airway resistance and responsiveness.

PubMed

Hjoberg, Josephine; Shore, Stephanie; Kobzik, Lester; Okinaga, Shoji; Hallock, Arlene; Vallone, Joseph; Subramaniam, Venkat; De Sanctis, George T; Elias, Jack A; Drazen, Jeffrey M; Silverman, Eric S

2004-07-01

Individuals with asthma have increased levels of nitric oxide in their exhaled air. To explore its role, we have developed a regulatable transgenic mouse capable of overexpressing inducible nitric oxide synthase in a lung-specific fashion. The CC10-rtTA-NOS-2 mouse contains two transgenes, a reverse tetracycline transactivator under the control of the Clara cell protein promoter and the mouse nitric oxide synthase-2 (NOS-2) coding region under control of a tetracycline operator. Addition of doxycycline to the drinking water of CC10-rtTA-NOS-2 mice causes an increase in nitric oxide synthase-2 that is largely confined to the airway epithelium. The fraction of expired nitric oxide increases over the first 24 h from approximately 10 parts per billion to a plateau of approximately 20 parts per billion. There were no obvious differences between CC10-rtTA-NOS-2 mice, with or without doxycycline, and wild-type mice in lung histology, bronchoalveolar protein, total cell count, or count differentials. However, airway resistance was lower in CC10-rtTA-NOS-2 mice with doxycycline than in CC10-rtTA-NOS-2 mice without doxycycline or wild-type mice with doxycycline. Moreover, doxycycline-treated CC10-rtTA-NOS-2 mice were hyporesponsive to methacholine compared with other groups. These data suggest that increased nitric oxide in the airways has no proinflammatory effects per se and may have beneficial effects on pulmonary function.

Profiling structured product labeling with NDF-RT and RxNorm

PubMed Central

2012-01-01

Background Structured Product Labeling (SPL) is a document markup standard approved by Health Level Seven (HL7) and adopted by United States Food and Drug Administration (FDA) as a mechanism for exchanging drug product information. The SPL drug labels contain rich information about FDA approved clinical drugs. However, the lack of linkage to standard drug ontologies hinders their meaningful use. NDF-RT (National Drug File Reference Terminology) and NLM RxNorm as standard drug ontology were used to standardize and profile the product labels. Methods In this paper, we present a framework that intends to map SPL drug labels with existing drug ontologies: NDF-RT and RxNorm. We also applied existing categorical annotations from the drug ontologies to classify SPL drug labels into corresponding classes. We established the classification and relevant linkage for SPL drug labels using the following three approaches. First, we retrieved NDF-RT categorical information from the External Pharmacologic Class (EPC) indexing SPLs. Second, we used the RxNorm and NDF-RT mappings to classify and link SPLs with NDF-RT categories. Third, we profiled SPLs using RxNorm term type information. In the implementation process, we employed a Semantic Web technology framework, in which we stored the data sets from NDF-RT and SPLs into a RDF triple store, and executed SPARQL queries to retrieve data from customized SPARQL endpoints. Meanwhile, we imported RxNorm data into MySQL relational database. Results In total, 96.0% SPL drug labels were mapped with NDF-RT categories whereas 97.0% SPL drug labels are linked to RxNorm codes. We found that the majority of SPL drug labels are mapped to chemical ingredient concepts in both drug ontologies whereas a relatively small portion of SPL drug labels are mapped to clinical drug concepts. Conclusions The profiling outcomes produced by this study would provide useful insights on meaningful use of FDA SPL drug labels in clinical applications through standard drug ontologies such as NDF-RT and RxNorm. PMID:23256517

Profiling structured product labeling with NDF-RT and RxNorm.

PubMed

Zhu, Qian; Jiang, Guoqian; Chute, Christopher G

2012-12-20

Structured Product Labeling (SPL) is a document markup standard approved by Health Level Seven (HL7) and adopted by United States Food and Drug Administration (FDA) as a mechanism for exchanging drug product information. The SPL drug labels contain rich information about FDA approved clinical drugs. However, the lack of linkage to standard drug ontologies hinders their meaningful use. NDF-RT (National Drug File Reference Terminology) and NLM RxNorm as standard drug ontology were used to standardize and profile the product labels. In this paper, we present a framework that intends to map SPL drug labels with existing drug ontologies: NDF-RT and RxNorm. We also applied existing categorical annotations from the drug ontologies to classify SPL drug labels into corresponding classes. We established the classification and relevant linkage for SPL drug labels using the following three approaches. First, we retrieved NDF-RT categorical information from the External Pharmacologic Class (EPC) indexing SPLs. Second, we used the RxNorm and NDF-RT mappings to classify and link SPLs with NDF-RT categories. Third, we profiled SPLs using RxNorm term type information. In the implementation process, we employed a Semantic Web technology framework, in which we stored the data sets from NDF-RT and SPLs into a RDF triple store, and executed SPARQL queries to retrieve data from customized SPARQL endpoints. Meanwhile, we imported RxNorm data into MySQL relational database. In total, 96.0% SPL drug labels were mapped with NDF-RT categories whereas 97.0% SPL drug labels are linked to RxNorm codes. We found that the majority of SPL drug labels are mapped to chemical ingredient concepts in both drug ontologies whereas a relatively small portion of SPL drug labels are mapped to clinical drug concepts. The profiling outcomes produced by this study would provide useful insights on meaningful use of FDA SPL drug labels in clinical applications through standard drug ontologies such as NDF-RT and RxNorm.

A Broadband Waveguide Transfer Standard for Dissemination of UK National Microwave Power Standards,

DTIC Science & Technology

1982-01-01

la )PT " RT a where RT is the resistance of the thermistor when the bridge is balanced. Although the thermistor mount is temperature controlled, some...voltage difference V1 - V and Vb - V2 - V then equation la 4 ... . .. mmm mmm mmmmmmmm m m mm mm mmmm m mm A becomes 2V(V - Vb) + V 2 - 2 P a b a b (lb...Weidman, "An international intercomparison of power standards in WR-28 waveguide". Metrologia , 17, June 1981. 4 G F Engen. "A refined X-band microwave

Friendly Extensible Transfer Tool Beta Version

DOE Office of Scientific and Technical Information (OSTI.GOV)

Collins, William P.; Gutierrez, Kenneth M.; McRee, Susan R.

2016-04-15

Often data transfer software is designed to meet specific requirements or apply to specific environments. Frequently, this requires source code integration for added functionality. An extensible data transfer framework is needed to more easily incorporate new capabilities, in modular fashion. Using FrETT framework, functionality may be incorporated (in many cases without need of source code) to handle new platform capabilities: I/O methods (e.g., platform specific data access), network transport methods, data processing (e.g., data compression.).

Scheduling observational and physical practice: influence on the coding of simple motor sequences.

PubMed

Ellenbuerger, Thomas; Boutin, Arnaud; Blandin, Yannick; Shea, Charles H; Panzer, Stefan

2012-01-01

The main purpose of the present experiment was to determine the coordinate system used in the development of movement codes when observational and physical practice are scheduled across practice sessions. The task was to reproduce a 1,300-ms spatial-temporal pattern of elbow flexions and extensions. An intermanual transfer paradigm with a retention test and two effector (contralateral limb) transfer tests was used. The mirror effector transfer test required the same pattern of homologous muscle activation and sequence of limb joint angles as that performed or observed during practice, and the non-mirror effector transfer test required the same spatial pattern movements as that performed or observed. The test results following the first acquisition session replicated the findings of Gruetzmacher, Panzer, Blandin, and Shea (2011) . The results following the second acquisition session indicated a strong advantage for participants who received physical practice in both practice sessions or received observational practice followed by physical practice. This advantage was found on both the retention and the mirror transfer tests compared to the non-mirror transfer test. These results demonstrate that codes based in motor coordinates can be developed relatively quickly and effectively for a simple spatial-temporal movement sequence when participants are provided with physical practice or observation followed by physical practice, but physical practice followed by observational practice or observational practice alone limits the development of codes based in motor coordinates.

RT DDA: A hybrid method for predicting the scattering properties by densely packed media

NASA Astrophysics Data System (ADS)

Ramezan Pour, B.; Mackowski, D.

2017-12-01

The most accurate approaches to predicting the scattering properties of particulate media are based on exact solutions of the Maxwell's equations (MEs), such as the T-matrix and discrete dipole methods. Applying these techniques for optically thick targets is challenging problem due to the large-scale computations and are usually substituted by phenomenological radiative transfer (RT) methods. On the other hand, the RT technique is of questionable validity in media with large particle packing densities. In recent works, we used numerically exact ME solvers to examine the effects of particle concentration on the polarized reflection properties of plane parallel random media. The simulations were performed for plane parallel layers of wavelength-sized spherical particles, and results were compared with RT predictions. We have shown that RTE results monotonically converge to the exact solution as the particle volume fraction becomes smaller and one can observe a nearly perfect fit for packing densities of 2%-5%. This study describes the hybrid technique composed of exact and numerical scalar RT methods. The exact methodology in this work is the plane parallel discrete dipole approximation whereas the numerical method is based on the adding and doubling method. This approach not only decreases the computational time owing to the RT method but also includes the interference and multiple scattering effects, so it may be applicable to large particle density conditions.

Bilingualism, Code-Switching, Language Mixing, Transfer and Borrowing; Clarifying Terminologies in the Literature.

ERIC Educational Resources Information Center

Yumoto, Kazuko

A study of second language acquisition in two Japanese children, and corresponding examination of research literature, led to this effort to clarify terminology related to cross-linguistic influence in language contact situations. Terms include: bilingualism, code-switching, language mixing, language transfer, and borrowing. Two forms of transfer…

A survey to identify the clinical coding and classification systems currently in use across Europe.

PubMed

de Lusignan, S; Minmagh, C; Kennedy, J; Zeimet, M; Bommezijn, H; Bryant, J

2001-01-01

This is a survey to identify what clinical coding systems are currently in use across the European Union, and the states seeking membership to it. We sought to identify what systems are currently used and to what extent they were subject to local adaptation. Clinical coding should facilitate identifying key medical events in a computerised medical record, and aggregating information across groups of records. The emerging new driver is as the enabler of the life-long computerised medical record. A prerequisite for this level of functionality is the transfer of information between different computer systems. This transfer can be facilitated either by working on the interoperability problems between disparate systems or by harmonising the underlying data. This paper examines the extent to which the latter has occurred across Europe. Literature and Internet search. Requests for information via electronic mail to pan-European mailing lists of health informatics professionals. Coding systems are now a de facto part of health information systems across Europe. There are relatively few coding systems in existence across Europe. ICD9 and ICD 10, ICPC and Read were the most established. However the local adaptation of these classification systems either on a by country or by computer software manufacturer basis; significantly reduces the ability for the meaning coded with patients computer records to be easily transferred from one medical record system to another. There is no longer any debate as to whether a coding or classification system should be used. Convergence of different classifications systems should be encouraged. Countries and computer manufacturers within the EU should be encouraged to stop making local modifications to coding and classification systems, as this practice risks significantly slowing progress towards easy transfer of records between computer systems.

A Very Efficient Transfer Function Bounding Technique on Bit Error Rate for Viterbi Decoded, Rate 1/N Convolutional Codes

NASA Technical Reports Server (NTRS)

Lee, P. J.

1984-01-01

For rate 1/N convolutional codes, a recursive algorithm for finding the transfer function bound on bit error rate (BER) at the output of a Viterbi decoder is described. This technique is very fast and requires very little storage since all the unnecessary operations are eliminated. Using this technique, we find and plot bounds on the BER performance of known codes of rate 1/2 with K 18, rate 1/3 with K 14. When more than one reported code with the same parameter is known, we select the code that minimizes the required signal to noise ratio for a desired bit error rate of 0.000001. This criterion of determining goodness of a code had previously been found to be more useful than the maximum free distance criterion and was used in the code search procedures of very short constraint length codes. This very efficient technique can also be used for searches of longer constraint length codes.

Improving Estimated Optical Constants With MSTM and DDSCAT Modeling

NASA Astrophysics Data System (ADS)

Pitman, K. M.; Wolff, M. J.

2015-12-01

We present numerical experiments to determine quantitatively the effects of mineral particle clustering on Mars spacecraft spectral signatures and to improve upon the values of refractive indices (optical constants n, k) derived from Mars dust laboratory analog spectra such as those from RELAB and MRO CRISM libraries. Whereas spectral properties for Mars analog minerals and actual Mars soil are dominated by aggregates of particles smaller than the size of martian atmospheric dust, the analytic radiative transfer (RT) solutions used to interpret planetary surfaces assume that individual, well-separated particles dominate the spectral signature. Both in RT models and in the refractive index derivation methods that include analytic RT approximations, spheres are also over-used to represent nonspherical particles. Part of the motivation is that the integrated effect over randomly oriented particles on quantities such as single scattering albedo and phase function are relatively less than for single particles. However, we have seen in previous numerical experiments that when varying the shape and size of individual grains within a cluster, the phase function changes in both magnitude and slope, thus the "relatively less" effect is more significant than one might think. Here we examine the wavelength dependence of the forward scattering parameter with multisphere T-matrix (MSTM) and discrete dipole approximation (DDSCAT) codes that compute light scattering by layers of particles on planetary surfaces to see how albedo is affected and integrate our model results into refractive index calculations to remove uncertainties in approximations and parameters that can lower the accuracy of optical constants. By correcting the single scattering albedo and phase function terms in the refractive index determinations, our data will help to improve the understanding of Mars in identifying, mapping the distributions, and quantifying abundances for these minerals and will address long-standing questions on fundamental physics in the martian surface (e.g., what is the fundamental scattering unit for closely packed dust or regolith grains?). This work was supported by NASA's Mars Fundamental Research Program and performed with the Pleiades cluster courtesy of NASA's Advanced Supercomputing Division.

FitSKIRT: genetic algorithms to automatically fit dusty galaxies with a Monte Carlo radiative transfer code

NASA Astrophysics Data System (ADS)

De Geyter, G.; Baes, M.; Fritz, J.; Camps, P.

2013-02-01

We present FitSKIRT, a method to efficiently fit radiative transfer models to UV/optical images of dusty galaxies. These images have the advantage that they have better spatial resolution compared to FIR/submm data. FitSKIRT uses the GAlib genetic algorithm library to optimize the output of the SKIRT Monte Carlo radiative transfer code. Genetic algorithms prove to be a valuable tool in handling the multi- dimensional search space as well as the noise induced by the random nature of the Monte Carlo radiative transfer code. FitSKIRT is tested on artificial images of a simulated edge-on spiral galaxy, where we gradually increase the number of fitted parameters. We find that we can recover all model parameters, even if all 11 model parameters are left unconstrained. Finally, we apply the FitSKIRT code to a V-band image of the edge-on spiral galaxy NGC 4013. This galaxy has been modeled previously by other authors using different combinations of radiative transfer codes and optimization methods. Given the different models and techniques and the complexity and degeneracies in the parameter space, we find reasonable agreement between the different models. We conclude that the FitSKIRT method allows comparison between different models and geometries in a quantitative manner and minimizes the need of human intervention and biasing. The high level of automation makes it an ideal tool to use on larger sets of observed data.

Cognitive and Neural Sciences Division 1989 Programs.

DTIC Science & Technology

1989-09-01

INVESTIGATOR: Herbert L. Roitblat University of Hawaii Department of Psychology (808) 948-8027 R&T PROJECT CODE: 4426707 CONTRACT No: N0001489J1093 CURRENT END...Posner, 76, 77 Fuster, 107 Kieras, 32 247 V Reckase, 54 Speidel, 96 Van Cott, 127 Robertson, 126 Sperling, 81 Van Essen, 85 Roitblat , 216 Squire, 153 Van

The cDNA-derived amino acid sequence of hemoglobin II from Lucina pectinata.

PubMed

Torres-Mercado, Elineth; Renta, Jessicca Y; Rodríguez, Yolanda; López-Garriga, Juan; Cadilla, Carmen L

2003-11-01

Hemoglobin II from the clam Lucina pectinata is an oxygen-reactive protein with a unique structural organization in the heme pocket involving residues Gln65 (E7), Tyr30 (B10), Phe44 (CD1), and Phe69 (E11). We employed the reverse transcriptase-polymerase chain reaction (RT-PCR) and methods to synthesize various cDNA(HbII). An initial 300-bp cDNA clone was amplified from total RNA by RT-PCR using degenerate oligonucleotides. Gene-specific primers derived from the HbII-partial cDNA sequence were used to obtain the 5' and 3' ends of the cDNA by RACE. The length of the HbII cDNA, estimated from overlapping clones, was approximately 2114 bases. Northern blot analysis revealed that the mRNA size of HbII agrees with the estimated size using cDNA data. The coding region of the full-length HbII cDNA codes for 151 amino acids. The calculated molecular weight of HbII, including the heme group and acetylated N-terminal residue, is 17,654.07 Da.

13 CFR 120.1709 - Transfers of Pool Certificates.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 13 Business Credit and Assistance 1 2012-01-01 2012-01-01 false Transfers of Pool Certificates... Transfers of Pool Certificates. (a) Transfer of Pool Certificates. A Pool Certificate is transferable. A transfer of a Pool Certificate must comply with Article 8 of the Uniform Commercial Code of the State of...

13 CFR 120.1709 - Transfers of Pool Certificates.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Transfers of Pool Certificates... Transfers of Pool Certificates. (a) Transfer of Pool Certificates. A Pool Certificate is transferable. A transfer of a Pool Certificate must comply with Article 8 of the Uniform Commercial Code of the State of...

13 CFR 120.1709 - Transfers of Pool Certificates.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 13 Business Credit and Assistance 1 2014-01-01 2014-01-01 false Transfers of Pool Certificates... Transfers of Pool Certificates. (a) Transfer of Pool Certificates. A Pool Certificate is transferable. A transfer of a Pool Certificate must comply with Article 8 of the Uniform Commercial Code of the State of...

13 CFR 120.1709 - Transfers of Pool Certificates.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 13 Business Credit and Assistance 1 2011-01-01 2011-01-01 false Transfers of Pool Certificates... Transfers of Pool Certificates. (a) Transfer of Pool Certificates. A Pool Certificate is transferable. A transfer of a Pool Certificate must comply with Article 8 of the Uniform Commercial Code of the State of...

Irreducible 3D Radiative Transfer Effects in Multi-angle/Multi-spectral Radio-Polarimetric Signals (Not Noise!) from a Mixture of Clouds and Aerosol in a Single Large-Footprint Pixel

NASA Astrophysics Data System (ADS)

Davis, A. B.; Qu, Z.; Emde, C.; Xu, F.; Marshak, A.

2013-12-01

Although the Glory satellite mission failed at launch, the atmospheric observation strategy implemented in its Aerosol Polarization Sensor (APS) is alive and well since it is at least possible that another one will be built and launched. This strategy is based on APS's along-track scanning spectro-polarimetric measurement system that captures the three main Stokes vector elements (I,Q,U) at a large number (>200) viewing directions for 9 wavelengths emanating from a single pixel that is ~7 km in diameter at nadir and stretches into a ~7 x 20 km^2 ellipse at the most oblique views to be considered (~70 degrees). Two cloud cameras (CCs) were also onboard Glory to provide spatial context. If the relatively large APS footprint is cloud-free or fully-cloudy, then a 1D vector radiative transfer (RT) model is adequate for predicting the APS signals and, upon iteration over its input parameters, aerosol and cloud property retrievals are expected to be of high quality. And this level of accuracy is indeed required to make a real breakthrough in climate modeling where the radiative properties of aerosols and clouds remain one of the main sources of uncertainty. However, the CCs will often show that the APS's field-of-view is a spatially complex cloud scene, but where we are mostly interested in the ambient aerosols. Moreover, it is precisely these aerosols in contact with clouds that will influence their microphysical and optical properties, leading to the manifold indirect aerosol effects on the climate system that need to be far better understood in order to improve their representation in climate models. Therefore, the research presented here addresses the challenge of characterizing simultaneously aerosols and clouds in a single APS observation. Access to polarization can, at least in principle, be used to separate clouds and aerosols using the cloud-bow directions that will often be sampled by APS. In practice, however, we need to assess the extent of 3D polarized RT unfolding inside the APS pixel that cannot be estimated using a linear mixture of 1D vector RT (vRT) computations assuming either aerosol or cloud is present. Differences between the 1D vRT-based prediction and simulated APS data derived from a high-fidelity 3D vRT model is what we call "irreducible" 3D RT effects. To this end, we have used the vMYSTIC Monte Carlo 3D vRT model. Based on computations for a typical scene with a 3D cumulus cloud field embedded in a horizontally uniform aerosol, we find that the irreducible 3D vRT effects are in the APS's signal--not its noise--especially if the aerosol burden is significant. The cloud-bow region, which is key to any practical cloud-aerosol unmixing algorithm, is particularly vulnerable. Moreover, the adopted 1D vRT-based forward model is assumed to be very well informed about the actual aerosol/cloud properties, meaning that the predicted irreducible 3D vRT effects are a best-case scenario. In reality, the problem will be far more severe. We will nonetheless describe a promising path toward a mitigation scheme. We will also assess the impact of the 3D vRT damage on the joint aerosol-cloud property retrieval.

Neoadjuvant radiotherapy followed by mastectomy and immediate breast reconstruction : An alternative treatment option for locally advanced breast cancer.

PubMed

Pazos, Montserrat; Corradini, Stefanie; Dian, Darius; von Bodungen, Vera; Ditsch, Nina; Wuerstlein, Rachel; Schönecker, Stephan; Harbeck, Nadia; Scheithauer, Heike; Belka, Claus

2017-04-01

The optimal sequence of mastectomy with immediate breast reconstruction (IBR) and radiotherapy (RT) for the treatment of locally advanced breast cancer (LABC) is still under debate. Increased rates of postoperative complications are described following postmastectomy RT. Neoadjuvant RT aims to improve the aesthetic results and simplify the reconstructive pathway. A total of 22 patients diagnosed with LABC and treated with neoadjuvant RT followed by mastectomy and IBR between 04/2012 and 03/2015 were retrospectively analyzed. RT consisted of external beam RT to the breast and the regional lymphatics, if indicated. Both implant-based and autologous tissue-transfer reconstruction techniques were used. At the time of RT, 10 patients had no prior surgery and 12 patients had previously undergone breast-conserving surgery (BCS) with positive resection margins without the possibility to perform a second BCS. Additional neoadjuvant chemotherapy was administered in 18 patients prior to RT. A complete pathological response was achieved in 55.0% of patients. The 2‑year overall survival rate was 89.3%, the 2‑year disease-free-survival 79.8% and the local-recurrence-free survival was 95.2%. The cosmetic result was excellent or good in 66% of the patients treated with upfront mastectomy and 37% of the patients who had previously undergone BCS. Among patients who received implant-based IBR, 4 patients developed serious wound-healing problems with implant loss. The most satisfactory results were achieved with autologous tissue reconstruction. A sequential neoadjuvant chemo-/radiotherapy to allow IBR following mastectomy in selected cases of LABC seems feasible and can be safely attempted. Careful patient selection, close monitoring, and continuous patient support is mandatory to ensure compliance in this treatment strategy.

Nucleocapsid Protein Annealing of a Primer-Template Enhances (+)-Strand DNA Synthesis and Fidelity by HIV-1 Reverse Transcriptase†

PubMed Central

Kim, Jiae; Roberts, Anne; Yuan, Hua; Xiong, Yong; Anderson, Karen S.

2012-01-01

Human immunodeficiency virus type-1 (HIV-1) requires reverse transcriptase (RT) and HIV-1 nucleocapsid protein (NCp7) for proper viral replication. HIV-1 NCp7 has been shown to enhance various steps in reverse transcription including tRNA initiation and strand transfer which may be mediated through interactions with RT as well as RNA and DNA oligonucleotides. With the use of DNA oligonucleotides, we have examined the interaction of NCp7 with RT and the kinetics of reverse transcription during (+)-strand synthesis with an NCp7-facilitated annealed primer-template. Using a pre-steady state kinetics approach, the NCp7-annealed primer-template has a substantial increase (3-7 fold) in the rate of incorporation (kpol) by RT as compared to heat annealed primer-template with single nucleotide incorporation. There was also a 2-fold increase in the binding affinity constant (Kd) of the nucleotide. These differences in kpol and Kd were not through direct interactions between HIV-1 RT and NCp7. When examining extension by RT, the data suggests that the NCp7-annealed primer-template facilitates the formation of a longer product more quickly compared to the heat annealed primer-template. This enhancement in rate is mediated through interactions with NCp7’s zinc fingers and N-terminal domain and nucleic acids. The NCp7-annealed primer-template also enhances the fidelity of RT (3-fold) by slowing the rate of incorporation of an incorrect nucleotide. Taken together, this study elucidates a new role of NCp7 by facilitating DNA-directed DNA synthesis during reverse transcription by HIV-1 RT that may translate into enhanced viral fitness and offers an avenue to exploit for targeted therapeutic intervention against HIV. PMID:22210155

Transfer reaction code with nonlocal interactions

DOE PAGES

Titus, L. J.; Ross, A.; Nunes, F. M.

2016-07-14

We present a suite of codes (NLAT for nonlocal adiabatic transfer) to calculate the transfer cross section for single-nucleon transfer reactions, (d,N)(d,N) or (N,d)(N,d), including nonlocal nucleon–target interactions, within the adiabatic distorted wave approximation. For this purpose, we implement an iterative method for solving the second order nonlocal differential equation, for both scattering and bound states. The final observables that can be obtained with NLAT are differential angular distributions for the cross sections of A(d,N)BA(d,N)B or B(N,d)AB(N,d)A. Details on the implementation of the TT-matrix to obtain the final cross sections within the adiabatic distorted wave approximation method are also provided.more » This code is suitable to be applied for deuteron induced reactions in the range of View the MathML sourceEd=10–70MeV, and provides cross sections with 4% accuracy.« less

First report of charge-transfer induced heat-set hydrogel. Structural insights and remarkable properties

NASA Astrophysics Data System (ADS)

Bhattacharjee, Subham; Maiti, Bappa; Bhattacharya, Santanu

2016-05-01

The remarkable ability of a charge-transfer (CT) complex prepared from a pyrene-based donor (Py-D) and a naphthalenediimide-based acceptor (NDI-A) led to the formation of a deep-violet in color, transparent hydrogel at room temperature (RT-gel). Simultaneously, the RT-gel was diluted beyond its critical gelator concentration (CGC) to obtain a transparent sol. Very interestingly, the resultant sol, on heating above 70 °C, transformed into a heat-set gel instantaneously with a hitherto unknown CGC value. Detailed studies revealed the smaller globular aggregates of the RT-gels fuse to form giant globules upon heating, which, in turn, resulted in heat-set gelation through further aggregation. The thermoresponsive property of Py-D alone and 1 : 1 Py-D : NDI-A CT complex was investigated in detail which revealed the hydrophobic collapse of the oxyethylene chains of the CT complex upon heating was mainly responsible for heat-set gelation. Thixotropy, injectability, as well as stimuli responsiveness of the RT-gels were also addressed. In contrast, heat-set gel did not show thixotropic behavior. The X-ray diffraction (XRD) patterns of the xerogel depicted lamellar packing of the CT stacks in the gel phase. Single crystal XRD studies further evidenced the 1 : 1 mixed CT stack formation in the lamellae and also ruled out orthogonal hydrogen bonding possibilities among the hydrazide unit in the CT gel although such interaction was observed in a single crystal of NDI-A alone. In addition, a Ag+-ion triggered metallogelation of NDI-A and nematic liquid-crystalline property of Py-D were also observed.The remarkable ability of a charge-transfer (CT) complex prepared from a pyrene-based donor (Py-D) and a naphthalenediimide-based acceptor (NDI-A) led to the formation of a deep-violet in color, transparent hydrogel at room temperature (RT-gel). Simultaneously, the RT-gel was diluted beyond its critical gelator concentration (CGC) to obtain a transparent sol. Very interestingly, the resultant sol, on heating above 70 °C, transformed into a heat-set gel instantaneously with a hitherto unknown CGC value. Detailed studies revealed the smaller globular aggregates of the RT-gels fuse to form giant globules upon heating, which, in turn, resulted in heat-set gelation through further aggregation. The thermoresponsive property of Py-D alone and 1 : 1 Py-D : NDI-A CT complex was investigated in detail which revealed the hydrophobic collapse of the oxyethylene chains of the CT complex upon heating was mainly responsible for heat-set gelation. Thixotropy, injectability, as well as stimuli responsiveness of the RT-gels were also addressed. In contrast, heat-set gel did not show thixotropic behavior. The X-ray diffraction (XRD) patterns of the xerogel depicted lamellar packing of the CT stacks in the gel phase. Single crystal XRD studies further evidenced the 1 : 1 mixed CT stack formation in the lamellae and also ruled out orthogonal hydrogen bonding possibilities among the hydrazide unit in the CT gel although such interaction was observed in a single crystal of NDI-A alone. In addition, a Ag+-ion triggered metallogelation of NDI-A and nematic liquid-crystalline property of Py-D were also observed. Electronic supplementary information (ESI) available: General experimental section, synthesis and characterization, single crystal X-ray data including CIF files and additional experimental results. See DOI: 10.1039/c6nr01128d

Radiation Therapy After Breast-Conserving Surgery: Does Hospital Surgical Volume Matter? A Population-Based Study in Taiwan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chien, Chun-Ru; Department of Radiation Oncology, China Medical University Hospital, and School of Medicine, China Medical University, Taichung, Taiwan; Pan, I-Wen

2012-01-01

Purpose: To examine the association between hospital surgical volume and the use of radiation therapy (RT) after breast-conserving surgery (BCS) in Taiwan. Methods and Materials: We used claims data from the National Health Insurance program in Taiwan (1997-2005) in this retrospective population-based study. We identified patients with breast cancer, receipt of BCS, use of radiation, and the factors that could potentially associated with the use of RT from enrollment records, and the ICD-9 and billing codes in claims. We conducted logistic regression to examine factors associated with RT use after BCS, and performed subgroup analyses to examine whether the associationmore » differs by medical center status or hospital volumes. Results: Among 5,094 patients with newly diagnosed invasive breast cancer who underwent BCS, the rate of RT was significantly lower in low-volume hospitals (74% vs. 82%, p < 0.01). Patients treated in low-volume hospitals were less likely to receive RT after BCS (odds ratio = 0.72, 95% confidence interval = 0.62-0.83). In addition, patients treated after the implementation of the voluntary pay-for-performance policy in 2001 were more likely to receive RT (odds ratio = 1.23; 95% confidence interval = 1.05-1.45). Subgroup analyses indicated that the high-volume effect was limited to hospitals accredited as non-medical centers, and that the effect of the pay-for-performance policy was most pronounced among low-volume hospitals. Conclusions: Using population-based data from Taiwan, our study concluded that hospital surgical volume and pay-for-performance policy are positively associated with RT use after BCS.« less

A fast code for channel limb radiances with gas absorption and scattering in a spherical atmosphere

NASA Astrophysics Data System (ADS)

Eluszkiewicz, Janusz; Uymin, Gennady; Flittner, David; Cady-Pereira, Karen; Mlawer, Eli; Henderson, John; Moncet, Jean-Luc; Nehrkorn, Thomas; Wolff, Michael

2017-05-01

We present a radiative transfer code capable of accurately and rapidly computing channel limb radiances in the presence of gaseous absorption and scattering in a spherical atmosphere. The code has been prototyped for the Mars Climate Sounder measuring limb radiances in the thermal part of the spectrum (200-900 cm-1) where absorption by carbon dioxide and water vapor and absorption and scattering by dust and water ice particles are important. The code relies on three main components: 1) The Gauss Seidel Spherical Radiative Transfer Model (GSSRTM) for scattering, 2) The Planetary Line-By-Line Radiative Transfer Model (P-LBLRTM) for gas opacity, and 3) The Optimal Spectral Sampling (OSS) for selecting a limited number of spectral points to simulate channel radiances and thus achieving a substantial increase in speed. The accuracy of the code has been evaluated against brute-force line-by-line calculations performed on the NASA Pleiades supercomputer, with satisfactory results. Additional improvements in both accuracy and speed are attainable through incremental changes to the basic approach presented in this paper, which would further support the use of this code for real-time retrievals and data assimilation. Both newly developed codes, GSSRTM/OSS for MCS and P-LBLRTM, are available for additional testing and user feedback.

Generalized Radiative Transfer as an Efficient Computational Tool for Spatial and/or Spectral Integration over Unresolved Variability in Multi-Angle Observations

NASA Astrophysics Data System (ADS)

Davis, A. B.; Xu, F.; Diner, D. J.

2017-12-01

Two perennial problems in applied theoretical and computational radiative transfer (RT) are: (1) the impact of unresolved spatial variability on large-scale fluxes (in climate models) or radiances (in remote sensing); and (2) efficient-yet-accurate estimation of broadband spectral integrals in radiant energy budget estimation as well as in remote sensing, in particular, of trace gases.Generalized RT (GRT) is a modification of classic RT in an optical medium with uniform extinction where Beer's exponential law for direct transmission is replaced by a monotonically decreasing function with a slower power-law decay. In a convenient parameterized version of GRT, mean extinction replaces the uniform value and just one new property is introduced. As a non-dimensional metric for the unresolved variability, we use the square of the mean extinction coefficient divided by its variance. This parameter is also the exponent of the power-law tail of the modified transmission law.This specific form of sub-exponential transmission has explored for almost two decades in application to spatial variability in the presence of long-range correlations, much like in turbulent media such as clouds, with a focus on multiple scattering. It has also been proposed by Conley and Collins (JQSRT, 112, 1525-, 2011) to improve on the standard (weak-line) implementation of the correlated-k technique for efficient spectral integration.We have merged these two applications within a rigorous formulation of the combined problem, and solve the new integral RT equations in the single-scattering limit. The result is illustrated by addressing practical problems in multi-angle remote sensing of aerosols using the O2 A-band, an emerging methodology for passive profiling of coarse aerosols and clouds.

A First-Order Radiative Transfer Model for Microwave Radiometry of Forest Canopies at L-Band

NASA Technical Reports Server (NTRS)

Kurum, Mehmet; Lang, Roger H.; O'Neill, Peggy E.; Joseph, Alicia T.; Jackson, Thomas J.; Cosh, Michael H.

2011-01-01

In this study, a first-order radiative transfer (RT) model is developed to more accurately account for vegetation canopy scattering by modifying the basic Tau-Omega model (the zero-order RT solution). In order to optimally utilize microwave radiometric data in soil moisture (SM) retrievals over vegetated landscapes, a quantitative understanding of the relationship between scattering mechanisms within vegetation canopies and the microwave brightness temperature is desirable. The first-order RT model is used to investigate this relationship and to perform a physical analysis of the scattered and emitted radiation from vegetated terrain. This model is based on an iterative solution (successive orders of scattering) of the RT equations up to the first order. This formulation adds a new scattering term to the . model. The additional term represents emission by particles (vegetation components) in the vegetation layer and emission by the ground that is scattered once by particles in the layer. The model is tested against 1.4-GHz brightness temperature measurements acquired over deciduous trees by a truck-mounted microwave instrument system called ComRAD in 2007. The model predictions are in good agreement with the data, and they give quantitative understanding for the influence of first-order scattering within the canopy on the brightness temperature. The model results show that the scattering term is significant for trees and modifications are necessary to the . model when applied to dense vegetation. Numerical simulations also indicate that the scattering term has a negligible dependence on SM and is mainly a function of the incidence angle and polarization of the microwave observation. Index Terms Emission,microwave radiometry, scattering, soil, vegetation.

A First-Order Radiative Transfer Model for Microwave Radiometry of Forest Canopies at L-Band

NASA Technical Reports Server (NTRS)

Kurum, Mehmet; Lang, Roger H.; O'Neill, Peggy E.; Joseph, Alicia T.; Jackson, Thomas J.; Cosh, Michael H.

2010-01-01

In this study, a new first-order radiative transfer (RT) model is developed to more accurately account for vegetation canopy scattering by modifying the basic r-co model (the zero-order RT solution). In order to optimally utilize microwave radiometric data in soil moisture (SM) retrievals over moderately to densely vegetated landscapes, a quantitative understanding of the relationship between scattering mechanisms within vegetation canopies and the microwave brightness temperature is desirable. A first-order RT model is used to investigate this relationship and to perform a physical analysis of the scattered and emitted radiation from vegetated terrain. The new model is based on an iterative solution (successive orders of scattering) of the RT equations up to the first order. This formulation adds a new scattering term to the i-w model. The additional term represents emission by particles (vegetation components) in the vegetation layer and emission by the ground that is scattered once by particles in the layer. The new model is tested against 1.4 GHz brightness temperature measurements acquired over deciduous trees by a truck-mounted microwave instrument system called ComRAD in 2007. The model predictions are in good agreement with the data and they give quantitative understanding for the influence of first-order scattering within the canopy on the brightness temperature. The model results show that the scattering term is significant for trees and modifications are necessary to the T-w model when applied to dense vegetation. Numerical simulations also indicate that the scattering term has a negligible dependence on SM and is mainly a function of the angle and polarization of the microwave observation.

Learning on the Big Bay

ERIC Educational Resources Information Center

Philp, Michael J.

1978-01-01

Anne Arundel Community College uses the Chesapeake Bay for a flexible ocean engineering technology program which includes mechanical, electrical, and environmental options for transfer and/or vocational students, and adult education programs covering such subjects as sailing, Bay history, boat building, scuba-diving, and marine biology. (RT)

The Electrification of Thunderstorms.

ERIC Educational Resources Information Center

Williams, Earle R.

1988-01-01

Discusses the natural phenomena of lightning. States that the exact microphysical processes responsible for the charging of storm clouds remain in dispute although for centuries it has been known that lightning is a form of electricity. Uses diagrams to explain the structures of thunderclouds and charge transfer. (RT)

Reverse transcriptase polymerase chain reaction on fine needle aspirates for rapid detection of translocations in synovial sarcoma.

PubMed

Nilsson, G; Wang, M; Wejde, J; Kanter, L; Karlén, J; Tani, E; Kreicbergs, A; Larsson, O

1998-01-01

To evaluate the utilization of fine needle aspiration (FNA) biopsy to obtain material for reverse-transcriptase polymerase chain reaction (RT-PCR) in the detection of the t(X;18)(p11.2;q11.2) translocation in synovial sarcomas. We applied RT-PCR to detection of synovial sarcoma fusion gene transcripts on fine needle aspirates. Five clinical samples were first analyzed: one was a tumor previously diagnosed as malignant hemangiopericytoma, one was a poorly defined tumor, and three were suspected synovial sarcomas. FNA material was transferred directly to the RT-PCR reaction tube without RNA extraction. The t(X;18) translocation could be detected on the limited amount of material that FNA provides. In each of the cases studied the representivity of the tumor samples was confirmed microscopically. Our protocol permits analysis directly on representative samples without extraction of RNA. The results imply that RT-PCR offers reliable detection of sarcoma fusion gene transcripts on fine needle aspirates. The procedure, apart from being applicable to outpatients, is rapid and sensitive.

Optical properties of mineral dust aerosol in the thermal infrared

NASA Astrophysics Data System (ADS)

Köhler, Claas H.

2017-02-01

The optical properties of mineral dust and biomass burning aerosol in the thermal infrared (TIR) are examined by means of Fourier Transform Infrared Spectrometer (FTIR) measurements and radiative transfer (RT) simulations. The measurements were conducted within the scope of the Saharan Mineral Dust Experiment 2 (SAMUM-2) at Praia (Cape Verde) in January and February 2008. The aerosol radiative effect in the TIR atmospheric window region 800-1200 cm-1 (8-12 µm) is discussed in two case studies. The first case study employs a combination of IASI measurements and RT simulations to investigate a lofted optically thin biomass burning layer with emphasis on its potential influence on sea surface temperature (SST) retrieval. The second case study uses ground based measurements to establish the importance of particle shape and refractive index for benchmark RT simulations of dust optical properties in the TIR domain. Our research confirms earlier studies suggesting that spheroidal model particles lead to a significantly improved agreement between RT simulations and measurements compared to spheres. However, room for improvement remains, as the uncertainty originating from the refractive index data for many aerosol constituents prohibits more conclusive results.

RAPTOR. I. Time-dependent radiative transfer in arbitrary spacetimes

NASA Astrophysics Data System (ADS)

Bronzwaer, T.; Davelaar, J.; Younsi, Z.; Mościbrodzka, M.; Falcke, H.; Kramer, M.; Rezzolla, L.

2018-05-01

Context. Observational efforts to image the immediate environment of a black hole at the scale of the event horizon benefit from the development of efficient imaging codes that are capable of producing synthetic data, which may be compared with observational data. Aims: We aim to present RAPTOR, a new public code that produces accurate images, animations, and spectra of relativistic plasmas in strong gravity by numerically integrating the equations of motion of light rays and performing time-dependent radiative transfer calculations along the rays. The code is compatible with any analytical or numerical spacetime. It is hardware-agnostic and may be compiled and run both on GPUs and CPUs. Methods: We describe the algorithms used in RAPTOR and test the code's performance. We have performed a detailed comparison of RAPTOR output with that of other radiative-transfer codes and demonstrate convergence of the results. We then applied RAPTOR to study accretion models of supermassive black holes, performing time-dependent radiative transfer through general relativistic magneto-hydrodynamical (GRMHD) simulations and investigating the expected observational differences between the so-called fast-light and slow-light paradigms. Results: Using RAPTOR to produce synthetic images and light curves of a GRMHD model of an accreting black hole, we find that the relative difference between fast-light and slow-light light curves is less than 5%. Using two distinct radiative-transfer codes to process the same data, we find integrated flux densities with a relative difference less than 0.01%. Conclusions: For two-dimensional GRMHD models, such as those examined in this paper, the fast-light approximation suffices as long as errors of a few percent are acceptable. The convergence of the results of two different codes demonstrates that they are, at a minimum, consistent. The public version of RAPTOR is available at the following URL: http://https://github.com/tbronzwaer/raptor

Duplication of SOX9 associated with 46,XX ovotesticular disorder of sex development.

PubMed

López-Hernández, Berenice; Méndez, Juan Pablo; Coral-Vázquez, Ramón Mauricio; Benítez-Granados, Jesús; Zenteno, Juan Carlos; Villegas-Ruiz, Vanessa; Calzada-León, Raúl; Soderlund, Daniela; Canto, Patricia

2018-04-04

The purpose of the present study was to investigate whether ten unrelated SRY-negative individuals with this sex differentiation disorder presented a double dose of SOX9 as the cause of their disease. Ten unrelated SRY-negative 46,XX ovotesticular disorder of sexual development (DSD) subjects were molecularly studied. Multiplex-ligation dependent probe amplification (MLPA) and quantitative real-time PCR analysis (qRT-PCR) for SOX9 were performed. The MLPA analysis demonstrated that one patient presented a heterozygous duplication of the entire SOX9 coding region (above 1.3 value of peak ratio), as well as at least a ~ 483 kb upstream duplication. Moreover, no duplication of other SOX9 probes was observed corresponding to the region between -1007 and -1500 kb upstream. A qRT-PCR analysis showed a duplication of at least -581 kb upstream and ~1.63 kb of the coding region that encompasses exon 3. The limits of the duplication were mapped approximately from ~71539762 to 72122741 of Chr17. No molecular abnormalities were found in the remaining nine patients. This study is thought to be the first report regarding a duplication of SOX9 that is associated with the presence of 46,XX ovotesticular DSD, encompassing at least -581 kb upstream, and the almost entire coding region of the gene. Copyright © 2018 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

Python Radiative Transfer Emission code (PyRaTE): non-LTE spectral lines simulations

NASA Astrophysics Data System (ADS)

Tritsis, A.; Yorke, H.; Tassis, K.

2018-05-01

We describe PyRaTE, a new, non-local thermodynamic equilibrium (non-LTE) line radiative transfer code developed specifically for post-processing astrochemical simulations. Population densities are estimated using the escape probability method. When computing the escape probability, the optical depth is calculated towards all directions with density, molecular abundance, temperature and velocity variations all taken into account. A very easy-to-use interface, capable of importing data from simulations outputs performed with all major astrophysical codes, is also developed. The code is written in PYTHON using an "embarrassingly parallel" strategy and can handle all geometries and projection angles. We benchmark the code by comparing our results with those from RADEX (van der Tak et al. 2007) and against analytical solutions and present case studies using hydrochemical simulations. The code will be released for public use.

An indicator gene to demonstrate intracellular transposition of defective retroviruses.

PubMed Central

Heidmann, T; Heidmann, O; Nicolas, J F

1988-01-01

An indicator gene for detection and quantitation of RNA-mediated transposition was constructed (neoRT). It was inserted into a Moloney murine leukemia provirus (Mo-MLV) deleted for the envelope gene to test for intracellular transposition of defective retroviruses [Mo-MLV(neo)RT]. NeoRT contains the selectable neo gene (which confers resistance to the drug G418), inactivated by a polyadenylylation sequence inserted between the neo promotor and coding sequence. The polyadenylylation sequence is flanked (on the antisense strand of the DNA) by a donor and an acceptor splice site so as to be removed upon passage of the provirus through an RNA intermediate. 3T3 cells transfected with the defective Mo-MLV(neo)RT provirus are sensitive to G418. After trans-complementation with Mo-MLV, viral transcripts confer resistance to G418 upon infection of test cells. In the resistant cells, the polyadenylylation sequence has been removed, as a result in most cases of precise splicing of the intronic domain. Retrotransposition of the defective Mo-MLV(neo)RT provirus was demonstrated by submitting transfected G418-sensitive clones to selection. Between 1 and 10 G418-resistant clones were obtained per 10(7) cells. Several possess additional copies, with evidence for precise removal of the intronic domain. By using target test cells in coculture experiments, extracellular intermediates of retrotransposition could not be detected. Images PMID:2832848

Integrated Technology Plan for the Civil Space Program, 1991

NASA Technical Reports Server (NTRS)

1991-01-01

The purpose of the Integrated Technology Plan (ITP) is to serve as a strategic plan for the OAST space research and technology (R&T) program, and as a strategic planning framework for other NASA and national participants in advocating and conducting technology developments that support future U.S. civil space missions. The ITP begins with a discussion of the national policy and NASA organization which establishes the overall framework for civil space R&T planning. The second chapter provides a top-level review of the potential users of civil space R&T, their strategic mission plans, and the technologies they have identified as needed to achieve those plans. The overall methodology used to develop a civil space technology strategy is discussed. The technical details of the 1991 strategic plan are described, ending with a review of civil space R&T priorities. The fourth chapter describes how the strategic plan is annually translated into the OAST Space R&T Program, with a summary of the fiscal year 1992 program. The ITP concludes with a discussion of requirements for technology development coordination and strategies for facilitating the transfer of civil space technology to the private sector. Several appendices also are attached that provide further information regarding budget implications of the strategic plan, organizational roles, and other topics.

Influence of flowfield and vehicle parameters on engineering aerothermal methods

NASA Technical Reports Server (NTRS)

Wurster, Kathryn E.; Zoby, E. Vincent; Thompson, Richard A.

1989-01-01

The reliability and flexibility of three engineering codes used in the aerosphace industry (AEROHEAT, INCHES, and MINIVER) were investigated by comparing the results of these codes with Reentry F flight data and ground-test heat-transfer data for a range of cone angles, and with the predictions obtained using the detailed VSL3D code; the engineering solutions were also compared. In particular, the impact of several vehicle and flow-field parameters on the heat transfer and the capability of the engineering codes to predict these results were determined. It was found that entropy, pressure gradient, nose bluntness, gas chemistry, and angle of attack all affect heating levels. A comparison of the results of the three engineering codes with Reentry F flight data and with the predictions obtained of the VSL3D code showed a very good agreement in the regions of the applicability of the codes. It is emphasized that the parameters used in this study can significantly influence the actual heating levels and the prediction capability of a code.

A code for optically thick and hot photoionized media

NASA Astrophysics Data System (ADS)

Dumont, A.-M.; Abrassart, A.; Collin, S.

2000-05-01

We describe a code designed for hot media (T >= a few 104 K), optically thick to Compton scattering. It computes the structure of a plane-parallel slab of gas in thermal and ionization equilibrium, illuminated on one or on both sides by a given spectrum. Contrary to the other photoionization codes, it solves the transfer of the continuum and of the lines in a two stream approximation, without using the local escape probability formalism to approximate the line transfer. We stress the importance of taking into account the returning flux even for small column densities (1022 cm-2), and we show that the escape probability approximation can lead to strong errors in the thermal and ionization structure, as well as in the emitted spectrum, for a Thomson thickness larger than a few tenths. The transfer code is coupled with a Monte Carlo code which allows to take into account Compton and inverse Compton diffusions, and to compute the spectrum emitted up to MeV energies, in any geometry. Comparisons with cloudy show that it gives similar results for small column densities. Several applications are mentioned.

Bayesian Atmospheric Radiative Transfer (BART)Thermochemical Equilibrium Abundance (TEA) Code and Application to WASP-43b

NASA Astrophysics Data System (ADS)

Blecic, Jasmina; Harrington, Joseph; Bowman, Matthew O.; Cubillos, Patricio E.; Stemm, Madison; Foster, Andrew

2014-11-01

We present a new, open-source, Thermochemical Equilibrium Abundances (TEA) code that calculates the abundances of gaseous molecular species. TEA uses the Gibbs-free-energy minimization method with an iterative Lagrangian optimization scheme. It initializes the radiative-transfer calculation in our Bayesian Atmospheric Radiative Transfer (BART) code. Given elemental abundances, TEA calculates molecular abundances for a particular temperature and pressure or a list of temperature-pressure pairs. The code is tested against the original method developed by White at al. (1958), the analytic method developed by Burrows and Sharp (1999), and the Newton-Raphson method implemented in the open-source Chemical Equilibrium with Applications (CEA) code. TEA is written in Python and is available to the community via the open-source development site GitHub.com. We also present BART applied to eclipse depths of WASP-43b exoplanet, constraining atmospheric thermal and chemical parameters. This work was supported by NASA Planetary Atmospheres grant NNX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G. JB holds a NASA Earth and Space Science Fellowship.

Intercomparison of three microwave/infrared high resolution line-by-line radiative transfer codes

NASA Astrophysics Data System (ADS)

Schreier, Franz; Milz, Mathias; Buehler, Stefan A.; von Clarmann, Thomas

2018-05-01

An intercomparison of three line-by-line (lbl) codes developed independently for atmospheric radiative transfer and remote sensing - ARTS, GARLIC, and KOPRA - has been performed for a thermal infrared nadir sounding application assuming a HIRS-like (High resolution Infrared Radiation Sounder) setup. Radiances for the 19 HIRS infrared channels and a set of 42 atmospheric profiles from the "Garand dataset" have been computed. The mutual differences of the equivalent brightness temperatures are presented and possible causes of disagreement are discussed. In particular, the impact of path integration schemes and atmospheric layer discretization is assessed. When the continuum absorption contribution is ignored because of the different implementations, residuals are generally in the sub-Kelvin range and smaller than 0.1 K for some window channels (and all atmospheric models and lbl codes). None of the three codes turned out to be perfect for all channels and atmospheres. Remaining discrepancies are attributed to different lbl optimization techniques. Lbl codes seem to have reached a maturity in the implementation of radiative transfer that the choice of the underlying physical models (line shape models, continua etc) becomes increasingly relevant.

User's manual for the one-dimensional hypersonic experimental aero-thermodynamic (1DHEAT) data reduction code

NASA Technical Reports Server (NTRS)

Hollis, Brian R.

1995-01-01

A FORTRAN computer code for the reduction and analysis of experimental heat transfer data has been developed. This code can be utilized to determine heat transfer rates from surface temperature measurements made using either thin-film resistance gages or coaxial surface thermocouples. Both an analytical and a numerical finite-volume heat transfer model are implemented in this code. The analytical solution is based on a one-dimensional, semi-infinite wall thickness model with the approximation of constant substrate thermal properties, which is empirically corrected for the effects of variable thermal properties. The finite-volume solution is based on a one-dimensional, implicit discretization. The finite-volume model directly incorporates the effects of variable substrate thermal properties and does not require the semi-finite wall thickness approximation used in the analytical model. This model also includes the option of a multiple-layer substrate. Fast, accurate results can be obtained using either method. This code has been used to reduce several sets of aerodynamic heating data, of which samples are included in this report.

Generalization of the Last Scattering Approximation for the Second Solar Spectrum Modeling: The Ca I 4227 Å Line as a Case Study

NASA Astrophysics Data System (ADS)

Anusha, L. S.; Nagendra, K. N.; Stenflo, J. O.; Bianda, M.; Sampoorna, M.; Frisch, H.; Holzreuter, R.; Ramelli, R.

2010-08-01

To model the second solar spectrum (the linearly polarized spectrum of the Sun that is due to coherent scattering processes), one needs to solve the polarized radiative transfer (RT) equation. For strong resonance lines, partial frequency redistribution (PRD) effects must be accounted for, which make the problem computationally demanding. The "last scattering approximation" (LSA) is a concept that has been introduced to make this highly complex problem more tractable. An earlier application of a simple LSA version could successfully model the wings of the strong Ca I 4227 Å resonance line in Stokes Q/I (fractional linear polarization), but completely failed to reproduce the observed Q/I peak in the line core. Since the magnetic field signatures from the Hanle effect only occur in the line core, we need to generalize the existing LSA approach if it is to be useful for the diagnostics of chromospheric and turbulent magnetic fields. In this paper, we explore three different approximation levels for LSA and compare each of them with the benchmark represented by the solution of the full polarized RT, including PRD effects. The simplest approximation level is LSA-1, which uses the observed center-to-limb variation of the intensity profile to obtain the anisotropy of the radiation field at the surface, without solving any transfer equation. In contrast, the next two approximation levels use the solution of the unpolarized transfer equation to derive the anisotropy of the incident radiation field and use it as an input. In the case of LSA-2, the anisotropy at level τλ = μ, the atmospheric level from which an observed photon is most likely to originate, is used. LSA-3, on the other hand, makes use of the full depth dependence of the radiation anisotropy. The Q/I formula for LSA-3 is obtained by keeping the first term in a series expansion of the Q-source function in powers of the mean number of scattering events. Computationally, LSA-1 is 21 times faster than LSA-2, which is 5 times faster than the more general LSA-3, which itself is 8 times faster than the polarized RT approach. A comparison of the calculated Q/I spectra with the RT benchmark shows excellent agreement for LSA-3, including good modeling of the Q/I core region with its PRD effects. In contrast, both LSA-1 and LSA-2 fail to model the core region. The RT and LSA-3 approaches are then applied to model the recently observed Q/I profile of the Ca I 4227 Å line in quiet regions of the Sun. Apart from a global scale factor both give a very good fit to the Q/I spectra for all the wavelengths, including the core peak and blend line depolarizations. We conclude that LSA-3 is an excellent substitute for the full polarized RT and can be used to interpret the second solar spectrum, including the Hanle effect with PRD. It also allows the techniques developed for unpolarized three-dimensional RT to be applied to the modeling of the second solar spectrum.

Numerical investigation of two- and three-dimensional heat transfer in expander cycle engines

NASA Technical Reports Server (NTRS)

Burch, Robert L.; Cheung, Fan-Bill

1993-01-01

The concept of using tube canting for enhancing the hot-side convective heat transfer in a cross-stream tubular rocket combustion chamber is evaluated using a CFD technique in this study. The heat transfer at the combustor wall is determined from the flow field generated by a modified version of the PARC Navier-Stokes Code, using the actual dimensions, fluid properties, and design parameters of a split-expander demonstrator cycle engine. The effects of artificial dissipation on convergence and solution accuracy are investigated. Heat transfer results predicted by the code are presented. The use of CFD in heat transfer calculations is critically examined to demonstrate the care needed in the use of artificial dissipation for good convergence and accurate solutions.

Poor Children in Rich Countries.

ERIC Educational Resources Information Center

Smeeding, Timothy M.; Torrey, Barbara Boyld

1988-01-01

Reports on a comparison of the poverty rates of families with children in six industrial countries. Discusses income and poverty, poverty among children, family poverty rates before and after taxes and income transfers, and conclusions. States that the poverty of children may affect long-term competitiveness with other countries. (RT)

Non-local gravity and comparison with observational datasets. II. Updated results and Bayesian model comparison with ΛCDM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dirian, Yves; Foffa, Stefano; Kunz, Martin

We present a comprehensive and updated comparison with cosmological observations of two non-local modifications of gravity previously introduced by our group, the so called RR and RT models. We implement the background evolution and the cosmological perturbations of the models in a modified Boltzmann code, using CLASS. We then test the non-local models against the Planck 2015 TT, TE, EE and Cosmic Microwave Background (CMB) lensing data, isotropic and anisotropic Baryonic Acoustic Oscillations (BAO) data, JLA supernovae, H {sub 0} measurements and growth rate data, and we perform Bayesian parameter estimation. We then compare the RR, RT and ΛCDM models,more » using the Savage-Dickey method. We find that the RT model and ΛCDM perform equally well, while the performance of the RR model with respect to ΛCDM depends on whether or not we include a prior on H {sub 0} based on local measurements.« less

Modeling variably saturated multispecies reactive groundwater solute transport with MODFLOW-UZF and RT3D

USGS Publications Warehouse

Bailey, Ryan T.; Morway, Eric D.; Niswonger, Richard G.; Gates, Timothy K.

2013-01-01

A numerical model was developed that is capable of simulating multispecies reactive solute transport in variably saturated porous media. This model consists of a modified version of the reactive transport model RT3D (Reactive Transport in 3 Dimensions) that is linked to the Unsaturated-Zone Flow (UZF1) package and MODFLOW. Referred to as UZF-RT3D, the model is tested against published analytical benchmarks as well as other published contaminant transport models, including HYDRUS-1D, VS2DT, and SUTRA, and the coupled flow and transport modeling system of CATHY and TRAN3D. Comparisons in one-dimensional, two-dimensional, and three-dimensional variably saturated systems are explored. While several test cases are included to verify the correct implementation of variably saturated transport in UZF-RT3D, other cases are included to demonstrate the usefulness of the code in terms of model run-time and handling the reaction kinetics of multiple interacting species in variably saturated subsurface systems. As UZF1 relies on a kinematic-wave approximation for unsaturated flow that neglects the diffusive terms in Richards equation, UZF-RT3D can be used for large-scale aquifer systems for which the UZF1 formulation is reasonable, that is, capillary-pressure gradients can be neglected and soil parameters can be treated as homogeneous. Decreased model run-time and the ability to include site-specific chemical species and chemical reactions make UZF-RT3D an attractive model for efficient simulation of multispecies reactive transport in variably saturated large-scale subsurface systems.

Anti-human immunodeficiency virus (HIV) activities of halogenated gomisin J derivatives, new nonnucleoside inhibitors of HIV type 1 reverse transcriptase.

PubMed

Fujihashi, T; Hara, H; Sakata, T; Mori, K; Higuchi, H; Tanaka, A; Kaji, H; Kaji, A

1995-09-01

Halogenated gomisin J (a derivative of lignan compound), represented by the bromine derivative 1506 [(6R, 7S, S-biar)-4,9-dibromo-3,10-dihydroxy-1,2,11,12-tetramethoxy-6, 7-dimethyl-5,6,7,8- tetrahydrodibenzo[a,c]cyclo-octene], was found to be a potent inhibitor of the cytopathic effects of human immunodeficiency virus type 1 (HIV-1) on MT-4 human T cells (50% effective dose, 0.1 to 0.5 microM). Gomisin J derivatives were active in preventing p24 production from acutely HIV-1-infected H9 cells. The selective indices (toxic dose/effective dose) of these compounds were as high as > 300 in some systems. 1506 was active against 3'-azido-3'-deoxythymidine-resistant HIV-1 and acted synergistically with AZT and 2',3'-ddC. 1506 inhibited HIV-1 reverse transcriptase (RT) in vitro but not HIV-1 protease. From the time-of-addition experiment, 1506 was found to inhibit the early phase of the HIV life cycle. A 1506-resistant HIV mutant was selected and shown to possess a mutation within the RT-coding region (at position 188 [Tyr to Leu]). The mutant RT expressed in Escherichia coli was resistant to 1506 in the in vitro RT assay. Some of the HIV strains resistant to other nonnucleoside HIV-1 RT inhibitors were also resistant to 1506. Comparison of various gomisin J derivatives with gomisin J showed that iodine, bromine, and chlorine in the fourth and ninth positions increased RT inhibitory activity as well as cytoprotective activity.

A Radiation-Induced Hippocampal Vascular Injury Surrogate Marker Predicts Late Neurocognitive Dysfunction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farjam, Reza; Pramanik, Priyanka; Aryal, Madhava P.

Purpose: We aimed to develop a hippocampal vascular injury surrogate marker for early prediction of late neurocognitive dysfunction in patients receiving brain radiation therapy (RT). Methods and Materials: Twenty-seven patients (17 males and 10 females, 31-80 years of age) were enrolled in an institutional review board-approved prospective longitudinal study. Patients received diagnoses of low-grade glioma or benign tumor and were treated by (3D) conformal or intensity-modulated RT with a median dose of 54 Gy (50.4-59.4 Gy in 1.8-Gy fractions). Six dynamic-contrast enhanced MRI scans were performed from pre-RT to 18-month post-RT, and quantified for vascular parameters related to blood-brain barrier permeability, K{sup trans},more » and the fraction of blood plasma volume, V{sub p}. The temporal changes in the means of hippocampal transfer constant K{sup trans} and V{sub p} after starting RT were modeled by integrating the dose effects with age, sex, hippocampal laterality, and presence of tumor or edema near a hippocampus. Finally, the early vascular dose response in hippocampi was correlated with neurocognitive dysfunction at 6 and 18 months post-RT. Results: The mean K{sup trans} Increased significantly from pre-RT to 1-month post-RT (P<.0004), which significantly depended on sex (P<.0007) and age (P<.00004), with the dose response more pronounced in older females. Also, the vascular dose response in the left hippocampus of females correlated significantly with changes in memory function at 6 (r=−0.95, P<.0006) and 18-months (r=−0.88, P<.02) post-RT. Conclusions: The early hippocampal vascular dose response could be a predictor of late neurocognitive dysfunction. A personalized hippocampus sparing strategy may be considered in the future.« less

Investigation of Advanced Counterrotation Blade Configuration Concepts for High Speed Turboprop Systems. Task 8: Cooling Flow/heat Transfer Analysis User's Manual

NASA Technical Reports Server (NTRS)

Hall, Edward J.; Topp, David A.; Heidegger, Nathan J.; Delaney, Robert A.

1994-01-01

The focus of this task was to validate the ADPAC code for heat transfer calculations. To accomplish this goal, the ADPAC code was modified to allow for a Cartesian coordinate system capability and to add boundary conditions to handle spanwise periodicity and transpiration boundaries. This user's manual describes how to use the ADPAC code as developed in Task 5, NAS3-25270, including the modifications made to date in Tasks 7 and 8, NAS3-25270.

Fractal Geometry in Physics

DTIC Science & Technology

1993-09-30

AD-A273 271 OFFICE OF NAVAL RESEARCH 3-0 1993 CONTRACT NUMBER: N00014-90-J- 1 30 MODIFICATION NO: P00005 19 R&T PROJECT: 4123041-10 & 11 A S.O. CODE...investigated. Indirectly related to these topics is a papaer by D. Stauffer, A. Aharony and B. Man- delbrot in Phy•sica A 196, 1993, 1-5. It evaluates

Low-Cost High-Speed Techniques for Real-Time Simulation of Power Electronic Systems

DTIC Science & Technology

2007-06-01

first implemented on the RT-Lab using Simulink S- fuctions . An effort was then initiated to code at least part of the simulation on the available FPGA. It...time simulation, and the use of simulation packages such as Matlab and Spice. The primary purpose of these calculations was to confirm that the

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires.

PubMed

Silas, Sukrit; Makarova, Kira S; Shmakov, Sergey; Páez-Espino, David; Mohr, Georg; Liu, Yi; Davison, Michelle; Roux, Simon; Krishnamurthy, Siddharth R; Fu, Becky Xu Hua; Hansen, Loren L; Wang, David; Sullivan, Matthew B; Millard, Andrew; Clokie, Martha R; Bhaya, Devaki; Lambowitz, Alan M; Kyrpides, Nikos C; Koonin, Eugene V; Fire, Andrew Z

2017-07-11

Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent) to a gene encoding a reverse transcriptase (RT) related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains. Nearly all such RTs are present within type III CRISPR-Cas loci, but their phylogeny does not parallel the CRISPR-Cas type classification, indicating that RT-Cas1 is an autonomous functional module that is disseminated by horizontal gene transfer and can function with diverse type III systems. To compare the sequence pools sampled by RT-Cas1-associated and RT-lacking CRISPR-Cas systems, we obtained samples of a commercially grown cyanobacterium- Arthrospira platensis Sequencing of the CRISPR arrays uncovered a highly diverse population of spacers. Spacer diversity was particularly striking for the RT-Cas1-containing type III-B system, where no saturation was evident even with millions of sequences analyzed. In contrast, analysis of the RT-lacking type III-D system yielded a highly diverse pool but reached a point where fewer novel spacers were recovered as sequencing depth was increased. Matches could be identified for a small fraction of the non-RT-Cas1-associated spacers, and for only a single RT-Cas1-associated spacer. Thus, the principal source(s) of the spacers, particularly the hypervariable spacer repertoire of the RT-associated arrays, remains unknown. IMPORTANCE While the majority of CRISPR-Cas immune systems adapt to foreign genetic elements by capturing segments of invasive DNA, some systems carry reverse transcriptases (RTs) that enable adaptation to RNA molecules. From analysis of available bacterial sequence data, we find evidence that RT-based RNA adaptation machinery has been able to join with CRISPR-Cas immune systems in many, diverse bacterial species. To investigate whether the abilities to adapt to DNA and RNA molecules are utilized for defense against distinct classes of invaders in nature, we sequenced CRISPR arrays from samples of commercial-scale open-air cultures of Arthrospira platensis , a cyanobacterium that contains both RT-lacking and RT-containing CRISPR-Cas systems. We uncovered a diverse pool of naturally occurring immune memories, with the RT-lacking locus acquiring a number of segments matching known viral or bacterial genes, while the RT-containing locus has acquired spacers from a distinct sequence pool for which the source remains enigmatic. Copyright © 2017 Silas et al.

Turbine Internal and Film Cooling Modeling For 3D Navier-Stokes Codes

NASA Technical Reports Server (NTRS)

DeWitt, Kenneth; Garg Vijay; Ameri, Ali

2005-01-01

The aim of this research project is to make use of NASA Glenn on-site computational facilities in order to develop, validate and apply aerodynamic, heat transfer, and turbine cooling models for use in advanced 3D Navier-Stokes Computational Fluid Dynamics (CFD) codes such as the Glenn-" code. Specific areas of effort include: Application of the Glenn-HT code to specific configurations made available under Turbine Based Combined Cycle (TBCC), and Ultra Efficient Engine Technology (UEET) projects. Validating the use of a multi-block code for the time accurate computation of the detailed flow and heat transfer of cooled turbine airfoils. The goal of the current research is to improve the predictive ability of the Glenn-HT code. This will enable one to design more efficient turbine components for both aviation and power generation. The models will be tested against specific configurations provided by NASA Glenn.

PARC Navier-Stokes code upgrade and validation for high speed aeroheating predictions

NASA Technical Reports Server (NTRS)

Liver, Peter A.; Praharaj, Sarat C.; Seaford, C. Mark

1990-01-01

Applications of the PARC full Navier-Stokes code for hypersonic flowfield and aeroheating predictions around blunt bodies such as the Aeroassist Flight Experiment (AFE) and Aeroassisted Orbital Transfer Vehicle (AOTV) are evaluated. Two-dimensional/axisymmetric and three-dimensional perfect gas versions of the code were upgraded and tested against benchmark wind tunnel cases of hemisphere-cylinder, three-dimensional AFE forebody, and axisymmetric AFE and AOTV aerobrake/wake flowfields. PARC calculations are in good agreement with experimental data and results of similar computer codes. Difficulties encountered in flowfield and heat transfer predictions due to effects of grid density, boundary conditions such as singular stagnation line axis and artificial dissipation terms are presented together with subsequent improvements made to the code. The experience gained with the perfect gas code is being currently utilized in applications of an equilibrium air real gas PARC version developed at REMTECH.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uchibori, Akihiro; Kurihara, Akikazu; Ohshima, Hiroyuki

A multiphysics analysis system for sodium-water reaction phenomena in a steam generator of sodium-cooled fast reactors was newly developed. The analysis system consists of the mechanistic numerical analysis codes, SERAPHIM, TACT, and RELAP5. The SERAPHIM code calculates the multicomponent multiphase flow and sodium-water chemical reaction caused by discharging of pressurized water vapor. Applicability of the SERAPHIM code was confirmed through the analyses of the experiment on water vapor discharging in liquid sodium. The TACT code was developed to calculate heat transfer from the reacting jet to the adjacent tube and to predict the tube failure occurrence. The numerical models integratedmore » into the TACT code were verified through some related experiments. The RELAP5 code evaluates thermal hydraulic behavior of water inside the tube. The original heat transfer correlations were corrected for the tube rapidly heated by the reacting jet. The developed system enables evaluation of the wastage environment and the possibility of the failure propagation.« less

Benchmarking a Visual-Basic based multi-component one-dimensional reactive transport modeling tool

NASA Astrophysics Data System (ADS)

Torlapati, Jagadish; Prabhakar Clement, T.

2013-01-01

We present the details of a comprehensive numerical modeling tool, RT1D, which can be used for simulating biochemical and geochemical reactive transport problems. The code can be run within the standard Microsoft EXCEL Visual Basic platform, and it does not require any additional software tools. The code can be easily adapted by others for simulating different types of laboratory-scale reactive transport experiments. We illustrate the capabilities of the tool by solving five benchmark problems with varying levels of reaction complexity. These literature-derived benchmarks are used to highlight the versatility of the code for solving a variety of practical reactive transport problems. The benchmarks are described in detail to provide a comprehensive database, which can be used by model developers to test other numerical codes. The VBA code presented in the study is a practical tool that can be used by laboratory researchers for analyzing both batch and column datasets within an EXCEL platform.

AccuRT: A versatile tool for radiative transfer simulations in the coupled atmosphere-ocean system

NASA Astrophysics Data System (ADS)

Hamre, Børge; Stamnes, Snorre; Stamnes, Knut; Stamnes, Jakob

2017-02-01

Reliable, accurate, and efficient modeling of the transport of electromagnetic radiation in turbid media has important applications in the study of the Earth's climate by remote sensing. For example, such modeling is needed to develop forward-inverse methods used to quantify types and concentrations of aerosol and cloud particles in the atmosphere, the dissolved organic and particulate biogeochemical matter in lakes, rivers, coastal, and open-ocean waters. It is also needed to simulate the performance of remote sensing detectors deployed on aircraft, balloons, and satellites as well as radiometric detectors deployed on buoys, gliders and other aquatic observing systems. Accurate radiative transfer modeling is also required to compute irradiances and scalar irradiances that are used to compute warming/cooling and photolysis rates in the atmosphere and primary production and warming/cooling rates in the water column. AccuRT is a radiative transfer model for the coupled atmosphere-water system that is designed to be a versatile tool for researchers in the ocean optics and remote sensing communities. It addresses the needs of researchers interested in analyzing irradiance and radiance measurements in the field and laboratory as well as those interested in making simulations of the top-of-the-atmosphere radiance in support of remote sensing algorithm development.

ASTRORAY: General relativistic polarized radiative transfer code

NASA Astrophysics Data System (ADS)

Shcherbakov, Roman V.

2014-07-01

ASTRORAY employs a method of ray tracing and performs polarized radiative transfer of (cyclo-)synchrotron radiation. The radiative transfer is conducted in curved space-time near rotating black holes described by Kerr-Schild metric. Three-dimensional general relativistic magneto hydrodynamic (3D GRMHD) simulations, in particular performed with variations of the HARM code, serve as an input to ASTRORAY. The code has been applied to reproduce the sub-mm synchrotron bump in the spectrum of Sgr A*, and to test the detectability of quasi-periodic oscillations in its light curve. ASTRORAY can be readily applied to model radio/sub-mm polarized spectra of jets and cores of other low-luminosity active galactic nuclei. For example, ASTRORAY is uniquely suitable to self-consistently model Faraday rotation measure and circular polarization fraction in jets.

Production of human CD59-transgenic pigs by embryonic germ cell nuclear transfer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahn, Kwang Sung; Won, Ji Young; Park, Jin-Ki

Research highlights: {yields} Human CD59 (hCD59) gene was introduced into porcine embryonic germ (EG) cells. {yields} hCD59-transgenic EG cells were resistant to hyperacute rejection in cytolytic assay. {yields} hCD59-transgenic pigs were produced by EG cell nuclear transfer. -- Abstract: This study was performed to produce transgenic pigs expressing the human complement regulatory protein CD59 (hCD59) using the nuclear transfer (NT) of embryonic germ (EG) cells, which are undifferentiated stem cells derived from primordial germ cells. Because EG cells can be cultured indefinitely in an undifferentiated state, they may provide an inexhaustible source of nuclear donor cells for NT to producemore » transgenic pigs. A total of 1980 NT embryos derived from hCD59-transgenic EG cells were transferred to ten recipients, resulting in the birth of fifteen piglets from three pregnancies. Among these offspring, ten were alive without overt health problems. Based on PCR analysis, all fifteen piglets were confirmed as hCD59 transgenic. The expression of the hCD59 transgene in the ten living piglets was verified by RT-PCR. Western analysis showed the expression of the hCD59 protein in four of the ten RT-PCR-positive piglets. These results demonstrate that hCD59-transgenic pigs could effectively be produced by EG cell NT and that such transgenic pigs may be used as organ donors in pig-to-human xenotransplantation.« less

Down-regulated PAR-2 is associated in part with interrupted melanosome transfer in pigmented basal cell epithelioma.

PubMed

Sakuraba, Kazuko; Hayashi, Nobukazu; Kawashima, Makoto; Imokawa, Genji

2004-08-01

In pigmented basal cell epithelioma (BCE), there seems to be an abnormal transfer of melanized melanosomes from proliferating melanocytes to basaloid tumor cells. In this study, the interruption of that melanosome transfer was studied with special respect to the altered function of a phagocytic receptor, protease-activated receptor (PAR)-2 in the basaloid tumor cells. We used electron microscopy to clarify the disrupted transfer at the ultrastructural level and then performed immunohistochemistry and reverse transcription-polymerase chain reaction (RT-PCR) to examine the regulation of a phagocytic receptor, PAR-2, expressed on basaloid tumor cells. Electron microscopic analysis revealed that basaloid tumor cells of pigmented BCE have a significantly lower population of melanosomes ( approximately 16.4%) than do normal keratinocytes located in the perilesional normal epidermis ( approximately 91.0%). In contrast, in pigmented seborrheic keratosis (SK), a similarly pigmented epidermal tumor, the distribution of melanin granules does not differ between the lesional ( approximately 93.9%) and the perilesional normal epidermis ( approximately 92.2 %), indicating that interrupted melanosome transfer occurs in BCE but not in all pigmented epithelial tumors. RT-PCR analysis demonstrated that the expression of PAR-2 mRNA transcripts in basaloid cells is significantly decreased in pigmented BCE compared with the perilesional normal epidermis. In contrast, in pigmented SK, where melanosome transfer to basaloid tumor cells is not interrupted, the expression of PAR-2 mRNA transcripts is comparable between the basaloid tumor cells and the perilesional normal epidermis. Immunohistochemistry demonstrated that basaloid cells in pigmented BCE have less immunostaining for PAR-2 than do keratinocytes in the perilesional normal epidermis whereas in pigmented SK, there is no difference in immunostaining for PAR-2 between the basaloid tumor and the perilesional normal epidermis. These findings suggest that the decreased expression of PAR-2 in the basaloid cells is associated in part with the observed interruption of melanosome transfer in pigmented BCE.

Radiative Transfer Modeling in Proto-planetary Disks

NASA Astrophysics Data System (ADS)

Kasper, David; Jang-Condell, Hannah; Kloster, Dylan

2016-01-01

Young Stellar Objects (YSOs) are rich astronomical research environments. Planets form in circumstellar disks of gas and dust around YSOs. With ever increasing capabilities of the observational instruments designed to look at these proto-planetary disks, most notably GPI, SPHERE, and ALMA, more accurate interfaces must be made to connect modeling of the disks with observation. PaRTY (Parallel Radiative Transfer in YSOs) is a code developed previously to model the observable density and temperature structure of such a disk by self-consistently calculating the structure of the disk based on radiative transfer physics. We present upgrades we are implementing to the PaRTY code to improve its accuracy and flexibility. These upgrades include: creating a two-sided disk model, implementing a spherical coordinate system, and implementing wavelength-dependent opacities. These upgrades will address problems in the PaRTY code of infinite optical thickness, calculation under/over-resolution, and wavelength-independent photon penetration depths, respectively. The upgraded code will be used to better model disk perturbations resulting from planet formation.

Analytical and Experimental Evaluation of the Heat Transfer Distribution over the Surfaces of Turbine Vanes

NASA Technical Reports Server (NTRS)

Hylton, L. D.; Mihelc, M. S.; Turner, E. R.; Nealy, D. A.; York, R. E.

1983-01-01

Three airfoil data sets were selected for use in evaluating currently available analytical models for predicting airfoil surface heat transfer distributions in a 2-D flow field. Two additional airfoils, representative of highly loaded, low solidity airfoils currently being designed, were selected for cascade testing at simulated engine conditions. Some 2-D analytical methods were examined and a version of the STAN5 boundary layer code was chosen for modification. The final form of the method utilized a time dependent, transonic inviscid cascade code coupled to a modified version of the STAN5 boundary layer code featuring zero order turbulence modeling. The boundary layer code is structured to accommodate a full spectrum of empirical correlations addressing the coupled influences of pressure gradient, airfoil curvature, and free-stream turbulence on airfoil surface heat transfer distribution and boundary layer transitional behavior. Comparison of pedictions made with the model to the data base indicates a significant improvement in predictive capability.

The Deceptively Simple N170 Reflects Network Information Processing Mechanisms Involving Visual Feature Coding and Transfer Across Hemispheres

PubMed Central

Ince, Robin A. A.; Jaworska, Katarzyna; Gross, Joachim; Panzeri, Stefano; van Rijsbergen, Nicola J.; Rousselet, Guillaume A.; Schyns, Philippe G.

2016-01-01

A key to understanding visual cognition is to determine “where”, “when”, and “how” brain responses reflect the processing of the specific visual features that modulate categorization behavior—the “what”. The N170 is the earliest Event-Related Potential (ERP) that preferentially responds to faces. Here, we demonstrate that a paradigmatic shift is necessary to interpret the N170 as the product of an information processing network that dynamically codes and transfers face features across hemispheres, rather than as a local stimulus-driven event. Reverse-correlation methods coupled with information-theoretic analyses revealed that visibility of the eyes influences face detection behavior. The N170 initially reflects coding of the behaviorally relevant eye contralateral to the sensor, followed by a causal communication of the other eye from the other hemisphere. These findings demonstrate that the deceptively simple N170 ERP hides a complex network information processing mechanism involving initial coding and subsequent cross-hemispheric transfer of visual features. PMID:27550865

Analytical and experimental evaluation of the heat transfer distribution over the surfaces of turbine vanes

NASA Astrophysics Data System (ADS)

Hylton, L. D.; Mihelc, M. S.; Turner, E. R.; Nealy, D. A.; York, R. E.

1983-05-01

Three airfoil data sets were selected for use in evaluating currently available analytical models for predicting airfoil surface heat transfer distributions in a 2-D flow field. Two additional airfoils, representative of highly loaded, low solidity airfoils currently being designed, were selected for cascade testing at simulated engine conditions. Some 2-D analytical methods were examined and a version of the STAN5 boundary layer code was chosen for modification. The final form of the method utilized a time dependent, transonic inviscid cascade code coupled to a modified version of the STAN5 boundary layer code featuring zero order turbulence modeling. The boundary layer code is structured to accommodate a full spectrum of empirical correlations addressing the coupled influences of pressure gradient, airfoil curvature, and free-stream turbulence on airfoil surface heat transfer distribution and boundary layer transitional behavior. Comparison of pedictions made with the model to the data base indicates a significant improvement in predictive capability.

Radiative transfer code SHARM-3D for radiance simulations over a non-Lambertian nonhomogeneous surface: intercomparison study.

PubMed

Lyapustin, Alexei

2002-09-20

Results of an extensive validation study of the new radiative transfer code SHARM-3D are described. The code is designed for modeling of unpolarized monochromatic radiative transfer in the visible and near-IR spectra in the laterally uniform atmosphere over an arbitrarily inhomogeneous anisotropic surface. The surface boundary condition is periodic. The algorithm is based on an exact solution derived with the Green's function method. Several parameterizations were introduced into the algorithm to achieve superior performance. As a result, SHARM-3D is 2-3 orders of magnitude faster than the rigorous code SHDOM. It can model radiances over large surface scenes for a number of incidence-view geometries simultaneously. Extensive comparisons against SHDOM indicate that SHARM-3D has an average accuracy of better than 1%, which along with the high speed of calculations makes it a unique tool for remote-sensing applications in land surface and related atmospheric radiation studies.

Radiative Transfer Code SHARM-3D for Radiance Simulations over a non-Lambertian Nonhomogeneous Surface: Intercomparison Study

NASA Astrophysics Data System (ADS)

Lyapustin, Alexei

2002-09-01

Results of an extensive validation study of the new radiative transfer code SHARM-3D are described. The code is designed for modeling of unpolarized monochromatic radiative transfer in the visible and near-IR spectra in the laterally uniform atmosphere over an arbitrarily inhomogeneous anisotropic surface. The surface boundary condition is periodic. The algorithm is based on an exact solution derived with the Green ’s function method. Several parameterizations were introduced into the algorithm to achieve superior performance. As a result, SHARM-3D is 2 -3 orders of magnitude faster than the rigorous code SHDOM. It can model radiances over large surface scenes for a number of incidence-view geometries simultaneously. Extensive comparisons against SHDOM indicate that SHARM-3D has an average accuracy of better than 1%, which along with the high speed of calculations makes it a unique tool for remote-sensing applications in land surface and related atmospheric radiation studies.

Retrieval of atmospheric properties from hyper and multispectral imagery with the FLAASH atmospheric correction algorithm

NASA Astrophysics Data System (ADS)

Perkins, Timothy; Adler-Golden, Steven; Matthew, Michael; Berk, Alexander; Anderson, Gail; Gardner, James; Felde, Gerald

2005-10-01

Atmospheric Correction Algorithms (ACAs) are used in applications of remotely sensed Hyperspectral and Multispectral Imagery (HSI/MSI) to correct for atmospheric effects on measurements acquired by air and space-borne systems. The Fast Line-of-sight Atmospheric Analysis of Spectral Hypercubes (FLAASH) algorithm is a forward-model based ACA created for HSI and MSI instruments which operate in the visible through shortwave infrared (Vis-SWIR) spectral regime. Designed as a general-purpose, physics-based code for inverting at-sensor radiance measurements into surface reflectance, FLAASH provides a collection of spectral analysis and atmospheric retrieval methods including: a per-pixel vertical water vapor column estimate, determination of aerosol optical depth, estimation of scattering for compensation of adjacency effects, detection/characterization of clouds, and smoothing of spectral structure resulting from an imperfect atmospheric correction. To further improve the accuracy of the atmospheric correction process, FLAASH will also detect and compensate for sensor-introduced artifacts such as optical smile and wavelength mis-calibration. FLAASH relies on the MODTRANTM radiative transfer (RT) code as the physical basis behind its mathematical formulation, and has been developed in parallel with upgrades to MODTRAN in order to take advantage of the latest improvements in speed and accuracy. For example, the rapid, high fidelity multiple scattering (MS) option available in MODTRAN4 can greatly improve the accuracy of atmospheric retrievals over the 2-stream approximation. In this paper, advanced features available in FLAASH are described, including the principles and methods used to derive atmospheric parameters from HSI and MSI data. Results are presented from processing of Hyperion, AVIRIS, and LANDSAT data.

Directional radiative transfer by SCOPE, SLC and DART using laser scan derived structural forest parameters

NASA Astrophysics Data System (ADS)

Timmermans, Joris; Gastellu-Etchegorry, Jean Philippe; van der Tol, Christiaan; Verhoef, Wout; Vekerdy, Zoltan; Su, Zhongbo

2017-04-01

Accurate estimation of the radiative transfer (RT) over vegetation is the corner stone of agricultural and hydrological remote sensing applications. Present remote sensing sensors mostly use traditional optical, thermal and microwave observations. However with these traditional observations characterization of the light efficiency and photosynthetic rate can only be accomplished indirectly. A promising new method of observing these processes is by using the fluorescent emitted radiation. This approach was recently highlighted due to the selection of the FLEX sensor as a future Earth Explorer by the European Space agency (ESA). Several modelling activities have been undertaken to better understand the technical feasibilities of this sensor. Within these studies, the SCOPE model has been chosen as the baseline algorithm. This model combines a detailed RT description of the canopy, using a discrete version of the SAIL model, with a description of photosynthetic processes (by use of the Farquhar/Ball-Berry model). Consequently, this model is capable of simulating simultaneously the biophysical processes and jointly the fluorescent, optical and thermal RT. The SAIL model however is a 1D RT model and consequently provides higher uncertainties with increasing vegetation structures. The main objective of this research is to investigate the limitations of the RT model component of the SCOPE model over complex canopies. In particular the aim of this research is to evaluate the validity for increasingly structural complex canopies', on the bidirectional reflectance distribution functions (BRDF) of these canopies. This was accomplished by evaluating the simulated outgoing radiation from SCOPE/SAIL against simulations of the DART 3D RT model. In total nine different scenarios were simulated with the DART RTM with increasing structural complexity, ranging from the simple 'Plot' scenario to the highly complex 'Multiple Crown' scenario. The canopy parameters are retrieved from a terrestrial laser scan of the Speulderbos in the Netherlands. The comparison between DART and SCOPE/SLC models showed a good match for the simple scenarios. Calculated rMSDs showed lower than 7.5% errors for crown coverage values lower than 0.87, with the Near-Hotspot viewing angles found to be the largest contributor to this deviation. For more complex scenarios (using Multiple Crowns), the comparison between SCOPE and DART showed mixed results. Good results were obtained for crown coverage values of 0.93, with rMSD (6.77% and 5.96%), lower than the defined threshold value, except near hotspot. For scenarios with crown coverages lower than 0.93 the rMSD were too large to validate the use of SCOPE model. When considering the Soil Leaf Canopy (SLC) model, an improved version of SAIL that considers the canopy clumping, better results were obtained for these complex scenarios, with good agreement for medium crown coverage values (0.93 and 0.87) with rMSD (6.33% and 5.99; 6.66% and 7.12%). This indicates that the radiative transfer model within SCOPE might be upgraded in the future.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steiner, Konstanze, E-mail: konstanze.steiner@uni-konstanz.de; Hagenbuch, Bruno, E-mail: bhagenbuch@kumc.edu; Dietrich, Daniel R., E-mail: daniel.dietrich@uni-konstanz.de

Cyanobacterial blooms have an impact on the aquatic ecosystem due to the production of toxins (e.g. microcystins, MCs), which constrain fish health or even cause fish death. However the toxicokinetics of the most abundant toxin, microcystin-LR (MC-LR), are not yet fully understood. To investigate the uptake mechanism, the novel Oatp1d1 in rainbow trout (rtOatp1d1) was cloned, identified and characterized. The cDNA isolated from a clone library consisted of 2772 bp containing a 2115 bp open reading frame coding for a 705 aa protein with an approximate molecular mass of 80 kDa. This fish specific transporter belongs to the OATP1 familymore » and has most likely evolved from a common ancestor of OATP1C1. Real time PCR analysis showed that rtOatp1d1 is predominantly expressed in the liver, followed by the brain while expression in other organs was not detectable. Transient transfection in HEK293 cells was used for further characterization. Like its human homologues OATP1A1, OATP1B1 and OATP1B3, rtOatp1d1 displayed multi-specific transport including endogenous and xenobiotic substrates. Kinetic analyses revealed a K{sub m} value of 13.9 μM and 13.4 μM for estrone-3-sulfate and methotrexate, respectively and a rather low affinity for taurocholate with a K{sub m} value of 103 μM. Furthermore, it was confirmed that rtOatp1d1 is a MC-LR transporter and therefore most likely plays a key role in the susceptibility of rainbow trout to MC intoxications. - Highlights: • A new Oatp1d1 in rainbow trout (rtOatp1d1) was cloned, identified and characterized. • rtOatp1d1 is predominantly expressed in the liver. • rtOatp1d1 displays multi-specific transport of endogenous and xenobiotic substrates. • rtOatp1d1 is a homologue of the OATP1A1, OATP1B1 and OATP1B3. • rtOatp1d1 is a microcystin (MC) transporter.« less

SU-E-J-93: Development of Pre-Contoured Human Model Library in DICOM-RT Format for the Epidemiological Study of the Radiotherapy Patients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pyakuryal, A; Lee, C; Lee, C

Purpose: Prior to 3D conformal radiation therapy planning, patient anatomy information was mostly limited to 2D beams-eye-view from the conventional simulator. To analyze the outcomes of such treatments for radiation late effects, 3D computational human models are often used in commercial treatment planning systems (TPSs). However, several underlying difficulties such as time-consuming manual delineation procedures of a large number of structures in the model have always limited its applications. Primary objective of this work was to develop a human model library for the epidemiological study by converting 3D-surface model organs to DICOM-RT format (DICOM-RT structure) using an in-house built software.more » We converted the ICRP reference human models to DICOM-RT models, which can be readily adopted for various dose calculations. Methods: MATLAB based code were utilized to convert the contour drawings extracted in text-format from the 3D graphic-tool, Rhinoceros into DICOM-RT structure format for 50 different organs of each model using a 16GB dual-core processor. The conversion periods were measured for each DICOM-RT models, and the reconstructed structure volumes were validated against the original 3D-surface models in the TPS. Ten reference hybrid whole-body models (8-pediatric and 2-adults) were automatically processed to create DICOM-RT computational human model library. Results: Mean contour conversion period was found to be 580 (N=2) and 394.5 (N=8) seconds for 50 organs in the adult and pediatric models respectively. A good agreement for large organs (NRMSD <1.0%) and small organs (NRMSD <7.7%) was also observed between the original volumes and corresponding DICOM-RT structure volumes of the organs. Conclusion: The ICRP reference human models were converted into DICOM-RT format to support the epidemiological study using a large cohort of conventional radiotherapy patients. Due to its DICOM-compatibility, the library may be implemented to many other different applications. We also expect to develop the library by including additional models in future.« less

Transferring Error Characteristics of Satellite Rainfall Data from Ground Validation (gauged) into Non-ground Validation (ungauged)

NASA Astrophysics Data System (ADS)

Tang, L.; Hossain, F.

2009-12-01

Understanding the error characteristics of satellite rainfall data at different spatial/temporal scales is critical, especially when the scheduled Global Precipitation Mission (GPM) plans to provide High Resolution Precipitation Products (HRPPs) at global scales. Satellite rainfall data contain errors which need ground validation (GV) data for characterization, while satellite rainfall data will be most useful in the regions that are lacking in GV. Therefore, a critical step is to develop a spatial interpolation scheme for transferring the error characteristics of satellite rainfall data from GV regions to Non-GV regions. As a prelude to GPM, The TRMM Multi-satellite Precipitation Analysis (TMPA) products of 3B41RT and 3B42RT (Huffman et al., 2007) over the US spanning a record of 6 years are used as a representative example of satellite rainfall data. Next Generation Radar (NEXRAD) Stage IV rainfall data are used as the reference for GV data. Initial work by the authors (Tang et al., 2009, GRL) has shown promise in transferring error from GV to Non-GV regions, based on a six-year climatologic average of satellite rainfall data assuming only 50% of GV coverage. However, this transfer of error characteristics needs to be investigated for a range of GV data coverage. In addition, it is also important to investigate if proxy-GV data from an accurate space-borne sensor, such as the TRMM PR (or the GPM DPR), can be leveraged for the transfer of error at sparsely gauged regions. The specific question we ask in this study is, “what is the minimum coverage of GV data required for error transfer scheme to be implemented at acceptable accuracy in hydrological relevant scale?” Three geostatistical interpolation methods are compared: ordinary kriging, indicator kriging and disjunctive kriging. Various error metrics are assessed for transfer such as, Probability of Detection for rain and no rain, False Alarm Ratio, Frequency Bias, Critical Success Index, RMSE etc. Understanding the proper space-time scales at which these metrics can be reasonably transferred is also explored in this study. Keyword: Satellite rainfall, error transfer, spatial interpolation, kriging methods.

Long noncoding RNA DANCR, working as a competitive endogenous RNA, promotes ROCK1-mediated proliferation and metastasis via decoying of miR-335-5p and miR-1972 in osteosarcoma.

PubMed

Wang, Yong; Zeng, Xiandong; Wang, Ningning; Zhao, Wei; Zhang, Xi; Teng, Songling; Zhang, Yueyan; Lu, Zhi

2018-05-12

Accumulating evidences indicate that non-coding RNAs (ncRNAs) including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) acting as crucial regulators in osteosarcoma (OS). Previously, we reported that Rho associated coiled-coil containing protein kinase 1 (ROCK1), a metastatic-related gene was negatively regulated by microRNA-335-5p (miR-335-5p) and work as an oncogene in osteosarcoma. Whether any long non-coding RNAs participate in the upstream of miR-335-5p/ROCK1 axial remains unclear. Expression of differentiation antagonizing non-protein coding RNA (DANCR) and miR-335-5p/miR-1972 in osteosarcoma tissues were determined by a qRT-PCR assay and an ISH assay. Osteosarcoma cells' proliferation and migration/invasion ability changes were measured by a CCK-8/EDU assay and a transwell assay respectively. ROCK1 expression changes were checked by a qRT-PCR assay and a western blot assay. Targeted binding effects between miR-335-5p/miR-1972 and ROCK1 or DANCR were verified by a dual luciferase reporter assay and a RIP assay. In vivo experiments including a nude formation assay as well as a CT scan were applied to detect tumor growth and metastasis changes in animal level. In the present study, an elevated DNACR was found in osteosarcoma tissue specimens and in osteosarcoma cell lines, and the elevated DNACR was closely correlated with poor prognosis in clinical patients. Functional experiments illustrated that a depression of DANCR suppressed ROCK1-mediated proliferation and metastasis in osteosarcoma cells. The results of western blot assays and qRT-PCR assays revealed that DANCR regulated ROCK1 via crosstalk with miR-335-5p and miR-1972. Further cellular behavioral experiments demonstrated that DNACR promoted ROCK1-meidated proliferation and metastasis through decoying both miR-335-5p and miR-1972. Finally, the outcomes of in vivo animal models showed that DANCR promoted tumor growth and lung metastasis of osteosarcoma. LncRNA DANCR work as an oncogene and promoted ROCK1-mediated proliferation and metastasis through acting as a competing endogenous RNA (ceRNA) in osteosarcoma.

Mutant type glutathione S-transferase theta 1 gene homologue to mTOR in myelodysplastic syndrome: possible clinical application of rapamycin.

PubMed

Maeda, Yasuhiro; Yamaguchi, Terufumi; Ueda, Satomi; Matsuo, Koki; Morita, Yasuyoshi; Naiki, Yoshito; Miyazato, Hajime; Shimada, Takahiro; Miyatake, Jun-Ichi; Matsuda, Mitsuhiro; Kanamaru, Akihisa

2003-07-01

In this study, we observed the expression of the GSTT-1 gene in patients with myelodysplastic syndrome (MDS) at the messenger RNA level. Reverse transcription-polymerase chain reaction (RT-PCR) for GSTT-1 was performed with a pair of primers complementary to the 5' coding section and the 3' coding section of the GSTT-1 cDNA for amplifying the 623-bp band. Among 20 patients with MDS, 8 patients showed the expected 623-bp band on RT-PCR, and 12 patients showed a 500-bp band on RT-PCR, indicating that a 123-bp sequence was deleted as a mutant of the GSTT-1 gene. Furthermore, a BLAST DNA search showed that the deletion of a 123 bp sequence creates a sequence that is 63% homologous to human FKBP-rapamycin associated protein (FRAP); this protein has been termed a mammalian target of rapamycin (mTOR). We respectively transfected the wild type and the mutant type GSTT-1 gene in an expression vector to two cell lines (K562 and HL-60). The stable transformants for the wild type and the mutant type GSTT-1 genes were made by G418 selection. Interestingly, rapamycin could induce significant growth inhibition of the stable transformants for mutant type GSTT-1, which was indicative of apoptosis, but not that of those for wild type GSTT-1. These results suggest that rapamycin could be included in the therapeutic modality for the patients with MDS who have the mTOR sequences in GSTT-1 gene.

Vector radiative transfer code SORD: Performance analysis and quick start guide

NASA Astrophysics Data System (ADS)

Korkin, Sergey; Lyapustin, Alexei; Sinyuk, Alexander; Holben, Brent; Kokhanovsky, Alexander

2017-10-01

We present a new open source polarized radiative transfer code SORD written in Fortran 90/95. SORD numerically simulates propagation of monochromatic solar radiation in a plane-parallel atmosphere over a reflecting surface using the method of successive orders of scattering (hence the name). Thermal emission is ignored. We did not improve the method in any way, but report the accuracy and runtime in 52 benchmark scenarios. This paper also serves as a quick start user's guide for the code available from ftp://maiac.gsfc.nasa.gov/pub/skorkin, from the JQSRT website, or from the corresponding (first) author.

Sensor Authentication: Embedded Processor Code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Svoboda, John

2012-09-25

Described is the c code running on the embedded Microchip 32bit PIC32MX575F256H located on the INL developed noise analysis circuit board. The code performs the following functions: Controls the noise analysis circuit board preamplifier voltage gains of 1, 10, 100, 000 Initializes the analog to digital conversion hardware, input channel selection, Fast Fourier Transform (FFT) function, USB communications interface, and internal memory allocations Initiates high resolution 4096 point 200 kHz data acquisition Computes complex 2048 point FFT and FFT magnitude. Services Host command set Transfers raw data to Host Transfers FFT result to host Communication error checking

Heat Transfer Computations of Internal Duct Flows With Combined Hydraulic and Thermal Developing Length

NASA Technical Reports Server (NTRS)

Wang, C. R.; Towne, C. E.; Hippensteele, S. A.; Poinsatte, P. E.

1997-01-01

This study investigated the Navier-Stokes computations of the surface heat transfer coefficients of a transition duct flow. A transition duct from an axisymmetric cross section to a non-axisymmetric cross section, is usually used to connect the turbine exit to the nozzle. As the gas turbine inlet temperature increases, the transition duct is subjected to the high temperature at the gas turbine exit. The transition duct flow has combined development of hydraulic and thermal entry length. The design of the transition duct required accurate surface heat transfer coefficients. The Navier-Stokes computational method could be used to predict the surface heat transfer coefficients of a transition duct flow. The Proteus three-dimensional Navier-Stokes numerical computational code was used in this study. The code was first studied for the computations of the turbulent developing flow properties within a circular duct and a square duct. The code was then used to compute the turbulent flow properties of a transition duct flow. The computational results of the surface pressure, the skin friction factor, and the surface heat transfer coefficient were described and compared with their values obtained from theoretical analyses or experiments. The comparison showed that the Navier-Stokes computation could predict approximately the surface heat transfer coefficients of a transition duct flow.

Multi-profile Bayesian alignment model for LC-MS data analysis with integration of internal standards

PubMed Central

Tsai, Tsung-Heng; Tadesse, Mahlet G.; Di Poto, Cristina; Pannell, Lewis K.; Mechref, Yehia; Wang, Yue; Ressom, Habtom W.

2013-01-01

Motivation: Liquid chromatography-mass spectrometry (LC-MS) has been widely used for profiling expression levels of biomolecules in various ‘-omic’ studies including proteomics, metabolomics and glycomics. Appropriate LC-MS data preprocessing steps are needed to detect true differences between biological groups. Retention time (RT) alignment, which is required to ensure that ion intensity measurements among multiple LC-MS runs are comparable, is one of the most important yet challenging preprocessing steps. Current alignment approaches estimate RT variability using either single chromatograms or detected peaks, but do not simultaneously take into account the complementary information embedded in the entire LC-MS data. Results: We propose a Bayesian alignment model for LC-MS data analysis. The alignment model provides estimates of the RT variability along with uncertainty measures. The model enables integration of multiple sources of information including internal standards and clustered chromatograms in a mathematically rigorous framework. We apply the model to LC-MS metabolomic, proteomic and glycomic data. The performance of the model is evaluated based on ground-truth data, by measuring correlation of variation, RT difference across runs and peak-matching performance. We demonstrate that Bayesian alignment model improves significantly the RT alignment performance through appropriate integration of relevant information. Availability and implementation: MATLAB code, raw and preprocessed LC-MS data are available at http://omics.georgetown.edu/alignLCMS.html Contact: hwr@georgetown.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24013927

grid-model: Semi-numerical reionization code

NASA Astrophysics Data System (ADS)

Hutter, Anne

2018-05-01

grid-model computes the time and spatially dependent ionization of neutral hydrogen (HI), neutral (HeI) and singly ionized helium (HeII) in the intergalactic medium (IGM). It accounts for recombinations and provides different descriptions for the photoionization rate that are used to calculate the residual HI fraction in ionized regions. The ionizing emissivity is directly derived from the RT simulation spectra.

Expression of an Mg2+-Dependent HIV-1 RNase H Construct for Drug Screening▿†

PubMed Central

Farias, Richard V.; Vargas, Deborah A.; Castillo, Andres E.; Valenzuela, Beatriz; Coté, Marie L.; Roth, Monica J.; Leon, Oscar

2011-01-01

A single polypeptide of the HIV-1 reverse transcriptase that reconstituted Mg2+-dependent RNase H activity has been made. Using molecular modeling, the construct was designed to encode the p51 subunit joined by a linker to the thumb (T), connection (C), and RNase H (R) domains of p66. This p51-G-TCR construct was purified from the soluble fraction of an Escherichia coli strain, MIC2067(DE3), lacking endogenous RNase HI and HII. The p51-G-TCR RNase H construct displayed Mg2+-dependent activity using a fluorescent nonspecific assay and showed the same cleavage pattern as HIV-1 reverse transcriptase (RT) on substrates that mimic the tRNA removal required for second-strand transfer reactions. The mutant E706Q (E478Q in RT) was purified under similar conditions and was not active. The RNase H of the p51-G-TCR RNase H construct and wild type HIV-1 RT had similar Kms for an RNA-DNA hybrid substrate and showed similar inhibition kinetics to two known inhibitors of the HIV-1 RT RNase H. PMID:21768506

Development and Implementation of Dynamic Scripts to Execute Cycled WRF/GSI Forecasts

NASA Technical Reports Server (NTRS)

Zavodsky, Bradley; Srikishen, Jayanthi; Berndt, Emily; Li, Quanli; Watson, Leela

2014-01-01

Automating the coupling of data assimilation (DA) and modeling systems is a unique challenge in the numerical weather prediction (NWP) research community. In recent years, the Development Testbed Center (DTC) has released well-documented tools such as the Weather Research and Forecasting (WRF) model and the Gridpoint Statistical Interpolation (GSI) DA system that can be easily downloaded, installed, and run by researchers on their local systems. However, developing a coupled system in which the various preprocessing, DA, model, and postprocessing capabilities are all integrated can be labor-intensive if one has little experience with any of these individual systems. Additionally, operational modeling entities generally have specific coupling methodologies that can take time to understand and develop code to implement properly. To better enable collaborating researchers to perform modeling and DA experiments with GSI, the Short-term Prediction Research and Transition (SPoRT) Center has developed a set of Perl scripts that couple GSI and WRF in a cycling methodology consistent with the use of real-time, regional observation data from the National Centers for Environmental Prediction (NCEP)/Environmental Modeling Center (EMC). Because Perl is open source, the code can be easily downloaded and executed regardless of the user's native shell environment. This paper will provide a description of this open-source code and descriptions of a number of the use cases that have been performed by SPoRT collaborators using the scripts on different computing systems.

Mutational analysis of the reverse transcriptase and ribonuclease H domains of the human foamy virus.

PubMed Central

Kögel, D; Aboud, M; Flügel, R M

1995-01-01

Human foamy or spuma virus (HFV) codes for a distinct set of pol gen products. To determine the minimal requirements for the HFV enzymatic activities, defined residues of the reverse transcriptase (RT) and ribo-nuclease H (RNase H) domain of the HFV pol gene were mutated by site-specific PCR mutagenesis. The mutant gene products were bacterially expressed, purified by Ni2+ chelate affinity chromatography and characterised by Western blotting. The enzymatic activities of the individual recombinant HFV pol mutant proteins were characterised by the situ RT, RNase H and RNase H assays. Two substitution mutants reached RT activity levels higher than that of the intact recombinant HFV RT-RH-His. When the catalytically essential D508 was substituted by A508, 5% of RNase H activity was retained while DNA polymerase activity increased 2-fold. A deletion of 11 amino acid residues in the hinge region completely abolished DNA polymerase while RNase H activity decreased 2-fold. A deletion mutant in the C-terminal RH domain showed no RNase H but retained RNase H activity indicating that the activities are genetically separable. The combined data reveal that the HFV DNA polymerase and RNase H activities are interdependent. Images PMID:7544460

Development and Evaluation of Reverse Transcription-Loop-Mediated Isothermal Amplification (RT-LAMP) Assay Coupled with a Portable Device for Rapid Diagnosis of Ebola Virus Disease in Guinea

PubMed Central

Kurosaki, Yohei; Magassouba, N’Faly; Oloniniyi, Olamide K.; Cherif, Mahamoud S.; Sakabe, Saori; Takada, Ayato; Hirayama, Kenji; Yasuda, Jiro

2016-01-01

Given the current absence of specific drugs or vaccines for Ebola virus disease (EVD), rapid, sensitive, and reliable diagnostic methods are required to stem the transmission chain of the disease. We have developed a rapid detection assay for Zaire ebolavirus based on reverse transcription-loop-mediated isothermal amplification (RT-LAMP) and coupled with a novel portable isothermal amplification and detection platform. The RT-LAMP assay is based on primer sets that target the untranscribed trailer region or nucleoprotein coding region of the viral RNA. The test could specifically detect viral RNAs of Central and West African Ebola virus strains within 15 minutes with no cross-reactivity to other hemorrhagic fever viruses and arboviruses, which cause febrile disease. The assay was evaluated using a total of 100 clinical specimens (serum, n = 44; oral swab, n = 56) collected from suspected EVD cases in Guinea. The specificity of this diagnostic test was 100% for both primer sets, while the sensitivity was 100% and 97.9% for the trailer and nucleoprotein primer sets, respectively, compared with a reference standard RT-PCR test. These observations suggest that our diagnostic assay is useful for identifying EVD cases, especially in the field or in settings with insufficient infrastructure. PMID:26900929

Development and Evaluation of Reverse Transcription-Loop-Mediated Isothermal Amplification (RT-LAMP) Assay Coupled with a Portable Device for Rapid Diagnosis of Ebola Virus Disease in Guinea.

PubMed

Kurosaki, Yohei; Magassouba, N'Faly; Oloniniyi, Olamide K; Cherif, Mahamoud S; Sakabe, Saori; Takada, Ayato; Hirayama, Kenji; Yasuda, Jiro

2016-02-01

Given the current absence of specific drugs or vaccines for Ebola virus disease (EVD), rapid, sensitive, and reliable diagnostic methods are required to stem the transmission chain of the disease. We have developed a rapid detection assay for Zaire ebolavirus based on reverse transcription-loop-mediated isothermal amplification (RT-LAMP) and coupled with a novel portable isothermal amplification and detection platform. The RT-LAMP assay is based on primer sets that target the untranscribed trailer region or nucleoprotein coding region of the viral RNA. The test could specifically detect viral RNAs of Central and West African Ebola virus strains within 15 minutes with no cross-reactivity to other hemorrhagic fever viruses and arboviruses, which cause febrile disease. The assay was evaluated using a total of 100 clinical specimens (serum, n = 44; oral swab, n = 56) collected from suspected EVD cases in Guinea. The specificity of this diagnostic test was 100% for both primer sets, while the sensitivity was 100% and 97.9% for the trailer and nucleoprotein primer sets, respectively, compared with a reference standard RT-PCR test. These observations suggest that our diagnostic assay is useful for identifying EVD cases, especially in the field or in settings with insufficient infrastructure.

Computer code for predicting coolant flow and heat transfer in turbomachinery

NASA Technical Reports Server (NTRS)

Meitner, Peter L.

1990-01-01

A computer code was developed to analyze any turbomachinery coolant flow path geometry that consist of a single flow passage with a unique inlet and exit. Flow can be bled off for tip-cap impingement cooling, and a flow bypass can be specified in which coolant flow is taken off at one point in the flow channel and reintroduced at a point farther downstream in the same channel. The user may either choose the coolant flow rate or let the program determine the flow rate from specified inlet and exit conditions. The computer code integrates the 1-D momentum and energy equations along a defined flow path and calculates the coolant's flow rate, temperature, pressure, and velocity and the heat transfer coefficients along the passage. The equations account for area change, mass addition or subtraction, pumping, friction, and heat transfer.

State-to-state rotational energy-transfer measurements in the nu(2) = 1 state of ammonia by infrared-infrared double resonance

NASA Technical Reports Server (NTRS)

Abel, Bernd; Coy, Stephen L.; Klaassen, Jody J.; Steinfeld, Jeffrey I.

1992-01-01

The state-resolved rotational (R-R, R-T) energy transfer in (N-14)H3 (for NH3-NH3 and NH3-Ar collisions) was studied using an IR double-resonance laser spectroscopic technique. Measurements of both the total rate of depopulation by collisions, and the rates of transfer into specific final rovibrational states (v,J,K) were performed using time-resolved tunable diode laser absorption spectroscopy. A kinetic master-equation analysis of time-resolved level populatons was carried out, yielding state-to-state rate constants and propensity rules for NH3-NH3 and NH3-Ar collisions.

Assessment of radiation-induced secondary cancer risk in the Brazilian population from left-sided breast-3D-CRT using MCNPX.

PubMed

Mendes, Bruno Melo; Trindade, Bruno Machado; Fonseca, Telma Cristina Ferreira; de Campos, Tarcisio Passos Ribeiro

2017-12-01

The aim of this work was to simulate a 6MV conventional breast 3D conformational radiation therapy (3D-CRT) with physical wedges (50 Gy/25#) in the left breast, calculate the mean absorbed dose in the body organs using robust models and computational tools and estimate the secondary cancer-incidence risk to the Brazilian population. The VW female phantom was used in the simulations. Planning target volume (PTV) was defined in the left breast. The 6MV parallel-opposed fields breast-radiotherapy (RT) protocol was simulated with MCNPx code. The absorbed doses were evaluated in all the organs. The secondary cancer-incidence risk induced by radiotherapy was calculated for different age groups according to the BEIR VII methodology. RT quality indexes indicated that the protocol was properly simulated. Significant absorbed dose values in red bone marrow, RBM (0.8 Gy) and stomach (0.6 Gy) were observed. The contralateral breast presented the highest risk of incidence of a secondary cancer followed by leukaemia, lung and stomach. The risk of a secondary cancer-incidence by breast-RT, for the Brazilian population, ranged between 2.2-1.7% and 0.6-0.4%. RBM and stomach, usually not considered as OAR, presented high second cancer incidence risks of 0.5-0.3% and 0.4-0.1%, respectively. This study may be helpful for breast-RT risk/benefit assessment. Advances in knowledge: MCNPX-dosimetry was able to provide the scatter radiation and dose for all body organs in conventional breast-RT. It was found a relevant risk up to 2.2% of induced-cancer from breast-RT, considering the whole thorax organs and Brazilian cancer-incidence.

Development of a new clot formation protocol for standardized in vitro investigations of sonothrombolysis.

PubMed

Roessler, Florian C; Teichert, Andrea; Ohlrich, Marcus; Marxsen, Jan H; Stellmacher, Florian; Tanislav, Christian; Seidel, Günter

2014-11-30

Agreement about the most suitable clot formation protocol for sonothrombolysis investigations is lacking. Lysis rates vary strongly owing to different test conditions and, thus, cannot be compared. We aim to establish a simple but physiologically grounded protocol for in vitro coagulation to enable standardized sonothrombolysis investigations. Clots were generated from platelet-rich plasma (PRP) obtained by centrifugation (10 min, 180 × g) of human venous blood (VB). PRP was mixed with the boundary layer formed between the supernatant and the erythrocyte layer. To achieve clots with different platelet counts, PRP was gradually substituted with platelet-free plasma (PFP), harvested from the supernatant of VB after centrifugation (10 min, 2570 × g). Clot types were examined for histological appearance, hydrodynamic resistance under physiological flows, and lysis rate measured by weight loss after a 2-h treatment with recombinant tissue plasminogen activator (rt-PA) (60 kU/ml). Lysis rates of the most suitable clot were measured after a 1-h treatment with rt-PA (60 kU/ml), and combined treatment with rt-PA and 2-MHz transcranial color-coded sonography (TCCS) (0.179 W/cm(2)) or 2-MHz transcranial Doppler (TCD) (0.457 W/cm(2)). With increased platelet count, the hydrodynamic resistance of the artificial clots increased, their histological appearance became more physiological, and lysis rates decreased. The most suitable clots consisted of 1.5-ml PRP, 2.0-ml PFP, and 0.5-ml boundary layer. Their lysis rates were 36.7 ± 7.8% (rt-PA), 40.8 ± 8.6% (rt-PA+TCCS), and 40.4 ± 8.3% (rt-PA+TCD). These systemic investigations were conducted for the first time. This protocol should be used for standardized sonothrombolysis investigations. Copyright © 2014 Elsevier B.V. All rights reserved.

Thermal finite-element analysis of space shuttle main engine turbine blade

NASA Technical Reports Server (NTRS)

Abdul-Aziz, Ali; Tong, Michael T.; Kaufman, Albert

1987-01-01

Finite-element, transient heat transfer analyses were performed for the first-stage blades of the space shuttle main engine (SSME) high-pressure fuel turbopump. The analyses were based on test engine data provided by Rocketdyne. Heat transfer coefficients were predicted by performing a boundary-layer analysis at steady-state conditions with the STAN5 boundary-layer code. Two different peak-temperature overshoots were evaluated for the startup transient. Cutoff transient conditions were also analyzed. A reduced gas temperature profile based on actual thermocouple data was also considered. Transient heat transfer analyses were conducted with the MARC finite-element computer code.

Validation of CFD/Heat Transfer Software for Turbine Blade Analysis

NASA Technical Reports Server (NTRS)

Kiefer, Walter D.

2004-01-01

I am an intern in the Turbine Branch of the Turbomachinery and Propulsion Systems Division. The division is primarily concerned with experimental and computational methods of calculating heat transfer effects of turbine blades during operation in jet engines and land-based power systems. These include modeling flow in internal cooling passages and film cooling, as well as calculating heat flux and peak temperatures to ensure safe and efficient operation. The branch is research-oriented, emphasizing the development of tools that may be used by gas turbine designers in industry. The branch has been developing a computational fluid dynamics (CFD) and heat transfer code called GlennHT to achieve the computational end of this analysis. The code was originally written in FORTRAN 77 and run on Silicon Graphics machines. However the code has been rewritten and compiled in FORTRAN 90 to take advantage of more modem computer memory systems. In addition the branch has made a switch in system architectures from SGI's to Linux PC's. The newly modified code therefore needs to be tested and validated. This is the primary goal of my internship. To validate the GlennHT code, it must be run using benchmark fluid mechanics and heat transfer test cases, for which there are either analytical solutions or widely accepted experimental data. From the solutions generated by the code, comparisons can be made to the correct solutions to establish the accuracy of the code. To design and create these test cases, there are many steps and programs that must be used. Before a test case can be run, pre-processing steps must be accomplished. These include generating a grid to describe the geometry, using a software package called GridPro. Also various files required by the GlennHT code must be created including a boundary condition file, a file for multi-processor computing, and a file to describe problem and algorithm parameters. A good deal of this internship will be to become familiar with these programs and the structure of the GlennHT code. Additional information is included in the original extended abstract.

National Aerospace Leadership Initiative - Phase I

DTIC Science & Technology

2008-09-30

Devised and validated CFD code for operation of a micro-channel heat exchanger. The work was published at the 2008 AIAA Annual Meeting and Exposition...and (3) preparation to implement this algorithm in TURBO. Heat Transfer Capability In the short and medium term, the following plan has been adopted...to provide heat transfer capability to the TURBO code: • Incorporation of a constant wall temperature boundary condition. This capability will be

Optimal trajectories for the aeroassisted flight experiment. Part 4: Data, tables, and graphs

NASA Technical Reports Server (NTRS)

Miele, A.; Wang, T.; Lee, W. Y.; Wang, H.; Wu, G. D.

1989-01-01

The determination of optimal trajectories for the aeroassisted flight experiment (AFE) is discussed. Data, tables, and graphs relative to the following transfers are presented: (IA) indirect ascent to a 178 NM perigee via a 197 NM apogee; and (DA) direct ascent to a 178 NM apogee. For both transfers, two cases are investigated: (1) the bank angle is continuously variable; and (2) the trajectory is divided into segments along which the bank angle is constant. For case (2), the following subcases are studied: two segments, three segments, four segments, and five segments; because the time duration of each segment is optimized, the above subcases involve four, six, eight, and ten parameters, respectively. Presented here are systematic data on a total of ten optimal trajectories (OT), five for Transfer IA and five for Transfer DA. For comparison purposes and only for Transfer IA, a five-segment reference trajectory RT is also considered.

Reverse Transcriptase Activity in Mature Spermatozoa of Mouse

PubMed Central

Giordano, Roberto; Magnano, Anna Rosa; Zaccagnini, Germana; Pittoggi, Carmine; Moscufo, Nicola; Lorenzini, Rodolfo; Spadafora, Corrado

2000-01-01

We show here that a reverse transcriptase (RT) activity is present in murine epididymal spermatozoa. Sperm cells incubated with human poliovirus RNA can take up exogenous RNA molecules and internalize them in nuclei. Direct PCR amplification of DNA extracted from RNA-incubated spermatozoa indicate that poliovirus RNA is reverse-transcribed in cDNA fragments. PCR analysis of two-cell embryos shows that poliovirus RNA-challenged spermatozoa transfer retrotranscribed cDNA molecules into eggs during in vitro fertilization. Finally, RT molecules can be visualized on sperm nuclear scaffolds by immunogold electron microscopy. These results, therefore, reveal a novel metabolic function in spermatozoa, which may play a role during early embryonic development. PMID:10725323

Consistent multiphysics simulation of a central tower CSP plant as applied to ISTORE

NASA Astrophysics Data System (ADS)

Votyakov, Evgeny V.; Papanicolas, Costas N.

2017-06-01

We present a unified consistent multiphysics approach to model a central tower CSP plant. The framework for the model includes Monte Carlo ray tracing (RT) and computational fluid dynamics (CFD) components utilizing the OpenFOAM C++ software library. The RT part works effectively with complex surfaces of engineering design given in CAD formats. The CFD simulation, which is based on 3D Navier-Stokes equations, takes into account all possible heat transfer mechanisms: radiation, conduction, and convection. Utilizing this package, the solar field of the experimental Platform for Research, Observation, and TEchnological Applications in Solar Energy (PROTEAS) and the Integrated STOrage and Receiver (ISTORE), developed at the Cyprus Institute, are being examined.

Immune mechanisms in organ allograft rejection. V. Pivotal role of the cytotoxic-suppressor T cell subset in the rejection of heart grafts bearing isolated class I disparities in the inbred rat

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lowry, R.P.; Forbes, R.D.; Blackburn, J.H.

1985-11-01

The cellular requirements for rejection of heart grafts bearing isolated major histocompatibility complex (MHC) subregion RT1A-encoded class I disparities was assessed by adoptive transfer. Sublethally irradiated (780 rads) (PVG X WF)F1 recipients of irradiated PVG-RT1r1 heart grafts were selectively reconstituted with spleen cells from syngeneic donors previously sensitized with two sequential PVG-RT1r1 skin grafts. PVG-RT1r1 heart grafts were rejected acutely in recipients reconstituted with 10 X 10(6) unfractionated immune spleen cells or inocula (5 X 10(6) cells) depleted of SIg+ cells, but additional depletion of cytotoxic T cells and their precursors resulted in marked prolongation of graft survival. Reducing themore » reconstituting inocula from 4 X 10(6) to 2.5 X 10(6) spleen cells prolonged graft survival to that observed in unreconstituted recipients. Additional studies were performed to define the immunologic basis for prolonged survival of PVG-RT1r1 heart grafts in homozygous PVG recipients. Although lymphoid cells of naive PVG failed to proliferate on coculture with irradiated PVG-RT1r1, bulk cultures yielding but weak and variable CTL generation, lymphoid cells from specifically sensitized PVG proliferated and generated greater cytotoxic T lymphocyte (CTL) activity under identical conditions, strongly suggesting, therefore, that prolonged heart graft survival in this strain combination is related to low CTL precursor frequency.« less

Hypo-Fractionated Conformal Radiation Therapy to the Tumor Bed After Segmental Mastectomy

DTIC Science & Technology

2004-07-01

conserving surgery for breast cancer were first offered slan- speed helical CT scanner . CT images were transferred to dard conventional 6-week RT. Only...Zhou S, Prosnitz RG, et al. The impact of breast cancer treated with breast conserving therapy. J Surg im, diated left ventricular volume on the

A comparison of transfer-appropriate processing and multi-process frameworks for prospective memory performance.

PubMed

McBride, Dawn M; Abney, Drew H

2012-01-01

We examined multi-process (MP) and transfer-appropriate processing descriptions of prospective memory (PM). Three conditions were compared that varied the overlap in processing type (perceptual/conceptual) between the ongoing and PM tasks such that two conditions involved a match of perceptual processing and one condition involved a mismatch in processing (conceptual ongoing task/perceptual PM task). One of the matched processing conditions also created a focal PM task, whereas the other two conditions were considered non-focal (Einstein & McDaniel, 2005). PM task accuracy and ongoing task completion speed in baseline and PM task conditions were measured. Accuracy results indicated a higher PM task completion rate for the focal condition than the non-focal conditions, a finding that is consistent with predictions made by the MP view. However, reaction time (RT) analyses indicated that PM task cost did not differ across conditions when practice effects are considered. Thus, the PM accuracy results are consistent with a MP description of PM, but RT results did not support the MP view predictions regarding PM cost.

SPAMCART: a code for smoothed particle Monte Carlo radiative transfer

NASA Astrophysics Data System (ADS)

Lomax, O.; Whitworth, A. P.

2016-10-01

We present a code for generating synthetic spectral energy distributions and intensity maps from smoothed particle hydrodynamics simulation snapshots. The code is based on the Lucy Monte Carlo radiative transfer method, I.e. it follows discrete luminosity packets as they propagate through a density field, and then uses their trajectories to compute the radiative equilibrium temperature of the ambient dust. The sources can be extended and/or embedded, and discrete and/or diffuse. The density is not mapped on to a grid, and therefore the calculation is performed at exactly the same resolution as the hydrodynamics. We present two example calculations using this method. First, we demonstrate that the code strictly adheres to Kirchhoff's law of radiation. Secondly, we present synthetic intensity maps and spectra of an embedded protostellar multiple system. The algorithm uses data structures that are already constructed for other purposes in modern particle codes. It is therefore relatively simple to implement.

Analysis of health care claims during the peri-transfer stage of transition from pediatric to adult care among juvenile idiopathic arthritis patients.

PubMed

Mannion, Melissa L; Xie, Fenglong; Baddley, John; Chen, Lang; Curtis, Jeffrey R; Saag, Kenneth; Zhang, Jie; Beukelman, Timothy

2016-09-05

To investigate the utilization of health care services before and after transfer from pediatric to adult rheumatology care in clinical practice. Using US commercial claims data from January 2005 through August 2012, we identified individuals with a JIA diagnosis code from a pediatric rheumatologist followed by any diagnosis code from an adult rheumatologist. Individuals had 6 months observable time before the last pediatric visit and 6 months after the first adult visit. Medication, emergency room, physical therapy use, and diagnosis codes were compared between the pediatric and adult interval using McNemar's test. The proportion of days covered (PDC) of TNFi for the time between last pediatric and first adult visit was calculated. We identified 58 individuals with JIA who transferred from pediatric to adult rheumatology care after the age of 14. The median age at the last pediatric rheumatology visit was 18.1 years old and the median transfer interval was 195 days. 29 % of patients received NSAIDs in the adult interval compared to 43 % in the pediatric interval (p = 0.06). In the pediatric interval, 71 % received a JRA and 0 % received an RA physician diagnosis code compared to 28 and 45 %, respectively, in the adult interval. The median PDC for patients receiving a TNFi was 0.75 during the transfer interval. Individuals with JIA who transferred to adult care were more likely receive a diagnosis of RA instead of JRA and were less likely to receive NSAIDs, but had no significant immediate changes to other medication use.

Evaluation of a GPS Receiver for Code and Carrier-Phase Time and Frequency Transfer

DTIC Science & Technology

2010-11-01

2], and carrier-phase [3]. NIST also employs GPS time transfer as the backup link to Two Way Satellite Time and Frequency Transfer ( TWSTFT ) [4...4] D. Kirchner, 1999, “Two-Way Satellite Time and Frequency Transfer ( TWSTFT ): Principle, Implementation, and Current Performance,” Review of

The Deceptively Simple N170 Reflects Network Information Processing Mechanisms Involving Visual Feature Coding and Transfer Across Hemispheres.

PubMed

Ince, Robin A A; Jaworska, Katarzyna; Gross, Joachim; Panzeri, Stefano; van Rijsbergen, Nicola J; Rousselet, Guillaume A; Schyns, Philippe G

2016-08-22

A key to understanding visual cognition is to determine "where", "when", and "how" brain responses reflect the processing of the specific visual features that modulate categorization behavior-the "what". The N170 is the earliest Event-Related Potential (ERP) that preferentially responds to faces. Here, we demonstrate that a paradigmatic shift is necessary to interpret the N170 as the product of an information processing network that dynamically codes and transfers face features across hemispheres, rather than as a local stimulus-driven event. Reverse-correlation methods coupled with information-theoretic analyses revealed that visibility of the eyes influences face detection behavior. The N170 initially reflects coding of the behaviorally relevant eye contralateral to the sensor, followed by a causal communication of the other eye from the other hemisphere. These findings demonstrate that the deceptively simple N170 ERP hides a complex network information processing mechanism involving initial coding and subsequent cross-hemispheric transfer of visual features. © The Author 2016. Published by Oxford University Press.

Surface reflectance retrieval from imaging spectrometer data using three atmospheric codes

NASA Astrophysics Data System (ADS)

Staenz, Karl; Williams, Daniel J.; Fedosejevs, Gunar; Teillet, Phil M.

1994-12-01

Surface reflectance retrieval from imaging spectrometer data has become important for quantitative information extraction in many application areas. In order to calculate surface reflectance from remotely measured radiance, radiative transfer codes play an important role for removal of the scattering and gaseous absorption effects of the atmosphere. The present study evaluates surface reflectances retrieved from airborne visible/infrared imaging spectrometer (AVIRIS) data using three radiative transfer codes: modified 5S (M5S), 6S, and MODTRAN2. Comparisons of the retrieved surface reflectance with ground-based reflectance were made for different target types such as asphalt, gravel, grass/soil mixture (soccer field), and water (Sooke Lake). The results indicate that the estimation of the atmospheric water vapor content is important for an accurate surface reflectance retrieval regardless of the radiative transfer code used. For the present atmospheric conditions, a difference of 0.1 in aerosol optical depth had little impact on the retrieved surface reflectance. The performance of MODTRAN2 is superior in the gas absorption regions compared to M5S and 6S.

Single-Pair Fret Analysis of mRNA Transcripts for Highly Sensitive Gene Expression Profiling in Near Real Time

PubMed Central

Peng, Zhiyong; Young, Brandon; Baird, Alison E.; Soper, Steven A.

2013-01-01

Expression analysis of mRNAs transcribed from certain genes can be used as important sources of biomarkers for in vitro diagnostics. While the use of reverse transcription quantitative PCR (RT-qPCR) can provide excellent analytical sensitivity for monitoring transcript numbers, more sensitive approaches for expression analysis that can report results in near real-time are needed for many critical applications. We report a novel assay that can provide exquisite limits-of-quantitation and consists of reverse transcription (RT) followed by a ligase detection reaction (LDR) with single-pair fluorescence resonance energy transfer (spFRET) to provide digital readout through molecular counting. For this assay, no PCR was employed, which enabled short assay turnaround times. To facilitate implementation of the assay, a cyclic olefin copolymer (COC) microchip, which was fabricated using hot embossing, was employed to carry out the LDR in a continuous flow format with on-line single-molecule detection following the LDR. As demonstrators of the assay's utility, MMP-7 mRNA was expression profiled from several colorectal cancer cell lines. It was found that the RT-LDR/spFRET assay produced highly linear calibration plots even in the low copy number regime. Comparison to RT-qPCR indicated a better linearity over the low copy number range investigated (10 − 10,000 copies) with an R2 = 0.9995 for RT-LDR/spFRET and R2 = 0.98 for RT-qPCR. In addition, differentiating between copy numbers of 10 and 50 could be performed with higher confidence using RT-LDR/spFRET. To demonstrate the short assay turnaround times obtainable using the RT-LDR/spFRET assay, a 2 thermal cycle LDR was carried out on amphiphysin gene transcripts that can serve as important diagnostic markers for ischemic stroke. The ability to supply diagnostic information on possible stroke events in short turnaround times using RT-LDR/spFRET will enable clinicians to treat patients effectively with appropriate time-sensitive therapeutics. PMID:23869556

Linear energy transfer in water phantom within SHIELD-HIT transport code

NASA Astrophysics Data System (ADS)

Ergun, A.; Sobolevsky, N.; Botvina, A. S.; Buyukcizmeci, N.; Latysheva, L.; Ogul, R.

2017-02-01

The effect of irradiation in tissue is important in hadron therapy for the dose measurement and treatment planning. This biological effect is defined by an equivalent dose H which depends on the Linear Energy Transfer (LET). Usually, H can be expressed in terms of the absorbed dose D and the quality factor K of the radiation under consideration. In literature, various types of transport codes have been used for modeling and simulation of the interaction of the beams of protons and heavier ions with tissue-equivalent materials. In this presentation we used SHIELD-HIT code to simulate decomposition of the absorbed dose by LET in water for 16O beams. A more detailed description of capabilities of the SHIELD-HIT code can be found in the literature.

Impact of Inner Surface Perturbations on the Stability of Cylindrical Liner Implosion

NASA Astrophysics Data System (ADS)

Weis, Matthew; Peterson, Kyle; Hess, Mark; Lau, Y. Y.; Zhang, Peng; Gilgenbach, Ronald

2015-11-01

This paper studies the effects of initial perturbations on the inner liner surface (ILS) of an imploding cylindrical liner. In MagLIF, nonuniform preheat of the fuel could provide an additional source of spatial nonuniformity on the ILS. A blast wave generated by the laser preheat might trigger the Richtmyer-Meshkov instability (RM) on the ILS which then serves as another seed to the Rayleigh-Taylor instability (RT) during the stagnation (deceleration) phase of the implosion. Another scenario is that the shock initiated from the outer liner surface, during current rise, propagates inward and is reflected at the ILS. This reflected shock would carry the initial ILS perturbations which then serve as an additional seed for the magneto-RT (MRT) during the acceleration phase of the implosion. These potentially dangerous interactions are analyzed using the 2D HYDRA code. The effects of axial magnetic fields, of the initial surface roughness spectrum, and of gas fill or water fill (to examine deceleration phase RT) are studied. M. R. Weis was supported by the Sandia National Laboratories. This work was also supported by DoE Grant DE-SC0012328.

Factor IX expression in skeletal muscle of a severe hemophilia B patient 10 years after AAV-mediated gene transfer.

PubMed

Buchlis, George; Podsakoff, Gregory M; Radu, Antonetta; Hawk, Sarah M; Flake, Alan W; Mingozzi, Federico; High, Katherine A

2012-03-29

In previous work we transferred a human factor IX-encoding adeno-associated viral vector (AAV) into skeletal muscle of men with severe hemophilia B. Biopsy of injected muscle up to 1 year after vector injection showed evidence of gene transfer by Southern blot and of protein expression by IHC and immunofluorescent staining. Although the procedure appeared safe, circulating F.IX levels remained subtherapeutic (< 1%). Recently, we obtained muscle tissue from a subject injected 10 years earlier who died of causes unrelated to gene transfer. Using Western blot, IHC, and immunofluorescent staining, we show persistent factor IX expression in injected muscle tissue. F.IX transcripts were detected in injected skeletal muscle using RT-PCR, and isolated whole genomic DNA tested positive for the presence of the transferred AAV vector sequence. This is the longest reported transgene expression to date from a parenterally administered AAV vector, with broad implications for the future of muscle-directed gene transfer.

Factor IX expression in skeletal muscle of a severe hemophilia B patient 10 years after AAV-mediated gene transfer

PubMed Central

Buchlis, George; Podsakoff, Gregory M.; Radu, Antonetta; Hawk, Sarah M.; Flake, Alan W.; Mingozzi, Federico

2012-01-01

In previous work we transferred a human factor IX–encoding adeno-associated viral vector (AAV) into skeletal muscle of men with severe hemophilia B. Biopsy of injected muscle up to 1 year after vector injection showed evidence of gene transfer by Southern blot and of protein expression by IHC and immunofluorescent staining. Although the procedure appeared safe, circulating F.IX levels remained subtherapeutic (< 1%). Recently, we obtained muscle tissue from a subject injected 10 years earlier who died of causes unrelated to gene transfer. Using Western blot, IHC, and immunofluorescent staining, we show persistent factor IX expression in injected muscle tissue. F.IX transcripts were detected in injected skeletal muscle using RT-PCR, and isolated whole genomic DNA tested positive for the presence of the transferred AAV vector sequence. This is the longest reported transgene expression to date from a parenterally administered AAV vector, with broad implications for the future of muscle-directed gene transfer. PMID:22271447

Cerebellar activation during motor sequence learning is associated with subsequent transfer to new sequences.

PubMed

Shimizu, Renee E; Wu, Allan D; Knowlton, Barbara J

2016-12-01

Effective learning results not only in improved performance on a practiced task, but also in the ability to transfer the acquired knowledge to novel, similar tasks. Using a modified serial reaction time (RT) task, the authors examined the ability to transfer to novel sequences after practicing sequences in a repetitive order versus a nonrepeating interleaved order. Interleaved practice resulted in better performance on new sequences than repetitive practice. In a second study, participants practiced interleaved sequences in a functional MRI (fMRI) scanner and received a transfer test of novel sequences. Transfer ability was positively correlated with cerebellar blood oxygen level dependent activity during practice, indicating that greater cerebellar engagement during training resulted in better subsequent transfer performance. Interleaved practice may thus result in a more generalized representation that is robust to interference, and the degree of activation in the cerebellum may be a reflection of the instantiation and engagement of internal models. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Warthog: Coupling Status Update

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hart, Shane W. D.; Reardon, Bradley T.

The Warthog code was developed to couple codes that are developed in both the Multi-Physics Object-Oriented Simulation Environment (MOOSE) from Idaho National Laboratory (INL) and SHARP from Argonne National Laboratory (ANL). The initial phase of this work, focused on coupling the neutronics code PROTEUS with the fuel performance code BISON. The main technical challenge involves mapping the power density solution determined by PROTEUS to the fuel in BISON. This presents a challenge since PROTEUS uses the MOAB mesh format, but BISON, like all other MOOSE codes, uses the libMesh format. When coupling the different codes, one must consider that Warthogmore » is a light-weight MOOSE-based program that uses the Data Transfer Kit (DTK) to transfer data between the various mesh types. Users set up inputs for the codes they want to run, and then Warthog transfers the data between them. Currently Warthog supports XSProc from SCALE or the Sub-Group Application Programming Interface (SGAPI) in PROTEUS for generating cross sections. It supports arbitrary geometries using PROTEUS and BISON. DTK will transfer power densities and temperatures between the codes where the domains overlap. In the past fiscal year (FY), much work has gone into demonstrating two-way coupling for simple pin cells of various materials. XSProc was used to calculate the cross sections, which were then passed to PROTEUS in an external file. PROTEUS calculates the fission/power density, and Warthog uses DTK to pass this information to BISON, where it is used as the heat source. BISON then calculates the temperature profile of the pin cell and sends it back to XSProc to obtain the temperature corrected cross sections. This process is repeated until the convergence criteria (tolerance on BISON solve, or number of time steps) is reached. Models have been constructed and run for both uranium oxide and uranium silicide fuels. These models demonstrate a clear difference in power shape that is not accounted for in a stand-alone BISON run. Future work involves improving the user interface (UI), likely through integration with the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Workbench. Furthermore, automating the input creation would ease the user experience. The next priority is to continue coupling the work with other codes in the SHARP package. Efforts on other projects include work to couple the Nek5000 thermo-hydraulics code to MOOSE, but this is in the preliminary stages.« less

Light scattering and absorption by space weathered planetary bodies: Novel numerical solution

NASA Astrophysics Data System (ADS)

Markkanen, Johannes; Väisänen, Timo; Penttilä, Antti; Muinonen, Karri

2017-10-01

Airless planetary bodies are exposed to space weathering, i.e., energetic electromagnetic and particle radiation, implantation and sputtering from solar wind particles, and micrometeorite bombardment.Space weathering is known to alter the physical and chemical composition of the surface of an airless body (C. Pieters et al., J. Geophys. Res. Planets, 121, 2016). From the light scattering perspective, one of the key effects is the production of nanophase iron (npFe0) near the exposed surfaces (B. Hapke, J. Geophys. Res., 106, E5, 2001). At visible and ultraviolet wavelengths these particles have a strong electromagnetic response which has a major impact on scattering and absorption features. Thus, to interpret the spectroscopic observations of space-weathered asteroids, the model should treat the contributions of the npFe0 particles rigorously.Our numerical approach is based on the hierarchical geometric optics (GO) and radiative transfer (RT). The modelled asteroid is assumed to consist of densely packed silicate grains with npFe0 inclusions. We employ our recently developed RT method for dense random media (K. Muinonen, et al., Radio Science, submitted, 2017) to compute the contributions of the npFe0 particles embedded in silicate grains. The dense media RT method requires computing interactions of the npFe0 particles in the volume element for which we use the exact fast superposition T-matrix method (J. Markkanen, and A.J. Yuffa, JQSRT 189, 2017). Reflections and refractions on the grain surface and propagation in the grain are addressed by the GO. Finally, the standard RT is applied to compute scattering by the entire asteroid.Our numerical method allows for a quantitative interpretation of the spectroscopic observations of space-weathered asteroids. In addition, it may be an important step towards more rigorous a thermophysical model of asteroids when coupled with the radiative and conductive heat transfer techniques.Acknowledgments. Research supported by European Research Council with Advanced Grant No. 320773 SAEMPL. Computational resources provided by CSC- IT Centre for Science Ltd, Finland.

From Geometry Optimization to Time Dependent Molecular Structure Modeling: Method Developments, ab initio Theories and Applications

NASA Astrophysics Data System (ADS)

Liang, Wenkel

This dissertation consists of two general parts: (I) developments of optimization algorithms (both nuclear and electronic degrees of freedom) for time-independent molecules and (II) novel methods, first-principle theories and applications in time dependent molecular structure modeling. In the first part, we discuss in specific two new algorithms for static geometry optimization, the eigenspace update (ESU) method in nonredundant internal coordinate that exhibits an enhanced performace with up to a factor of 3 savings in computational cost for large-sized molecular systems; the Car-Parrinello density matrix search (CP-DMS) method that enables direct minimization of the SCF energy as an effective alternative to conventional diagonalization approach. For the second part, we consider the time dependence and first presents two nonadiabatic dynamic studies that model laser controlled molecular photo-dissociation for qualitative understandings of intense laser-molecule interaction, using ab initio direct Ehrenfest dynamics scheme implemented with real-time time-dependent density functional theory (RT-TDDFT) approach developed in our group. Furthermore, we place our special interest on the nonadiabatic electronic dynamics in the ultrafast time scale, and presents (1) a novel technique that can not only obtain energies but also the electron densities of doubly excited states within a single determinant framework, by combining methods of CP-DMS with RT-TDDFT; (2) a solvated first-principles electronic dynamics method by incorporating the polarizable continuum solvation model (PCM) to RT-TDDFT, which is found to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution. (3) applications of the PCM-RT-TDDFT method to study the intramolecular charge-transfer (CT) dynamics in a C60 derivative. Such work provides insights into the characteristics of ultrafast dynamics in photoexcited fullerene derivatives, and aids in the rational design for pre-dissociative exciton in the intramolecular CT process in organic solar cells.

WINCLR: a Computer Code for Heat Transfer and Clearance Calculation in a Compressor

NASA Technical Reports Server (NTRS)

Bose, T. K.; Murthy, S. N. B.

1994-01-01

One of the concerns during inclement weather operation of aircraft in rain and hail storm conditions is the nature and extent of changes in compressor casing clearance. An increase in clearance affects efficiency while a decrease may cause blade rubbing with the casing. The change in clearance is the result of geometrical dimensional changes in the blades, the casing and the rotor due to heat transfer between those parts and the two-phase working fluid. The heat transfer interacts nonlinearly with the performance of the compressor, and, therefore, the determination of clearance changes necessitates a simultaneous determination of change in performance of the compressor. A computer code the WINCLR has been designed for the determination of casing clearance, that is operated interactively with the PURDU-WINCOF I code designed previously for determining the performance of a compressor. A detailed description of the WINCLR code is provided in a companion report. The current report provides details of the code with an illustrative example of application to the case of a multistage compressor. It is found in the example case that under given ingestion and operational conditions, it is possible for a compressor to undergo changes in performance in the front stages and rubbing in the back stages.

Genome-Wide Analysis of Long Noncoding RNA (lncRNA) Expression in Hepatoblastoma Tissues

PubMed Central

Xue, Ping; Cui, Ximao; Li, Kai; Zheng, Shan; He, Xianghuo; Dong, Kuiran

2014-01-01

Long noncoding RNAs (lncRNAs) have crucial roles in cancer biology. We performed a genome-wide analysis of lncRNA expression in hepatoblastoma tissues to identify novel targets for further study of hepatoblastoma. Hepatoblastoma and normal liver tissue samples were obtained from hepatoblastoma patients. The genome-wide analysis of lncRNA expression in these tissues was performed using a 4×180 K lncRNA microarray and Sureprint G3 Human lncRNA Chips. Quantitative RT-PCR (qRT-PCR) was performed to confirm these results. The differential expressions of lncRNAs and mRNAs were identified through fold-change filtering. Gene Ontology (GO) and pathway analyses were performed using the standard enrichment computation method. Associations between lncRNAs and adjacent protein-coding genes were determined through complex transcriptional loci analysis. We found that 2736 lncRNAs were differentially expressed in hepatoblastoma tissues. Among these, 1757 lncRNAs were upregulated more than two-fold relative to normal tissues and 979 lncRNAs were downregulated. Moreover, in hepatoblastoma there were 420 matched lncRNA-mRNA pairs for 120 differentially expressed lncRNAs, and 167 differentially expressed mRNAs. The co-expression network analysis predicted 252 network nodes and 420 connections between 120 lncRNAs and 132 coding genes. Within this co-expression network, 369 pairs were positive, and 51 pairs were negative. Lastly, qRT-PCR data verified six upregulated and downregulated lncRNAs in hepatoblastoma, plus endothelial cell-specific molecule 1 (ESM1) mRNA. Our results demonstrated that expression of these aberrant lncRNAs could respond to hepatoblastoma development. Further study of these lncRNAs could provide useful insight into hepatoblastoma biology. PMID:24465615

78 FR 46688 - Proposed Collection; Comment Request for Form 706

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-01

... 706, United States Estate (and Generation-Skipping Transfer) Tax Return. DATES: Written comments... INFORMATION: Title: United States Estate (and Generation-Skipping Transfer) Tax Return. OMB Number: 1545-0015... imposed by Internal Revenue Code section 2001 and the Federal generation-skipping transfer (GST) tax...

Unsupervised Transfer Learning via Multi-Scale Convolutional Sparse Coding for Biomedical Applications

PubMed Central

Chang, Hang; Han, Ju; Zhong, Cheng; Snijders, Antoine M.; Mao, Jian-Hua

2017-01-01

The capabilities of (I) learning transferable knowledge across domains; and (II) fine-tuning the pre-learned base knowledge towards tasks with considerably smaller data scale are extremely important. Many of the existing transfer learning techniques are supervised approaches, among which deep learning has the demonstrated power of learning domain transferrable knowledge with large scale network trained on massive amounts of labeled data. However, in many biomedical tasks, both the data and the corresponding label can be very limited, where the unsupervised transfer learning capability is urgently needed. In this paper, we proposed a novel multi-scale convolutional sparse coding (MSCSC) method, that (I) automatically learns filter banks at different scales in a joint fashion with enforced scale-specificity of learned patterns; and (II) provides an unsupervised solution for learning transferable base knowledge and fine-tuning it towards target tasks. Extensive experimental evaluation of MSCSC demonstrates the effectiveness of the proposed MSCSC in both regular and transfer learning tasks in various biomedical domains. PMID:28129148

Three-dimensional Navier-Stokes analysis of turbine passage heat transfer

NASA Technical Reports Server (NTRS)

Ameri, Ali A.; Arnone, Andrea

1991-01-01

The three-dimensional Reynolds-averaged Navier-Stokes equations are numerically solved to obtain the pressure distribution and heat transfer rates on the endwalls and the blades of two linear turbine cascades. The TRAF3D code which has recently been developed in a joint project between researchers from the University of Florence and NASA Lewis Research Center is used. The effect of turbulence is taken into account by using the eddy viscosity hypothesis and the two-layer mixing length model of Baldwin and Lomax. Predictions of surface heat transfer are made for Langston's cascade and compared with the data obtained for that cascade by Graziani. The comparison was found to be favorable. The code is also applied to a linear transonic rotor cascade to predict the pressure distributions and heat transfer rates.

FluorWPS: A Monte Carlo ray-tracing model to compute sun-induced chlorophyll fluorescence of three-dimensional canopy

USDA-ARS?s Scientific Manuscript database

A model to simulate radiative transfer (RT) of sun-induced chlorophyll fluorescence (SIF) of three-dimensional (3-D) canopy, FluorWPS, was proposed and evaluated. The inclusion of fluorescence excitation was implemented with the ‘weight reduction’ and ‘photon spread’ concepts based on Monte Carlo ra...

Preliminary Assessment of Turbomachinery Codes

NASA Technical Reports Server (NTRS)

Mazumder, Quamrul H.

2007-01-01

This report assesses different CFD codes developed and currently being used at Glenn Research Center to predict turbomachinery fluid flow and heat transfer behavior. This report will consider the following codes: APNASA, TURBO, GlennHT, H3D, and SWIFT. Each code will be described separately in the following section with their current modeling capabilities, level of validation, pre/post processing, and future development and validation requirements. This report addresses only previously published and validations of the codes. However, the codes have been further developed to extend the capabilities of the codes.

TH-E-BRF-03: A Multivariate Interaction Model for Assessment of Hippocampal Vascular Dose-Response and Early Prediction of Radiation-Induced Neurocognitive Dysfunction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farjam, R; Pramanik, P; Srinivasan, A

Purpose: Vascular injury could be a cause of hippocampal dysfunction leading to late neurocognitive decline in patients receiving brain radiotherapy (RT). Hence, our aim was to develop a multivariate interaction model for characterization of hippocampal vascular dose-response and early prediction of radiation-induced late neurocognitive impairments. Methods: 27 patients (17 males and 10 females, age 31–80 years) were enrolled in an IRB-approved prospective longitudinal study. All patients were diagnosed with a low-grade glioma or benign tumor and treated by 3-D conformal or intensity-modulated RT with a median dose of 54 Gy (50.4–59.4 Gy in 1.8− Gy fractions). Six DCE-MRI scans weremore » performed from pre-RT to 18 months post-RT. DCE data were fitted to the modified Toft model to obtain the transfer constant of gadolinium influx from the intravascular space into the extravascular extracellular space, Ktrans, and the fraction of blood plasma volume, Vp. The hippocampus vascular property alterations after starting RT were characterized by changes in the hippocampal mean values of, μh(Ktrans)τ and μh(Vp)τ. The dose-response, Δμh(Ktrans/Vp)pre->τ, was modeled using a multivariate linear regression considering integrations of doses with age, sex, hippocampal laterality and presence of tumor/edema near a hippocampus. Finally, the early vascular dose-response in hippocampus was correlated with neurocognitive decline 6 and 18 months post-RT. Results: The μh(Ktrans) increased significantly from pre-RT to 1 month post-RT (p<0.0004). The multivariate model showed that the dose effect on Δμh(Ktrans)pre->1M post-RT was interacted with sex (p<0.0007) and age (p<0.00004), with the dose-response more pronounced in older females. Also, the vascular dose-response in the left hippocampus of females was significantly correlated with memory function decline at 6 (r = − 0.95, p<0.0006) and 18 (r = −0.88, p<0.02) months post-RT. Conclusion: The hippocampal vascular response to radiation could be sex and age dependent. The early hippocampal vascular dose-response could predict late neurocognitive dysfunction. (Support: NIH-RO1NS064973)« less

Survival Outcomes of Whole-Pelvic Versus Prostate-Only Radiation Therapy for High-Risk Prostate Cancer Patients With Use of the National Cancer Data Base

DOE Office of Scientific and Technical Information (OSTI.GOV)

Amini, Arya; Jones, Bernard L.; Yeh, Norman

Purpose/Objectives: The addition of whole pelvic (WP) compared with prostate-only (PO) radiation therapy (RT) for clinically node-negative prostate cancer remains controversial. The purpose of our study was to evaluate the survival benefit of adding WPRT versus PO-RT for high-risk, node-negative prostate cancer, using the National Cancer Data Base (NCDB). Methods and Materials: Patients with high-risk prostate cancer treated from 2004 to 2006, with available data for RT volume, coded as prostate and pelvis (WPRT) or prostate alone (PO-RT) were included. Multivariate analysis (MVA) and propensity-score matched analysis (PSM) were performed. Recursive partitioning analysis (RPA) based on overall survival (OS) usingmore » Gleason score (GS), T stage, and pretreatment prostate-specific antigen (PSA) was also conducted. Results: A total of 14,817 patients were included: 7606 (51.3%) received WPRT, and 7211 (48.7%) received PO-RT. The median follow-up time was 81 months (range, 2-122 months). Under MVA, the addition of WPRT for high-risk patients had no OS benefit compared with PO-RT (HR 1.05; P=.100). On subset analysis, patients receiving dose-escalated RT also did not benefit from WPRT (HR 1.01; P=.908). PSM confirmed no survival benefit with the addition of WPRT for high-risk patients (HR 1.05; P=.141). In addition, RPA was unable to demonstrate a survival benefit of WPRT for any subset. Other prognostic factors for inferior OS under MVA included older age (HR 1.25; P<.001), increasing comorbidity scores (HR 1.46; P<.001), higher T stage (HR 1.17; P<.001), PSA (HR 1.81; P<.001), and GS (HR 1.29; P<.001), and decreasing median county household income (HR 1.15; P=.011). Factors improving OS included the addition of androgen deprivation therapy (HR 0.92; P=.033), combination external beam RT plus brachytherapy boost (HR 0.71; P<.001), and treatment at an academic/research institution (HR 0.84; P=.002). Conclusion: In the largest reported analysis of WPRT for patients with high-risk prostate cancer treated in the dose-escalated era, the addition of WPRT demonstrated no survival advantage compared with PO-RT.« less

Boundary layer simulator improvement

NASA Technical Reports Server (NTRS)

Praharaj, S. C.; Schmitz, C.; Frost, C.; Engel, C. D.; Fuller, C. E.; Bender, R. L.; Pond, J.

1984-01-01

High chamber pressure expander cycles proposed for orbit transfer vehicles depend primarily on the heat energy transmitted from the combustion products through the thrust wall chamber wall. The heat transfer to the nozzle wall is affected by such variables as wall roughness, relamarization, and the presence of particles in the flow. Motor performance loss for these nozzles with thick boundary layers is inaccurate using the existing procedure coded BLIMPJ. Modifications and innovations to the code are examined. Updated routines are listed.

Two-Way Satellite Time and Frequency Transfer Using 1 MChips/s Codes

DTIC Science & Technology

2009-11-01

Abstract The Ku-band transatlantic and Europe-to-Europe two-way satellite time and frequency transfer ( TWSTFT ) operations used 2.5 MChip/s...pseudo-random codes with 3.5 MHz bandwidth until the end of July 2009. The cost of TWSTFT operation is associated with the bandwidth used on a...geostationary satellite. The transatlantic and Europe-to-Europe TWSTFT operations faced a significant increase in cost for using 3.5 MHz bandwidth on a new

Forward Monte Carlo Computations of Polarized Microwave Radiation

NASA Technical Reports Server (NTRS)

Battaglia, A.; Kummerow, C.

2000-01-01

Microwave radiative transfer computations continue to acquire greater importance as the emphasis in remote sensing shifts towards the understanding of microphysical properties of clouds and with these to better understand the non linear relation between rainfall rates and satellite-observed radiance. A first step toward realistic radiative simulations has been the introduction of techniques capable of treating 3-dimensional geometry being generated by ever more sophisticated cloud resolving models. To date, a series of numerical codes have been developed to treat spherical and randomly oriented axisymmetric particles. Backward and backward-forward Monte Carlo methods are, indeed, efficient in this field. These methods, however, cannot deal properly with oriented particles, which seem to play an important role in polarization signatures over stratiform precipitation. Moreover, beyond the polarization channel, the next generation of fully polarimetric radiometers challenges us to better understand the behavior of the last two Stokes parameters as well. In order to solve the vector radiative transfer equation, one-dimensional numerical models have been developed, These codes, unfortunately, consider the atmosphere as horizontally homogeneous with horizontally infinite plane parallel layers. The next development step for microwave radiative transfer codes must be fully polarized 3-D methods. Recently a 3-D polarized radiative transfer model based on the discrete ordinate method was presented. A forward MC code was developed that treats oriented nonspherical hydrometeors, but only for plane-parallel situations.

Numerical Investigation of Radiative Heat Transfer in Laser Induced Air Plasmas

NASA Technical Reports Server (NTRS)

Liu, J.; Chen, Y. S.; Wang, T. S.; Turner, James E. (Technical Monitor)

2001-01-01

Radiative heat transfer is one of the most important phenomena in the laser induced plasmas. This study is intended to develop accurate and efficient methods for predicting laser radiation absorption and plasma radiative heat transfer, and investigate the plasma radiation effects in laser propelled vehicles. To model laser radiation absorption, a ray tracing method along with the Beer's law is adopted. To solve the radiative transfer equation in the air plasmas, the discrete transfer method (DTM) is selected and explained. The air plasma radiative properties are predicted by the LORAN code. To validate the present nonequilibrium radiation model, several benchmark problems are examined and the present results are found to match the available solutions. To investigate the effects of plasma radiation in laser propelled vehicles, the present radiation code is coupled into a plasma aerodynamics code and a selected problem is considered. Comparisons of results at different cases show that plasma radiation plays a role of cooling plasma and it lowers the plasma temperature by about 10%. This change in temperature also results in a reduction of the coupling coefficient by about 10-20%. The present study indicates that plasma radiation modeling is very important for accurate modeling of aerodynamics in a laser propelled vehicle.

In vivo dosimetry in UK external beam radiotherapy: current and future usage.

PubMed

MacDougall, Niall D; Graveling, Michael; Hansen, Vibeke N; Brownsword, Kevin; Morgan, Andrew

2017-04-01

Towards Safer Radiotherapy recommended that radiotherapy (RT) centres should have protocols in place for in vivo dosimetry (IVD) monitoring at the beginning of patient treatment courses (Donaldson S. Towards safer radiotherapy. R Coll Radiol 2008). This report determines IVD implementation in the UK in 2014, the methods used and makes recommendations on future use. Evidence from peer-reviewed journals was used in conjunction with the first survey of UK RT centre IVD practice since the publication of Towards Safer Radiotherapy. In March 2014, profession-specific questionnaires were sent to radiographer, clinical oncologist and physics staff groups in each of the 66 UK RT centres. Response rates from each group were 74%, 45% and 74%, respectively. 73% of RT centres indicated that they performed IVD. Diodes are the most popular IVD device. Thermoluminescent dosimeter (TLD) is still in use in a number of centres but not as a sole modality, being used in conjunction with diodes and/or electronic portal imaging device (EPID). The use of EPID dosimetry is increasing and is considered of most potential value for both geometric and dosimetric verification. Owing to technological advances, such as electronic data transfer, independent monitor unit checking and daily image-guided radiotherapy, the overall risk of adverse treatment events in RT has been substantially reduced. However, the use of IVD may prevent a serious radiation incident. Point dose IVD is not considered suited to the requirements of verifying advanced RT techniques, leaving EPID dosimetry as the current modality likely to be developed as a future standard. Advances in knowledge: An updated perspective on UK IVD use and provision of professional guidelines for future implementation.

In vivo dosimetry in UK external beam radiotherapy: current and future usage

PubMed Central

Graveling, Michael; Hansen, Vibeke N; Brownsword, Kevin; Morgan, Andrew

2017-01-01

Objective: Towards Safer Radiotherapy recommended that radiotherapy (RT) centres should have protocols in place for in vivo dosimetry (IVD) monitoring at the beginning of patient treatment courses (Donaldson S. Towards safer radiotherapy. R Coll Radiol 2008). This report determines IVD implementation in the UK in 2014, the methods used and makes recommendations on future use. Methods: Evidence from peer-reviewed journals was used in conjunction with the first survey of UK RT centre IVD practice since the publication of Towards Safer Radiotherapy. In March 2014, profession-specific questionnaires were sent to radiographer, clinical oncologist and physics staff groups in each of the 66 UK RT centres. Results: Response rates from each group were 74%, 45% and 74%, respectively. 73% of RT centres indicated that they performed IVD. Diodes are the most popular IVD device. Thermoluminescent dosimeter (TLD) is still in use in a number of centres but not as a sole modality, being used in conjunction with diodes and/or electronic portal imaging device (EPID). The use of EPID dosimetry is increasing and is considered of most potential value for both geometric and dosimetric verification. Conclusion: Owing to technological advances, such as electronic data transfer, independent monitor unit checking and daily image-guided radiotherapy, the overall risk of adverse treatment events in RT has been substantially reduced. However, the use of IVD may prevent a serious radiation incident. Point dose IVD is not considered suited to the requirements of verifying advanced RT techniques, leaving EPID dosimetry as the current modality likely to be developed as a future standard. Advances in knowledge: An updated perspective on UK IVD use and provision of professional guidelines for future implementation. PMID:28205452

Number of blastocysts biopsied as a predictive indicator to obtain at least one normal/balanced embryo following preimplantation genetic diagnosis with single nucleotide polymorphism microarray in translocation cases.

PubMed

Wang, Yi-Zi; Ding, Chen-Hui; Wang, Jing; Zeng, Yan-Hong; Zhou, Wen; Li, Rong; Zhou, Can-Quan; Deng, Ming-Fen; Xu, Yan-Wen

2017-01-01

The aim of this study is to investigate the minimum number of blastocysts for biopsy to increase the likelihood of obtaining at least one normal/balanced embryo in preimplantation genetic diagnosis (PGD) for translocation carriers. This blinded retrospective study included 55 PGD cycles for Robertsonian translocation (RT) and 181 cycles for reciprocal translocation (rcp) to indicate when only one of the couples carried a translocation. Single-nucleotide polymorphism microarray after trophectoderm biopsy was performed. Reliable results were obtained for 355/379 (93.7 %) biopsied blastocysts in RT group and 986/1053 (93.6 %) in rcp group. Mean numbers of biopsied embryos per patient, normal/balanced embryos per patient, and mean normal/balanced embryo rate per patient were 7.4, 3.1, and 40.7 % in RT group and 8.0, 2.1, and 27.3 %, respectively, in rcp group. In a regression model, three factors significantly affected the number of genetically transferrable embryos: number of biopsied embryos (P = 0.001), basal FSH level (P = 0.040), and maternal age (P = 0.027). ROC analysis with a cutoff of 1.5 was calculated for the number of biopsied embryos required to obtain at least one normal/balanced embryo for RT carriers. For rcp carriers, the cutoff was 3.5. The clinical pregnancy rate per embryo transfer was 44.2 and 42.6 % in RT and rcp groups (P = 0.836). The minimum numbers of blastocysts to obtain at least one normal/balanced embryo for RT and rcp were 2 and 4 under the conditions of female age < 37 years with a basal FSH level < 11.4 IU/L.

mRNA trans-splicing in gene therapy for genetic diseases.

PubMed

Berger, Adeline; Maire, Séverine; Gaillard, Marie-Claude; Sahel, José-Alain; Hantraye, Philippe; Bemelmans, Alexis-Pierre

2016-07-01

Spliceosome-mediated RNA trans-splicing, or SMaRT, is a promising strategy to design innovative gene therapy solutions for currently intractable genetic diseases. SMaRT relies on the correction of mutations at the post-transcriptional level by modifying the mRNA sequence. To achieve this, an exogenous RNA is introduced into the target cell, usually by means of gene transfer, to induce a splice event in trans between the exogenous RNA and the target endogenous pre-mRNA. This produces a chimeric mRNA composed partly of exons of the latter, and partly of exons of the former, encoding a sequence free of mutations. The principal challenge of SMaRT technology is to achieve a reaction as complete as possible, i.e., resulting in 100% repairing of the endogenous mRNA target. The proof of concept of SMaRT feasibility has already been established in several models of genetic diseases caused by recessive mutations. In such cases, in fact, the repair of only a portion of the mutant mRNA pool may be sufficient to obtain a significant therapeutic effect. However in the case of dominant mutations, the target cell must be freed from the majority of mutant mRNA copies, requiring a highly efficient trans-splicing reaction. This likely explains why only a few examples of SMaRT approaches targeting dominant mutations are reported in the literature. In this review, we explain in details the mechanism of trans-splicing, review the different strategies that are under evaluation to lead to efficient trans-splicing, and discuss the advantages and limitations of SMaRT. WIREs RNA 2016, 7:487-498. doi: 10.1002/wrna.1347 For further resources related to this article, please visit the WIREs website. © 2016 The Authors. WIREs RNA published by Wiley Periodicals, Inc.

A Validation Study of the Compressible Rayleigh–Taylor Instability Comparing the Ares and Miranda Codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rehagen, Thomas J.; Greenough, Jeffrey A.; Olson, Britton J.

In this paper, the compressible Rayleigh–Taylor (RT) instability is studied by performing a suite of large eddy simulations (LES) using the Miranda and Ares codes. A grid convergence study is carried out for each of these computational methods, and the convergence properties of integral mixing diagnostics and late-time spectra are established. A comparison between the methods is made using the data from the highest resolution simulations in order to validate the Ares hydro scheme. We find that the integral mixing measures, which capture the global properties of the RT instability, show good agreement between the two codes at this resolution.more » The late-time turbulent kinetic energy and mass fraction spectra roughly follow a Kolmogorov spectrum, and drop off as k approaches the Nyquist wave number of each simulation. The spectra from the highest resolution Miranda simulation follow a Kolmogorov spectrum for longer than the corresponding spectra from the Ares simulation, and have a more abrupt drop off at high wave numbers. The growth rate is determined to be between around 0.03 and 0.05 at late times; however, it has not fully converged by the end of the simulation. Finally, we study the transition from direct numerical simulation (DNS) to LES. The highest resolution simulations become LES at around t/τ ≃ 1.5. Finally, to have a fully resolved DNS through the end of our simulations, the grid spacing must be 3.6 (3.1) times finer than our highest resolution mesh when using Miranda (Ares).« less

A Validation Study of the Compressible Rayleigh–Taylor Instability Comparing the Ares and Miranda Codes

DOE PAGES

Rehagen, Thomas J.; Greenough, Jeffrey A.; Olson, Britton J.

2017-04-20

In this paper, the compressible Rayleigh–Taylor (RT) instability is studied by performing a suite of large eddy simulations (LES) using the Miranda and Ares codes. A grid convergence study is carried out for each of these computational methods, and the convergence properties of integral mixing diagnostics and late-time spectra are established. A comparison between the methods is made using the data from the highest resolution simulations in order to validate the Ares hydro scheme. We find that the integral mixing measures, which capture the global properties of the RT instability, show good agreement between the two codes at this resolution.more » The late-time turbulent kinetic energy and mass fraction spectra roughly follow a Kolmogorov spectrum, and drop off as k approaches the Nyquist wave number of each simulation. The spectra from the highest resolution Miranda simulation follow a Kolmogorov spectrum for longer than the corresponding spectra from the Ares simulation, and have a more abrupt drop off at high wave numbers. The growth rate is determined to be between around 0.03 and 0.05 at late times; however, it has not fully converged by the end of the simulation. Finally, we study the transition from direct numerical simulation (DNS) to LES. The highest resolution simulations become LES at around t/τ ≃ 1.5. Finally, to have a fully resolved DNS through the end of our simulations, the grid spacing must be 3.6 (3.1) times finer than our highest resolution mesh when using Miranda (Ares).« less

WE-H-207B-00: MRgRT

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

2016-06-15

In recent years, steady progress has been made towards the implementation of MRI in external beam radiation therapy for processes ranging from treatment simulation to in-room guidance. Novel procedures relying mostly on MR data are currently implemented in the clinic. This session will cover topics such as (a) commissioning and quality control of the MR in-room imagers and simulators specific to RT, (b) treatment planning requirements, constraints and challenges when dealing with various MR data, (c) quantification of organ motion with an emphasis on treatment delivery guidance, and (d) MR-driven strategies for adaptive RT workflows. The content of the sessionmore » was chosen to address both educational and practical key aspects of MR guidance. Learning Objectives: Good understanding of MR testing recommended for in-room MR imaging as well as image data validation for RT chain (e.g. image transfer, filtering for consistency, spatial accuracy, manipulation for task specific); Familiarity with MR-based planning procedures: motivation, core workflow requirements, current status, challenges; Overview of the current methods for the quantification of organ motion; Discussion on approaches for adaptive treatment planning and delivery. T. Stanescu - License agreement with Modus Medical Devices to develop a phantom for the quantification of MR image system-related distortions.; T. Stanescu, N/A.« less

WE-H-207B-04: Strategies for Adaptive RT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Green, O.

2016-06-15

In recent years, steady progress has been made towards the implementation of MRI in external beam radiation therapy for processes ranging from treatment simulation to in-room guidance. Novel procedures relying mostly on MR data are currently implemented in the clinic. This session will cover topics such as (a) commissioning and quality control of the MR in-room imagers and simulators specific to RT, (b) treatment planning requirements, constraints and challenges when dealing with various MR data, (c) quantification of organ motion with an emphasis on treatment delivery guidance, and (d) MR-driven strategies for adaptive RT workflows. The content of the sessionmore » was chosen to address both educational and practical key aspects of MR guidance. Learning Objectives: Good understanding of MR testing recommended for in-room MR imaging as well as image data validation for RT chain (e.g. image transfer, filtering for consistency, spatial accuracy, manipulation for task specific); Familiarity with MR-based planning procedures: motivation, core workflow requirements, current status, challenges; Overview of the current methods for the quantification of organ motion; Discussion on approaches for adaptive treatment planning and delivery. T. Stanescu - License agreement with Modus Medical Devices to develop a phantom for the quantification of MR image system-related distortions.; T. Stanescu, N/A.« less

Assessment of the prevailing physics codes: LEOPARD, LASER, and EPRI-CELL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lan, J.S.

1981-01-01

In order to analyze core performance and fuel management, it is necessary to verify reactor physics codes in great detail. This kind of work not only serves the purpose of understanding and controlling the characteristics of each code, but also ensures the reliability as codes continually change due to constant modifications and machine transfers. This paper will present the results of a comprehensive verification of three code packages - LEOPARD, LASER, and EPRI-CELL.

Simultaneous multislice diffusion-weighted MRI of the liver: Analysis of different breathing schemes in comparison to standard sequences.

PubMed

Taron, Jana; Martirosian, Petros; Erb, Michael; Kuestner, Thomas; Schwenzer, Nina F; Schmidt, Holger; Honndorf, Valerie S; Weiβ, Jakob; Notohamiprodjo, Mike; Nikolaou, Konstantin; Schraml, Christina

2016-10-01

To systematically evaluate image characteristics of simultaneous-multislice (SMS)-accelerated diffusion-weighted imaging (DWI) of the liver using different breathing schemes in comparison to standard sequences. DWI of the liver was performed in 10 healthy volunteers and 12 patients at 1.5T using an SMS-accelerated echo planar imaging sequence performed with respiratory-triggering and free breathing (SMS-RT, SMS-FB). Standard DWI sequences served as reference (STD-RT, STD-FB). Reduction of scan time by SMS-acceleration was measured. Image characteristics of SMS-DWI and STD-DWI with both breathing schemes were analyzed quantitatively (apparent diffusion coefficient [ADC], signal-to-noise ratio [SNR]) and qualitatively (5-point Likert scale, 5 = excellent). Qualitative and quantitative parameters were compared using Friedman test and Dunn-Bonferroni post-hoc method with P-values < 0.05 considered statistically significant. SMS-DWI provided diagnostic image quality in volunteers and patients both with RT and FB with a reduction of scan time of 70% (0:56 vs. 3:20 min in FB). Overall image quality did not significantly differ between FB and RT acquisition in both STD and SMS sequences (median STD-RT 5.0, STD-FB 4.5, SMS-RT: 4.75; SMS-FB: 4.5; P = 0.294). SNR in the right hepatic lobe was comparable between the four tested sequences. ADC values were significantly lower in SMS-DWI compared to STD-DWI irrespective of the breathing scheme (1.2 ± 0.2 × 10(-3) mm(2) /s vs. 1.0 ± 0.2 × 10(-3) mm(2) /s; P < 0.001). SMS-acceleration provides considerable scan time reduction for hepatic DWI with equivalent image quality compared to the STD technique both using RT and FB. Discrepancies in ADC between STD-DWI and SMS-DWI need to be considered when transferring the SMS technique to clinical routine reading. J. MAGN. RESON. IMAGING 2016;44:865-879. © 2016 International Society for Magnetic Resonance in Medicine.

Coding as a Trojan Horse for Mathematics Education Reform

ERIC Educational Resources Information Center

Gadanidis, George

2015-01-01

The history of mathematics educational reform is replete with innovations taken up enthusiastically by early adopters without significant transfer to other classrooms. This paper explores the coupling of coding and mathematics education to create the possibility that coding may serve as a Trojan Horse for mathematics education reform. That is,…

Validation of a vector version of the 6S radiative transfer code for atmospheric correction of satellite data. Part I: Path radiance

NASA Astrophysics Data System (ADS)

Kotchenova, Svetlana Y.; Vermote, Eric F.; Matarrese, Raffaella; Klemm, Frank J., Jr.

2006-09-01

A vector version of the 6S (Second Simulation of a Satellite Signal in the Solar Spectrum) radiative transfer code (6SV1), which enables accounting for radiation polarization, has been developed and validated against a Monte Carlo code, Coulson's tabulated values, and MOBY (Marine Optical Buoy System) water-leaving reflectance measurements. The developed code was also tested against the scalar codes SHARM, DISORT, and MODTRAN to evaluate its performance in scalar mode and the influence of polarization. The obtained results have shown a good agreement of 0.7% in comparison with the Monte Carlo code, 0.2% for Coulson's tabulated values, and 0.001-0.002 for the 400-550 nm region for the MOBY reflectances. Ignoring the effects of polarization led to large errors in calculated top-of-atmosphere reflectances: more than 10% for a molecular atmosphere and up to 5% for an aerosol atmosphere. This new version of 6S is intended to replace the previous scalar version used for calculation of lookup tables in the MODIS (Moderate Resolution Imaging Spectroradiometer) atmospheric correction algorithm.

Validation of a vector version of the 6S radiative transfer code for atmospheric correction of satellite data. Part I: path radiance.

PubMed

Kotchenova, Svetlana Y; Vermote, Eric F; Matarrese, Raffaella; Klemm, Frank J

2006-09-10

A vector version of the 6S (Second Simulation of a Satellite Signal in the Solar Spectrum) radiative transfer code (6SV1), which enables accounting for radiation polarization, has been developed and validated against a Monte Carlo code, Coulson's tabulated values, and MOBY (Marine Optical Buoy System) water-leaving reflectance measurements. The developed code was also tested against the scalar codes SHARM, DISORT, and MODTRAN to evaluate its performance in scalar mode and the influence of polarization. The obtained results have shown a good agreement of 0.7% in comparison with the Monte Carlo code, 0.2% for Coulson's tabulated values, and 0.001-0.002 for the 400-550 nm region for the MOBY reflectances. Ignoring the effects of polarization led to large errors in calculated top-of-atmosphere reflectances: more than 10% for a molecular atmosphere and up to 5% for an aerosol atmosphere. This new version of 6S is intended to replace the previous scalar version used for calculation of lookup tables in the MODIS (Moderate Resolution Imaging Spectroradiometer) atmospheric correction algorithm.

Murt user`s guide: A hybrid Lagrangian-Eulerian finite element model of multiple-pore-region solute transport through subsurface media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gwo, J.P.; Jardine, P.M.; Yeh, G.T.

Matrix diffusion, a diffusive mass transfer process,in the structured soils and geologic units at ORNL, is believe to be an important subsurface mass transfer mechanism; it may affect off-site movement of radioactive wastes and remediation of waste disposal sites by locally exchanging wastes between soil/rock matrix and macropores/fractures. Advective mass transfer also contributes to waste movement but is largely neglected by researchers. This report presents the first documented 2-D multiregion solute transport code (MURT) that incorporates not only diffusive but also advective mass transfer and can be applied to heterogeneous porous media under transient flow conditions. In this report, theoreticalmore » background is reviewed and the derivation of multiregion solute transport equations is presented. Similar to MURF (Gwo et al. 1994), a multiregion subsurface flow code, multiplepore domains as suggested by previous investigators (eg, Wilson and Luxmoore 1988) can be implemented in MURT. Transient or steady-state flow fields of the pore domains can be either calculated by MURF or by modelers. The mass transfer process is briefly discussed through a three-pore-region multiregion solute transport mechanism. Mass transfer equations that describe mass flux across pore region interfaces are also presented and parameters needed to calculate mass transfer coefficients detailed. Three applications of MURT (tracer injection problem, sensitivity analysis of advective and diffusive mass transfer, hillslope ponding infiltration and secondary source problem) were simulated and results discussed. Program structure of MURT and functions of MURT subroutiness are discussed so that users can adapt the code; guides for input data preparation are provided in appendices.« less

Efficiency transfer using the GEANT4 code of CERN for HPGe gamma spectrometry.

PubMed

Chagren, S; Tekaya, M Ben; Reguigui, N; Gharbi, F

2016-01-01

In this work we apply the GEANT4 code of CERN to calculate the peak efficiency in High Pure Germanium (HPGe) gamma spectrometry using three different procedures. The first is a direct calculation. The second corresponds to the usual case of efficiency transfer between two different configurations at constant emission energy assuming a reference point detection configuration and the third, a new procedure, consists on the transfer of the peak efficiency between two detection configurations emitting the gamma ray in different energies assuming a "virtual" reference point detection configuration. No pre-optimization of the detector geometrical characteristics was performed before the transfer to test the ability of the efficiency transfer to reduce the effect of the ignorance on their real magnitude on the quality of the transferred efficiency. The obtained and measured efficiencies were found in good agreement for the two investigated methods of efficiency transfer. The obtained agreement proves that Monte Carlo method and especially the GEANT4 code constitute an efficient tool to obtain accurate detection efficiency values. The second investigated efficiency transfer procedure is useful to calibrate the HPGe gamma detector for any emission energy value for a voluminous source using one point source detection efficiency emitting in a different energy as a reference efficiency. The calculations preformed in this work were applied to the measurement exercise of the EUROMET428 project. A measurement exercise where an evaluation of the full energy peak efficiencies in the energy range 60-2000 keV for a typical coaxial p-type HpGe detector and several types of source configuration: point sources located at various distances from the detector and a cylindrical box containing three matrices was performed. Copyright © 2015 Elsevier Ltd. All rights reserved.

Ultrasonic Imaging and Automated Flaw Detection System

DTIC Science & Technology

1986-03-01

176 007 !----------------------------- DS 176 500 ------------------------- ! STEPPER MOOC TOR MAP 176 ~ ~ IGR 509------------------- I I28 * 4W...ATTN: SMCAR-CCB-R 2 -R (ELLEN FOGARTY) 1 -RA 1 -RM 1 -RP I -RT TECHNICAL LIBRARY 5 ATTN: SMCAR-CCB-TL TECHNICAL PUBLICATIONS & EDITING UNIT 2 ATTN...WEAPONS CTR ATTN: TECHNICAL LIBRARY CODE X212 DAIILGREN, VA 22448 ’.1 -_ NOTE: PLEASE NOTIFY COMMANDER, ARMAMENT RESEARCH AND DEVELOPMENT CENTER, US

Validation of the SINDA/FLUINT code using several analytical solutions

NASA Technical Reports Server (NTRS)

Keller, John R.

1995-01-01

The Systems Improved Numerical Differencing Analyzer and Fluid Integrator (SINDA/FLUINT) code has often been used to determine the transient and steady-state response of various thermal and fluid flow networks. While this code is an often used design and analysis tool, the validation of this program has been limited to a few simple studies. For the current study, the SINDA/FLUINT code was compared to four different analytical solutions. The thermal analyzer portion of the code (conduction and radiative heat transfer, SINDA portion) was first compared to two separate solutions. The first comparison examined a semi-infinite slab with a periodic surface temperature boundary condition. Next, a small, uniform temperature object (lumped capacitance) was allowed to radiate to a fixed temperature sink. The fluid portion of the code (FLUINT) was also compared to two different analytical solutions. The first study examined a tank filling process by an ideal gas in which there is both control volume work and heat transfer. The final comparison considered the flow in a pipe joining two infinite reservoirs of pressure. The results of all these studies showed that for the situations examined here, the SINDA/FLUINT code was able to match the results of the analytical solutions.

Validation of a vector version of the 6S radiative transfer code for atmospheric correction of satellite data. Part II. Homogeneous Lambertian and anisotropic surfaces.

PubMed

Kotchenova, Svetlana Y; Vermote, Eric F

2007-07-10

This is the second part of the validation effort of the recently developed vector version of the 6S (Second Simulation of a Satellite Signal in the Solar Spectrum) radiative transfer code (6SV1), primarily used for the calculation of look-up tables in the Moderate Resolution Imaging Spectroradiometer (MODIS) atmospheric correction algorithm. The 6SV1 code was tested against a Monte Carlo code and Coulson's tabulated values for molecular and aerosol atmospheres bounded by different Lambertian and anisotropic surfaces. The code was also tested in scalar mode against the scalar code SHARM to resolve the previous 6S accuracy issues in the case of an anisotropic surface. All test cases were characterized by good agreement between the 6SV1 and the other codes: The overall relative error did not exceed 0.8%. The study also showed that ignoring the effects of radiation polarization in the atmosphere led to large errors in the simulated top-of-atmosphere reflectances: The maximum observed error was approximately 7.2% for both Lambertian and anisotropic surfaces.

Validation of a vector version of the 6S radiative transfer code for atmospheric correction of satellite data. Part II. Homogeneous Lambertian and anisotropic surfaces

NASA Astrophysics Data System (ADS)

Kotchenova, Svetlana Y.; Vermote, Eric F.

2007-07-01

This is the second part of the validation effort of the recently developed vector version of the 6S (Second Simulation of a Satellite Signal in the Solar Spectrum) radiative transfer code (6SV1), primarily used for the calculation of look-up tables in the Moderate Resolution Imaging Spectroradiometer (MODIS) atmospheric correction algorithm. The 6SV1 code was tested against a Monte Carlo code and Coulson's tabulated values for molecular and aerosol atmospheres bounded by different Lambertian and anisotropic surfaces. The code was also tested in scalar mode against the scalar code SHARM to resolve the previous 6S accuracy issues in the case of an anisotropic surface. All test cases were characterized by good agreement between the 6SV1 and the other codes: The overall relative error did not exceed 0.8%. The study also showed that ignoring the effects of radiation polarization in the atmosphere led to large errors in the simulated top-of-atmosphere reflectances: The maximum observed error was approximately 7.2% for both Lambertian and anisotropic surfaces.

DOE Office of Scientific and Technical Information (OSTI.GOV)

BRISC is a developmental prototype for a nextgeneration “systems-level” integrated performance and safety code (IPSC) for nuclear reactors. Its development served to demonstrate how a lightweight multi-physics coupling approach can be used to tightly couple the physics models in several different physics codes (written in a variety of languages) into one integrated package for simulating accident scenarios in a liquid sodium cooled “burner” nuclear reactor. For example, the RIO Fluid Flow and Heat transfer code developed at Sandia (SNL: Chris Moen, Dept. 08005) is used in BRISC to model fluid flow and heat transfer, as well as conduction heat transfermore » in solids. Because BRISC is a prototype, its most practical application is as a foundation or starting point for developing a true production code. The sub-codes and the associated models and correlations currently employed within BRISC were chosen to cover the required application space and demonstrate feasibility, but were not optimized or validated against experimental data within the context of their use in BRISC.« less

NESSY: NLTE spectral synthesis code for solar and stellar atmospheres

NASA Astrophysics Data System (ADS)

Tagirov, R. V.; Shapiro, A. I.; Schmutz, W.

2017-07-01

Context. Physics-based models of solar and stellar magnetically-driven variability are based on the calculation of synthetic spectra for various surface magnetic features as well as quiet regions, which are a function of their position on the solar or stellar disc. Such calculations are performed with radiative transfer codes tailored for modeling broad spectral intervals. Aims: We aim to present the NLTE Spectral SYnthesis code (NESSY), which can be used for modeling of the entire (UV-visible-IR and radio) spectra of solar and stellar magnetic features and quiet regions. Methods: NESSY is a further development of the COde for Solar Irradiance (COSI), in which we have implemented an accelerated Λ-iteration (ALI) scheme for co-moving frame (CMF) line radiation transfer based on a new estimate of the local approximate Λ-operator. Results: We show that the new version of the code performs substantially faster than the previous one and yields a reliable calculation of the entire solar spectrum. This calculation is in a good agreement with the available observations.

TRUST-tPA trial: Telemedicine for remote collaboration with urgentists for stroke-tPA treatment.

PubMed

Mazighi, Mikael; Meseguer, Elena; Labreuche, Julien; Miroux, Patrick; Le Gall, Catherine; Roy, Patricia; Tubach, Florence; Amarenco, Pierre

2017-01-01

Background Previous observational studies have shown that telemedicine is feasible and safe to deliver intravenous (IV) recombinant tissue plasminogen activator (rt-PA). However, implementation of telemedicine may be challenging. To illustrate this fact, we report a study showing that telemedicine failed to improve clinical outcome and analyze the reasons for this shortcoming. Methods We established a tele-stroke network of 10 emergency rooms (ERs) of community hospitals connected to a stroke center to perform a randomized, open-label clinical trial with blinded outcome evaluation. Eligible patients were randomly assigned to either a usual care arm (i.e. immediate transfer to the stroke center and administration of IV rt-PA if indication was confirmed upon stroke arrival) or tele-thrombolysis arm (i.e. immediate administration of IV rt-PA in ER and transfer to the stroke center). The primary efficacy outcome was an excellent outcome (modified Rankin scale (mRS) 0-1 at 90 days). Secondary endpoints included favorable outcome (90-day mRS 0-2) and early neurological improvement (NIHSS score 0-1 at 24 hours or a decrease of ≥ 4 points within 24 hours). Safety outcomes included symptomatic intracerebral hemorrhage (ICH) per ECASS II definition, any ICH and all-cause mortality. Results During an accrual time of 48 months, because of a slow enrollment rate, only 49 of 270 patients initially planned for inclusion were randomized into usual care ( n = 23) and tele-thrombolysis ( n = 26). Despite random assignment, patients allocated to tele-thrombolysis were older and had more severe stroke than patients allocated to usual care. The median duration of video-conference was 23 minutes in the usual care arm and 73 minutes in the tele-thrombolysis arm. Eighty-four percent of patients in the tele-thrombolysis arm were treated by IV rt-PA in comparison to 18% in the usual care arm. In univariate analysis but not after adjustment for age and baseline NIHSS, patients allocated in the usual care arm had a higher rate of excellent or favorable outcome. There were no differences in safety outcomes, with only one symptomatic ICH occurring in the tele-thrombolysis arm. Conclusions Stroke patients included in the telemedicine arm of the TRUST-tPA trial increased their rt-PA eligibility five-fold. However, the efficacy and safety remains to be determined (ClinicalTrials.org, NCT00279149).

A new transmission methodology for quality assurance in radiotherapy based on radiochromic film measurements

PubMed Central

do Amaral, Leonardo L.; Pavoni, Juliana F.; Sampaio, Francisco; Netto, Thomaz Ghilardi

2015-01-01

Despite individual quality assurance (QA) being recommended for complex techniques in radiotherapy (RT) treatment, the possibility of errors in dose delivery during therapeutic application has been verified. Therefore, it is fundamentally important to conduct in vivo QA during treatment. This work presents an in vivo transmission quality control methodology, using radiochromic film (RCF) coupled to the linear accelerator (linac) accessory holder. This QA methodology compares the dose distribution measured by the film in the linac accessory holder with the dose distribution expected by the treatment planning software. The calculated dose distribution is obtained in the coronal and central plane of a phantom with the same dimensions of the acrylic support used for positioning the film but in a source‐to‐detector distance (SDD) of 100 cm, as a result of transferring the IMRT plan in question with all the fields positioned with the gantry vertically, that is, perpendicular to the phantom. To validate this procedure, first of all a Monte Carlo simulation using PENELOPE code was done to evaluate the differences between the dose distributions measured by the film in a SDD of 56.8 cm and 100 cm. After that, several simple dose distribution tests were evaluated using the proposed methodology, and finally a study using IMRT treatments was done. In the Monte Carlo simulation, the mean percentage of points approved in the gamma function comparing the dose distribution acquired in the two SDDs were 99.92%±0.14%. In the simple dose distribution tests, the mean percentage of points approved in the gamma function were 99.85%±0.26% and the mean percentage differences in the normalization point doses were −1.41%. The transmission methodology was approved in 24 of 25 IMRT test irradiations. Based on these results, it can be concluded that the proposed methodology using RCFs can be applied for in vivo QA in RT treatments. PACS number: 87.55.Qr, 87.55.km, 87.55.N‐ PMID:26699306

Harmful and favourable ultraviolet conditions for human health over Northern Eurasia

NASA Astrophysics Data System (ADS)

Chubarova, Nataly; Zhdanova, Ekaterina

2014-05-01

We provide the analysis of the spatial and temporal distribution of ultraviolet (UV) radiation over Northern Eurasia taking into account for both its detrimental (erythema and eye-damage effects) and favourable (vitamin D synthesis) influence on human health. The UV effects on six different skin types are considered in order to cover the variety of skin types of European and Asian inhabitants. To better quantifying the vitamin D irradiance threshold we accounted for an open body fraction S as a function of effective air temperature. The spatial and temporal distribution of UV resources was estimated by radiative transfer (RT) modeling (8 stream DISORT RT code) with 1x 1 degree grid and monthly resolution. For this purpose special datasets of main input geophysical parameters (total ozone content, aerosol characteristics, surface UV albedo, UV cloud modification factor) have been created over the territory of Northern Eurasia, which can be of separate interest for the different multidisciplinary scientific applications over the PEEX domain. The new approaches were used to retrieve aerosol and cloud transmittance from different satellite and re-analysis datasets for calculating the solar UV irradiance at ground. Using model simulations and some experimental data we provide the altitude parameterization for different types of biologically active irradiance in mountainous area taking into account not only for the effects of molecular scattering but for the altitude dependence of aerosol parameters and surface albedo. Based on the new classification of UV resources (Chubarova, Zhdanova, 2013) we show that the distribution of harmful (UV deficiency and UV excess) and favorable UV conditions is regulated by various geophysical parameters (mainly, total ozone, cloudiness and open body fraction) and can significantly deviate from latitudinal dependence. The interactive tool for providing simulations of biologically active irradiance and its attribution to the different classes of UV resources is demonstrated. Reference: Natalia Chubarova, Yekaterina Zhdanova. Ultraviolet resources over Northern Eurasia, Photochemistry and Photobiology, Elsevier, 127, 2013, p. 38-51

A Radiation Solver for the National Combustion Code

NASA Technical Reports Server (NTRS)

Sockol, Peter M.

2015-01-01

A methodology is given that converts an existing finite volume radiative transfer method that requires input of local absorption coefficients to one that can treat a mixture of combustion gases and compute the coefficients on the fly from the local mixture properties. The Full-spectrum k-distribution method is used to transform the radiative transfer equation (RTE) to an alternate wave number variable, g . The coefficients in the transformed equation are calculated at discrete temperatures and participating species mole fractions that span the values of the problem for each value of g. These results are stored in a table and interpolation is used to find the coefficients at every cell in the field. Finally, the transformed RTE is solved for each g and Gaussian quadrature is used to find the radiant heat flux throughout the field. The present implementation is in an existing cartesian/cylindrical grid radiative transfer code and the local mixture properties are given by a solution of the National Combustion Code (NCC) on the same grid. Based on this work the intention is to apply this method to an existing unstructured grid radiation code which can then be coupled directly to NCC.

Recent horizontal transfer of mellifera subfamily mariner transposons into insect lineages representing four different orders shows that selection acts only during horizontal transfer.

PubMed

Lampe, David J; Witherspoon, David J; Soto-Adames, Felipe N; Robertson, Hugh M

2003-04-01

We report the isolation and sequencing of genomic copies of mariner transposons involved in recent horizontal transfers into the genomes of the European earwig, Forficula auricularia; the European honey bee, Apis mellifera; the Mediterranean fruit fly, Ceratitis capitata; and a blister beetle, Epicauta funebris, insects from four different orders. These elements are in the mellifera subfamily and are the second documented example of full-length mariner elements involved in this kind of phenomenon. We applied maximum likelihood methods to the coding sequences and determined that the copies in each genome were evolving neutrally, whereas reconstructed ancestral coding sequences appeared to be under selection, which strengthens our previous hypothesis that the primary selective constraint on mariner sequence evolution is the act of horizontal transfer between genomes.

On the potential of Galileo E5 for time transfer.

PubMed

Martínez-Belda, Mari Carmen; Defraigne, Pascale; Bruyninx, Carine

2013-01-01

The main global navigation satellite systems (GNSS) technique currently used for accurate time and frequency transfer is based on an analysis of the ionosphere-free combinations of dual-frequency code and carrier phase measurements in a precise point positioning (PPP) mode. This technique analyses the observations of one GNSS station using external products for satellite clocks and orbits to determine the position and clock synchronization errors of this station. The frequency stability of this time transfer is limited by the noise and multipath of the Global Positioning System (GPS) and Globalnaya Navigatsionnaya Sputnikovaya Sistema (GLONASS) codes. In the near future, Galileo will offer a broadband signal E5, with low noise in the centimeter range and with the lowest multipath error ever observed. This paper investigates new analysis procedures based on the E5 codeplus- carrier (CPC) combination for time transfer. The CPC combination with E5 provides a noise level 10 times lower than the ionosphere-free combination of Galileo E1 and E5, which is very promising for improving GNSS time transfer performances. From some tests with simulated Galileo data, it is shown here that the use of the CPC combination with E5 does not improve, at present, the medium- and long-term stability of time transfer with respect to the ionosphere-free combination of Galileo E1 and E5 codes, because of the need for a second frequency signal to correct for the ionospheric delays and ambiguities.

Application of the TEMPEST computer code to canister-filling heat transfer problems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farnsworth, R.K.; Faletti, D.W.; Budden, M.J.

Pacific Northwest Laboratory (PNL) researchers used the TEMPEST computer code to simulate thermal cooldown behavior of nuclear waste glass after it was poured into steel canisters for long-term storage. The objective of this work was to determine the accuracy and applicability of the TEMPEST code when used to compute canister thermal histories. First, experimental data were obtained to provide the basis for comparing TEMPEST-generated predictions. Five canisters were instrumented with appropriately located radial and axial thermocouples. The canister were filled using the pilot-scale ceramic melter (PSCM) at PNL. Each canister was filled in either a continous or a batch fillingmore » mode. One of the canisters was also filled within a turntable simulant (a group of cylindrical shells with heat transfer resistances similar to those in an actual melter turntable). This was necessary to provide a basis for assessing the ability of the TEMPEST code to also model the transient cooling of canisters in a melter turntable. The continous-fill model, Version M, was found to predict temperatures with more accuracy. The turntable simulant experiment demonstrated that TEMPEST can adequately model the asymmetric temperature field caused by the turntable geometry. Further, TEMPEST can acceptably predict the canister cooling history within a turntable, despite code limitations in computing simultaneous radiation and convection heat transfer between shells, along with uncertainty in stainless-steel surface emissivities. Based on the successful performance of TEMPEST Version M, development was initiated to incorporate 1) full viscous glass convection, 2) a dynamically adaptive grid that automatically follows the glass/air interface throughout the transient, and 3) a full enclosure radiation model to allow radiation heat transfer to non-nearest neighbor cells. 5 refs., 47 figs., 17 tabs.« less

Dynamics of pulsed expansion of polyatomic gas cloud: Internal-translational energy transfer contribution

NASA Astrophysics Data System (ADS)

Morozov, A. A.

2007-08-01

Polyatomic gas cloud expansion under pulsed laser evaporation is studied on the basis of one-dimensional direct Monte Carlo simulation. The effect of rotational-translational (RT) and vibrational-translational (VT) energy transfer on dynamics of the cloud expansion is considered. Efficiency of VT energy transfer dependence on the amount of evaporated matter is discussed. To analyze VT energy transfer impact, the number of collisions per molecule during the expansion is calculated. The data are generally in good agreement with available analytical and numerical predictions. Dependencies of the effective number of vibrational degrees of freedom on the number of vibrationally inelastic collisions are obtained and generalized. The importance of the consideration of energy transfer from the internal degrees of freedom to the translational ones is illustrated by an example of pulsed laser evaporation of polytetrafluoroethylene (PTFE). Based on the obtained regularities, analysis of experimental data on pulsed laser evaporation of aniline is performed. The calculated aniline vibrational temperature correlates well with the experimentally measured one.

Analytical Solutions for Radiative Transfer: Implications for Giant Planet Formation by Disk Instability

NASA Astrophysics Data System (ADS)

Boss, Alan P.

2009-03-01

The disk instability mechanism for giant planet formation is based on the formation of clumps in a marginally gravitationally unstable protoplanetary disk, which must lose thermal energy through a combination of convection and radiative cooling if they are to survive and contract to become giant protoplanets. While there is good observational support for forming at least some giant planets by disk instability, the mechanism has become theoretically contentious, with different three-dimensional radiative hydrodynamics codes often yielding different results. Rigorous code testing is required to make further progress. Here we present two new analytical solutions for radiative transfer in spherical coordinates, suitable for testing the code employed in all of the Boss disk instability calculations. The testing shows that the Boss code radiative transfer routines do an excellent job of relaxing to and maintaining the analytical results for the radial temperature and radiative flux profiles for a spherical cloud with high or moderate optical depths, including the transition from optically thick to optically thin regions. These radial test results are independent of whether the Eddington approximation, diffusion approximation, or flux-limited diffusion approximation routines are employed. The Boss code does an equally excellent job of relaxing to and maintaining the analytical results for the vertical (θ) temperature and radiative flux profiles for a disk with a height proportional to the radial distance. These tests strongly support the disk instability mechanism for forming giant planets.

Clinical and Social Outcomes five years after closing a mental hospital: a trial of cognitive behavioural interventions

PubMed Central

2005-01-01

Background To investigate the outcome of patients transferred from hospital to community care in Como, Italy after 6 months intensive psychosocial rehabilitation prior to discharge. Method All 149 residents with a primary psychiatric diagnosis were assigned to receive either a 6-month pre-discharge course of goal-oriented rehabilitation, (IT), or routine management, (RT). BPRS and GAF ratings were made by blind, independent assessors before and at 12, 24, 36, 48, and 60 months after discharge and the results examined with repeated measures analysis of variance. Results Overall change in residence was achieved without any major detriment to the health and welfare of most patients. The cohort of patients who received intensive rehabilitation, (IT), prior to discharge showed significantly lower impairment and disability throughout the five years compared to the cohort receiving routine management, (RT), prior to discharge. Total BPRS scores remained significant when initial differences in the cohorts were covaried, whereas GAF failed to remain significant (p = 0.051). Conclusion The treatment provided prior to transfer from long-stay hospital to community residence may have long-term clinical benefits for chronically disabled patients. PMID:16305738

A Ratio-Analysis Method to the Dynamics of Excited State Proton Transfer: Pyranine in Water and Micelles.

PubMed

Sahu, Kalyanasis; Nandi, Nilanjana; Dolai, Suman; Bera, Avisek

2018-06-05

Emission spectrum of a fluorophore undergoing excited state proton transfer (ESPT) often exhibits two distinct bands each representing emissions from protonated and deprotonated forms. The relative contribution of the two bands, best represented by an emission intensity ratio (R) (intensity maximum of the protonated band / intensity maximum of the deprotonated band), is an important parameter which usually denotes feasibility or promptness of the ESPT process. However, the use of ratio is only limited to the interpretation of steady-state fluorescence spectra. Here, for the first time, we exploit the time-dependence of the ratio (R(t)), calculated from time-resolved emission spectra (TRES) at different times, to analyze ESPT dynamics. TRES at different times were fitted with a sum of two lognormal-functions representing each peaks and then, the peak intensity ratio, R(t) was calculated and further fitted with an analytical function. Recently, a time-resolved area-normalized emission spectra (TRANES)-based analysis was presented where the decay of protonated emission or the rise of deprotonated emission intensity conveniently accounts for the ESPT dynamics. We show that these two methods are equivalent but the new method provides more insights on the nature of the ESPT process.

Analysis of film cooling in rocket nozzles

NASA Technical Reports Server (NTRS)

Woodbury, Keith A.

1992-01-01

Computational Fluid Dynamics (CFD) programs are customarily used to compute details of a flow field, such as velocity fields or species concentrations. Generally they are not used to determine the resulting conditions at a solid boundary such as wall shear stress or heat flux. However, determination of this information should be within the capability of a CFD code, as the code supposedly contains appropriate models for these wall conditions. Before such predictions from CFD analyses can be accepted, the credibility of the CFD codes upon which they are based must be established. This report details the progress made in constructing a CFD model to predict the heat transfer to the wall in a film cooled rocket nozzle. Specifically, the objective of this work is to use the NASA code FDNS to predict the heat transfer which will occur during the upcoming hot-firing of the Pratt & Whitney 40K subscale nozzle (1Q93). Toward this end, an M = 3 wall jet is considered, and the resulting heat transfer to the wall is computed. The values are compared against experimental data available in Reference 1. Also, FDNS's ability to compute heat flux in a reacting flow will be determined by comparing the code's predictions against calorimeter data from the hot firing of a 40K combustor. The process of modeling the flow of combusting gases through the Pratt & Whitney 40K subscale combustor and nozzle is outlined. What follows in this report is a brief description of the FDNS code, with special emphasis on how it handles solid wall boundary conditions. The test cases and some FDNS solution are presented next, along with comparison to experimental data. The process of modeling the flow through a chamber and a nozzle using the FDNS code will also be outlined.

Accounting for the Effect of Noncondensing Gases on Interphasic Heat and Mass Transfer in the Two-Fluid Model Used in the KORSAR Code

NASA Astrophysics Data System (ADS)

Yudov, Yu. V.

2018-03-01

A model is presented of the interphasic heat and mass transfer in the presence of noncondensable gases for the KORSAR/GP design code. This code was developed by FGUP NITI and the special design bureau OKB Gidropress. It was certified by Rostekhnadzor in 2009 for numerical substantiation of the safety of reactor installations with VVER reactors. The model is based on the assumption that there are three types of interphasic heat and mass transfer of the vapor component: vapor condensation or evaporation on the interphase under any thermodynamic conditions of the phases, pool boiling of the liquid superheated above the saturation temperature at the total pressure, and spontaneous condensation in the volume of gas phase supercooled below the saturation temperature at the vapor partial pressure. Condensation and evaporation on the interphase continuously occur in a two-phase flow and control the time response of the interphase heat and mass transfer. Boiling and spontaneous condensation take place only at the metastable condition of the phases and run at a quite high speed. The procedure used for calculating condensation and evaporation on the interphase accounts for the combined diffusion and thermal resistance of mass transfer in all regimes of the two-phase flow. The proposed approach accounts for, in a natural manner, a decrease in the rate of steam condensation (or generation) in the presence of noncondensing components in the gas phase due to a decrease (or increase) in the interphase temperature relative to the saturation temperature at the vapor partial pressure. The model of the interphase heat transfer also accounts for the processes of dissolution or release of noncondensing components in or from the liquid. The gas concentration at the interphase and on the saturation curve is calculated by the Henry law. The mass transfer coefficient in gas dissolution is based on the heat and mass transfer analogy. Results are presented of the verification of the interphase heat and mass transfer used in the KORSAR/GP code based on the data on film condensation of steam-air flows in vertical pipes. The proposed model was also tested by solving a problem of nitrogen release from a supersaturated water solution.

Neutron transport analysis for nuclear reactor design

DOEpatents

Vujic, Jasmina L.

1993-01-01

Replacing regular mesh-dependent ray tracing modules in a collision/transfer probability (CTP) code with a ray tracing module based upon combinatorial geometry of a modified geometrical module (GMC) provides a general geometry transfer theory code in two dimensions (2D) for analyzing nuclear reactor design and control. The primary modification of the GMC module involves generation of a fixed inner frame and a rotating outer frame, where the inner frame contains all reactor regions of interest, e.g., part of a reactor assembly, an assembly, or several assemblies, and the outer frame, with a set of parallel equidistant rays (lines) attached to it, rotates around the inner frame. The modified GMC module allows for determining for each parallel ray (line), the intersections with zone boundaries, the path length between the intersections, the total number of zones on a track, the zone and medium numbers, and the intersections with the outer surface, which parameters may be used in the CTP code to calculate collision/transfer probability and cross-section values.

Neutron transport analysis for nuclear reactor design

DOEpatents

Vujic, J.L.

1993-11-30

Replacing regular mesh-dependent ray tracing modules in a collision/transfer probability (CTP) code with a ray tracing module based upon combinatorial geometry of a modified geometrical module (GMC) provides a general geometry transfer theory code in two dimensions (2D) for analyzing nuclear reactor design and control. The primary modification of the GMC module involves generation of a fixed inner frame and a rotating outer frame, where the inner frame contains all reactor regions of interest, e.g., part of a reactor assembly, an assembly, or several assemblies, and the outer frame, with a set of parallel equidistant rays (lines) attached to it, rotates around the inner frame. The modified GMC module allows for determining for each parallel ray (line), the intersections with zone boundaries, the path length between the intersections, the total number of zones on a track, the zone and medium numbers, and the intersections with the outer surface, which parameters may be used in the CTP code to calculate collision/transfer probability and cross-section values. 28 figures.

Thermal-Flow Code for Modeling Gas Dynamics and Heat Transfer in Space Shuttle Solid Rocket Motor Joints

NASA Technical Reports Server (NTRS)

Wang, Qunzhen; Mathias, Edward C.; Heman, Joe R.; Smith, Cory W.

2000-01-01

A new, thermal-flow simulation code, called SFLOW. has been developed to model the gas dynamics, heat transfer, as well as O-ring and flow path erosion inside the space shuttle solid rocket motor joints by combining SINDA/Glo, a commercial thermal analyzer. and SHARPO, a general-purpose CFD code developed at Thiokol Propulsion. SHARP was modified so that friction, heat transfer, mass addition, as well as minor losses in one-dimensional flow can be taken into account. The pressure, temperature and velocity of the combustion gas in the leak paths are calculated in SHARP by solving the time-dependent Navier-Stokes equations while the heat conduction in the solid is modeled by SINDA/G. The two codes are coupled by the heat flux at the solid-gas interface. A few test cases are presented and the results from SFLOW agree very well with the exact solutions or experimental data. These cases include Fanno flow where friction is important, Rayleigh flow where heat transfer between gas and solid is important, flow with mass addition due to the erosion of the solid wall, a transient volume venting process, as well as some transient one-dimensional flows with analytical solutions. In addition, SFLOW is applied to model the RSRM nozzle joint 4 subscale hot-flow tests and the predicted pressures, temperatures (both gas and solid), and O-ring erosions agree well with the experimental data. It was also found that the heat transfer between gas and solid has a major effect on the pressures and temperatures of the fill bottles in the RSRM nozzle joint 4 configuration No. 8 test.

Development of a thermal and structural analysis procedure for cooled radial turbines

NASA Technical Reports Server (NTRS)

Kumar, Ganesh N.; Deanna, Russell G.

1988-01-01

A procedure for computing the rotor temperature and stress distributions in a cooled radial turbine is considered. Existing codes for modeling the external mainstream flow and the internal cooling flow are used to compute boundary conditions for the heat transfer and stress analyses. An inviscid, quasi three-dimensional code computes the external free stream velocity. The external velocity is then used in a boundary layer analysis to compute the external heat transfer coefficients. Coolant temperatures are computed by a viscous one-dimensional internal flow code for the momentum and energy equation. These boundary conditions are input to a three-dimensional heat conduction code for calculation of rotor temperatures. The rotor stress distribution may be determined for the given thermal, pressure and centrifugal loading. The procedure is applied to a cooled radial turbine which will be tested at the NASA Lewis Research Center. Representative results from this case are included.

Transferring Standard English Braille Skills to the Unified English Braille Code: A Pilot Study

ERIC Educational Resources Information Center

Steinman, Bernard A.; Kimbrough, B. T.; Johnson, Franklin; LeJeune, B. J.

2004-01-01

The enormously complex and sometimes controversial project to unify the traditional literary Braille code used in English-speaking countries with the technical and mathematical codes authorized by the Braille Authority of North America (BANA) and the Braille Authority of the United Kingdom (BAUK) proposes to change English Grade Two Braille on a…

Resonant Inductive Power Transfer for Noncontact Launcher-Missile Interface

DTIC Science & Technology

2016-08-01

implementation of a wireless power transfer system based on the concept of non-radiating inductive coupling. 14. SUBJECT TERMS Resonant Inductive Coupling... Wireless Power Transfer 15. NUMBER OF PAGES 18 16. PRICE CODE 17. SECURITY CLASSIFICATION OF REPORT UNCLASSIFIED 18. SECURITY...2 In contrast to the ideal transformer, wireless inductive power transfer assumes that the coils are no longer physically connected by an iron core

Modeling lidar waveforms with time-dependent stochastic radiative transfer theory for remote estimations of forest structure

NASA Astrophysics Data System (ADS)

Kotchenova, Svetlana Y.; Shabanov, Nikolay V.; Knyazikhin, Yuri; Davis, Anthony B.; Dubayah, Ralph; Myneni, Ranga B.

2003-08-01

Large footprint waveform-recording laser altimeters (lidars) have demonstrated a potential for accurate remote sensing of forest biomass and structure, important for regional and global climate studies. Currently, radiative transfer analyses of lidar data are based on the simplifying assumption that only single scattering contributes to the return signal, which may lead to errors in the modeling of the lower portions of recorded waveforms in the near-infrared spectrum. In this study we apply time-dependent stochastic radiative transfer (RT) theory to model the propagation of lidar pulses through forest canopies. A time-dependent stochastic RT equation is formulated and solved numerically. Such an approach describes multiple scattering events, allows for realistic representation of forest structure including foliage clumping and gaps, simulates off-nadir and multiangular observations, and has the potential to provide better approximations of return waveforms. The model was tested with field data from two conifer forest stands (southern old jack pine and southern old black spruce) in central Canada and two closed canopy deciduous forest stands (with overstory dominated by tulip poplar) in eastern Maryland. Model-simulated signals were compared with waveforms recorded by the Scanning Lidar Imager of Canopies by Echo Recovery (SLICER) over these regions. Model simulations show good agreement with SLICER signals having a slow decay of the waveform. The analysis of the effects of multiple scattering shows that multiply scattered photons magnify the amplitude of the reflected signal, especially that originating from the lower portions of the canopy.

Effect of Speed of Processing Training on Older Driver Screening Measures.

PubMed

Eramudugolla, Ranmalee; Kiely, Kim M; Chopra, Sidhant; Anstey, Kaarin J

2017-01-01

Objective: Computerized training for cognitive enhancement is of great public interest, however, there is inconsistent evidence for the transfer of training gains to every day activity. Several large trials have focused on speed of processing (SOP) training with some promising findings for long-term effects on daily activity, but no immediate transfer to other cognitive tests. Here, we examine the transfer of SOP training gains to cognitive measures that are known predictors of driving safety in older adults. Methods: Fifty-three adults aged 65-87 years who were current drivers participated in a two group non-randomized design with repeated measures and a no-contact matched control group. The Intervention group completed an average of 7.9 ( SD = 3.0) hours of self-administered online SOP training at home. Control group was matched on age, gender and test-re-test interval. Measures included the Useful Field of View (UFOV) test, a Hazard Perception test, choice reaction time (Cars RT), Trail Making Test B, a Maze test, visual motion threshold, as well as road craft and road knowledge tests. Results: Speed of processing training resulted in significant improvement in processing speed on the UFOV test relative to controls, with an average change of -45.8 ms ( SE = 14.5), and effect size of ω 2 = 0.21. Performance on the Maze test also improved, but significant slowing on the Hazard Perception test was observed after SOP training. Training effects on the UFOV task was associated with similar effects on the Cars RT, but not the Hazard Perception and Maze tests, suggesting transfer to some but not all driving related measures. There were no effects of training on any of the other measures examined. Conclusion: Speed of processing training effects on the UFOV task can be achieved with self-administered, online training at home, with some transfer to other cognitive tests. However, differential effects of training may be observed for tasks requiring goal-directed search strategies rather than diffuse attention.

General relativistic radiative transfer code in rotating black hole space-time: ARTIST

NASA Astrophysics Data System (ADS)

Takahashi, Rohta; Umemura, Masayuki

2017-02-01

We present a general relativistic radiative transfer code, ARTIST (Authentic Radiative Transfer In Space-Time), that is a perfectly causal scheme to pursue the propagation of radiation with absorption and scattering around a Kerr black hole. The code explicitly solves the invariant radiation intensity along null geodesics in the Kerr-Schild coordinates, and therefore properly includes light bending, Doppler boosting, frame dragging, and gravitational redshifts. The notable aspect of ARTIST is that it conserves the radiative energy with high accuracy, and is not subject to the numerical diffusion, since the transfer is solved on long characteristics along null geodesics. We first solve the wavefront propagation around a Kerr black hole that was originally explored by Hanni. This demonstrates repeated wavefront collisions, light bending, and causal propagation of radiation with the speed of light. We show that the decay rate of the total energy of wavefronts near a black hole is determined solely by the black hole spin in late phases, in agreement with analytic expectations. As a result, the ARTIST turns out to correctly solve the general relativistic radiation fields until late phases as t ˜ 90 M. We also explore the effects of absorption and scattering, and apply this code for a photon wall problem and an orbiting hotspot problem. All the simulations in this study are performed in the equatorial plane around a Kerr black hole. The ARTIST is the first step to realize the general relativistic radiation hydrodynamics.

Numerical prediction of turbulent oscillating flow and associated heat transfer

NASA Technical Reports Server (NTRS)

Koehler, W. J.; Patankar, S. V.; Ibele, W. E.

1991-01-01

A crucial point for further development of engines is the optimization of its heat exchangers which operate under oscillatory flow conditions. It has been found that the most important thermodynamic uncertainties in the Stirling engine designs for space power are in the heat transfer between gas and metal in all engine components and in the pressure drop across the heat exchanger components. So far, performance codes cannot predict the power output of a Stirling engine reasonably enough if used for a wide variety of engines. Thus, there is a strong need for better performance codes. However, a performance code is not concerned with the details of the flow. This information must be provided externally. While analytical relationships exist for laminar oscillating flow, there has been hardly any information about transitional and turbulent oscillating flow, which could be introduced into the performance codes. In 1986, a survey by Seume and Simon revealed that most Stirling engine heat exchangers operate in the transitional and turbulent regime. Consequently, research has since focused on the unresolved issue of transitional and turbulent oscillating flow and heat transfer. Since 1988, the University of Minnesota oscillating flow facility has obtained experimental data about transitional and turbulent oscillating flow. However, since the experiments in this field are extremely difficult, lengthy, and expensive, it is advantageous to numerically simulate the flow and heat transfer accurately from first principles. Work done at the University of Minnesota on the development of such a numerical simulation is summarized.

The Reverse Transcriptases Associated with CRISPR-Cas Systems.

PubMed

Toro, Nicolás; Martínez-Abarca, Francisco; González-Delgado, Alejandro

2017-08-02

CRISPR (clustered regularly interspaced short palindromic repeats) and associated proteins (Cas) act as adaptive immune systems in bacteria and archaea. Some CRISPR-Cas systems have been found to be associated with putative reverse transcriptases (RT), and an RT-Cas1 fusion associated with a type III-B system has been shown to acquire RNA spacers in vivo. Nevertheless, the origin and evolutionary relationships of these RTs and associated CRISPR-Cas systems remain largely unknown. We performed a comprehensive phylogenetic analysis of these RTs and associated Cas1 proteins, and classified their CRISPR-Cas modules. These systems were found predominantly in bacteria, and their presence in archaea may be due to a horizontal gene transfer event. These RTs cluster into 12 major clades essentially restricted to particular phyla, suggesting host-dependent functioning. The RTs and associated Cas1 proteins may have largely coevolved. They are, therefore, subject to the same selection pressures, which may have led to coadaptation within particular protein complexes. Furthermore, our results indicate that the association of an RT with a CRISPR-Cas system has occurred on multiple occasions during evolution.

Assessment of research and technology transfer needs for wood-frame housing

Treesearch

Kevin Powell; David Tilotta; Karen Martinson

2008-01-01

Improvements to housing will require both research and the transfer of that research to homebuilders, homebuyers, and others in need of technology. This report summarizes results of a national survey on research and technology transfer needs for housing and prioritizes those needs. Survey participants included academicians, builders, code officials, government...

48 CFR 252.232-7011 - Payments in Support of Emergencies and Contingency Operations.

Code of Federal Regulations, 2011 CFR

2011-10-01

.... Internal Revenue Code. (ix) Electronic funds transfer banking information. (A) The Contractor shall include electronic funds transfer banking information on the invoice only if required elsewhere in this contract. (B) If electronic funds transfer banking information is not required to be on the invoice, in order for...

25 CFR 11.907 - Transfer to Court of Indian Offenses.

Code of Federal Regulations, 2010 CFR

2010-04-01

....907 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAW AND ORDER COURTS OF INDIAN OFFENSES AND LAW AND ORDER CODE Children's Court § 11.907 Transfer to Court of Indian Offenses. (a) The presenting officer or the minor may file a petition requesting the children's court to transfer the minor to...

12 CFR 210.26 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

...) Article 4A means article 4A of the Uniform Commercial Code as set forth in appendix B of this subpart. (b... Reserve Bank, or that receives a payment order from a Federal Reserve Bank, in lieu of an interest charge... clearing house transfers. (f) Interdistrict transfer means a funds transfer involving entries to accounts...

Adjuvant Brachytherapy Removes Survival Disadvantage of Local Disease Extension in Stage IIIC Endometrial Cancer: A SEER Registry Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rossi, Peter J.; Jani, Ashesh B.; Horowitz, Ira R.

2008-01-01

Purpose: To assess the role of radiotherapy (RT) in women with Stage IIIC endometrial cancer. Methods and Materials: The 17-registry Survival, Epidemiology, and End Results (SEER) database was searched for patients with lymph node-positive non-Stage IV epithelial endometrial cancer diagnosed and treated between 1988 and 1998. Two subgroups were identified: those with organ-confined Stage IIIC endometrial cancer and those with Stage IIIC endometrial cancer with direct extension of the primary tumor. RT was coded as external beam RT (EBRT) or brachytherapy (BT). Observed survival (OS) was reported with a minimum of 5 years of follow-up; the survival curves were comparedmore » using the log-rank test. Results: The therapy data revealed 611 women with Stage IIIC endometrial cancer during this period. Of these women, 51% were treated with adjuvant EBRT, 21% with EBRT and BT, and 28% with no additional RT (NAT). Of the 611 patients, 293 had organ-confined Stage IIIC endometrial cancer and 318 patients had Stage IIIC endometrial cancer with direct extension of the primary tumor. The 5-year OS rate for all patients was 40% with NAT, 56% after EBRT, and 64% after EBRT/BT. Adjuvant RT improved survival compared with NAT (p <0.001). In patients with organ-confined Stage IIIC endometrial cancer, the 5-year OS rate was 50% for NAT, 64% for EBRT, and 67% for EBRT/BT. Again, adjuvant RT contributed to improved survival compared with NAT (p = 0.02). In patients with Stage IIIC endometrial cancer and direct tumor extension, the 5-year OS rate was 34% for NAT, 47% for EBRT, and 63% for EBRT/BT. RT improved OS compared with NAT (p <0.001). Also, in this high-risk subgroup, adding BT to EBRT was superior to EBRT alone (p = 0.002). Conclusion: Women with Stage IIIC endometrial cancer receiving adjuvant EBRT and EBRT/BT had improved OS compared with patients receiving NAT. When direct extension of the primary tumor was present, the addition of BT to EBRT was even more beneficial.« less

Adjuvant brachytherapy removes survival disadvantage of local disease extension in stage IIIC endometrial cancer: a SEER registry analysis.

PubMed

Rossi, Peter J; Jani, Ashesh B; Horowitz, Ira R; Johnstone, Peter A S

2008-01-01

To assess the role of radiotherapy (RT) in women with Stage IIIC endometrial cancer. The 17-registry Survival, Epidemiology, and End Results (SEER) database was searched for patients with lymph node-positive non-Stage IV epithelial endometrial cancer diagnosed and treated between 1988 and 1998. Two subgroups were identified: those with organ-confined Stage IIIC endometrial cancer and those with Stage IIIC endometrial cancer with direct extension of the primary tumor. RT was coded as external beam RT (EBRT) or brachytherapy (BT). Observed survival (OS) was reported with a minimum of 5 years of follow-up; the survival curves were compared using the log-rank test. The therapy data revealed 611 women with Stage IIIC endometrial cancer during this period. Of these women, 51% were treated with adjuvant EBRT, 21% with EBRT and BT, and 28% with no additional RT (NAT). Of the 611 patients, 293 had organ-confined Stage IIIC endometrial cancer and 318 patients had Stage IIIC endometrial cancer with direct extension of the primary tumor. The 5-year OS rate for all patients was 40% with NAT, 56% after EBRT, and 64% after EBRT/BT. Adjuvant RT improved survival compared with NAT (p <0.001). In patients with organ-confined Stage IIIC endometrial cancer, the 5-year OS rate was 50% for NAT, 64% for EBRT, and 67% for EBRT/BT. Again, adjuvant RT contributed to improved survival compared with NAT (p = 0.02). In patients with Stage IIIC endometrial cancer and direct tumor extension, the 5-year OS rate was 34% for NAT, 47% for EBRT, and 63% for EBRT/BT. RT improved OS compared with NAT (p <0.001). Also, in this high-risk subgroup, adding BT to EBRT was superior to EBRT alone (p = 0.002). Women with Stage IIIC endometrial cancer receiving adjuvant EBRT and EBRT/BT had improved OS compared with patients receiving NAT. When direct extension of the primary tumor was present, the addition of BT to EBRT was even more beneficial.

Extracellular Vesicle-Associated RNA as a Carrier of Epigenetic Information

PubMed Central

2017-01-01

Post-transcriptional regulation of messenger RNA (mRNA) metabolism and subcellular localization is of the utmost importance both during development and in cell differentiation. Besides carrying genetic information, mRNAs contain cis-acting signals (zip codes), usually present in their 5′- and 3′-untranslated regions (UTRs). By binding to these signals, trans-acting factors, such as RNA-binding proteins (RBPs), and/or non-coding RNAs (ncRNAs), control mRNA localization, translation and stability. RBPs can also form complexes with non-coding RNAs of different sizes. The release of extracellular vesicles (EVs) is a conserved process that allows both normal and cancer cells to horizontally transfer molecules, and hence properties, to neighboring cells. By interacting with proteins that are specifically sorted to EVs, mRNAs as well as ncRNAs can be transferred from cell to cell. In this review, we discuss the mechanisms underlying the sorting to EVs of different classes of molecules, as well as the role of extracellular RNAs and the associated proteins in altering gene expression in the recipient cells. Importantly, if, on the one hand, RBPs play a critical role in transferring RNAs through EVs, RNA itself could, on the other hand, function as a carrier to transfer proteins (i.e., chromatin modifiers, and transcription factors) that, once transferred, can alter the cell’s epigenome. PMID:28937658

Virus-like attachment sites as structural landmarks of plants retrotransposons.

PubMed

Ochoa Cruz, Edgar Andres; Cruz, Guilherme Marcello Queiroga; Vieira, Andréia Prata; Van Sluys, Marie-Anne

2016-01-01

The genomic data available nowadays has enabled the study of repetitive sequences and their relationship to viruses. Among them, long terminal repeat retrotransposons (LTR-RTs) are the largest component of most plant genomes, the Gypsy and Copia superfamilies being the most common. Recently it has been found that Del lineage, an LTR-RT of Gypsy superfamily, has putative virus-like attachment (vl-att) sites. This signature, originally described for retroviruses, is recognized by retroviral integrase conferring specificity to the integration process. Here we retrieved 26,092 putative complete LTR-RTs from 10 lineages found in 10 fully sequenced angiosperm genomes and found putative vl-att sites that are a conserved structural landmark across these genomes. Furthermore, we reveal that each plant genome has a distinguishable LTR-RT lineage amplification pattern that could be related to the vl-att sites diversity. We used these patterns to generate a specific quick-response (QR) code for each genome that could be used as a barcode of identification of plants in the future. The universal distribution of vl-att sites represents a new structural feature common to plant LTR-RTs and retroviruses. This is an important finding that expands the information about the structural similarity between LTR-RT and retroviruses. We speculate that the sequence diversity of vl-att sites could be important for the life cycle of retrotransposons, as it was shown for retroviruses. All the structural vl-att site signatures are strong candidates for further functional studies. Moreover, this is the first identification of specific LTR-RT content and their amplification patterns in a large dataset of LTR-RT lineages and angiosperm genomes. These distribution patterns could be used in the future with biotechnological identification purposes.

Application of thin plate splines for accurate regional ionosphere modeling with multi-GNSS data

NASA Astrophysics Data System (ADS)

Krypiak-Gregorczyk, Anna; Wielgosz, Pawel; Borkowski, Andrzej

2016-04-01

GNSS-derived regional ionosphere models are widely used in both precise positioning, ionosphere and space weather studies. However, their accuracy is often not sufficient to support precise positioning, RTK in particular. In this paper, we presented new approach that uses solely carrier phase multi-GNSS observables and thin plate splines (TPS) for accurate ionospheric TEC modeling. TPS is a closed solution of a variational problem minimizing both the sum of squared second derivatives of a smoothing function and the deviation between data points and this function. This approach is used in UWM-rt1 regional ionosphere model developed at UWM in Olsztyn. The model allows for providing ionospheric TEC maps with high spatial and temporal resolutions - 0.2x0.2 degrees and 2.5 minutes, respectively. For TEC estimation, EPN and EUPOS reference station data is used. The maps are available with delay of 15-60 minutes. In this paper we compare the performance of UWM-rt1 model with IGS global and CODE regional ionosphere maps during ionospheric storm that took place on March 17th, 2015. During this storm, the TEC level over Europe doubled comparing to earlier quiet days. The performance of the UWM-rt1 model was validated by (a) comparison to reference double-differenced ionospheric corrections over selected baselines, and (b) analysis of post-fit residuals to calibrated carrier phase geometry-free observational arcs at selected test stations. The results show a very good performance of UWM-rt1 model. The obtained post-fit residuals in case of UWM maps are lower by one order of magnitude comparing to IGS maps. The accuracy of UWM-rt1 -derived TEC maps is estimated at 0.5 TECU. This may be directly translated to the user positioning domain.

PURDU-WINCOF: A computer code for establishing the performance of a fan-compressor unit with water ingestion

NASA Technical Reports Server (NTRS)

Leonardo, M.; Tsuchiya, T.; Murthy, S. N. B.

1982-01-01

A model for predicting the performance of a multi-spool axial-flow compressor with a fan during operation with water ingestion was developed incorporating several two-phase fluid flow effects as follows: (1) ingestion of water, (2) droplet interaction with blades and resulting changes in blade characteristics, (3) redistribution of water and water vapor due to centrifugal action, (4) heat and mass transfer processes, and (5) droplet size adjustment due to mass transfer and mechanical stability considerations. A computer program, called the PURDU-WINCOF code, was generated based on the model utilizing a one-dimensional formulation. An illustrative case serves to show the manner in which the code can be utilized and the nature of the results obtained.

A Steady State and Quasi-Steady Interface Between the Generalized Fluid System Simulation Program and the SINDA/G Thermal Analysis Program

NASA Technical Reports Server (NTRS)

Schallhorn, Paul; Majumdar, Alok; Tiller, Bruce

2001-01-01

A general purpose, one dimensional fluid flow code is currently being interfaced with the thermal analysis program SINDA/G. The flow code, GFSSP, is capable of analyzing steady state and transient flow in a complex network. The flow code is capable of modeling several physical phenomena including compressibility effects, phase changes, body forces (such as gravity and centrifugal) and mixture thermodynamics for multiple species. The addition of GFSSP to SINDA/G provides a significant improvement in convective heat transfer modeling for SINDA/G. The interface development is conducted in multiple phases. This paper describes the first phase of the interface which allows for steady and quasisteady (unsteady solid, steady fluid) conjugate heat transfer modeling.

Energy balance in a Z pinch with suppressed Rayleigh-Taylor instability

NASA Astrophysics Data System (ADS)

Baksht, R. B.; Oreshkin, V. I.; Rousskikh, A. G.; Zhigalin, A. S.

2018-03-01

At present Z-pinch has evolved into a powerful plasma source of soft x-ray. This paper considers the energy balance in a radiating metallic gas-puff Z pinch. In this type of Z pinch, a power-law density distribution is realized, promoting suppression of Rayleigh-Taylor (RT) instabilities that occur in the pinch plasma during compression. The energy coupled into the pinch plasma, is determined as the difference between the total energy delivered to the load from the generator and the magnetic energy of the load inductance. A calibrated voltage divider and a Rogowski coil were used to determine the coupled energy and the load inductance. Time-gated optical imaging of the pinch plasma showed its stable compression up to the stagnation phase. The pinch implosion was simulated using a 1D two-temperature radiative magnetohydrodynamic code. Comparison of the experimental and simulation results has shown that the simulation adequately describes the pinch dynamics for conditions in which RT instability is suppressed. It has been found that the proportion of the Ohmic heating in the energy balance of a Z pinch with suppressed RT instability is determined by Spitzer resistance and makes no more than ten percent.

Application Programming in AWIPS II

NASA Technical Reports Server (NTRS)

Smit, Matt; McGrath, Kevin; Burks, Jason; Carcione, Brian

2012-01-01

Since its inception almost 8 years ago, NASA's Short-term Prediction Research and Transition (SPoRT) Center has integrated NASA data into the National Weather Service's decision support system (DSS) the Advanced Weather Interactive Processing System (AWIPS). SPoRT has, in some instances, had to shape and transform data sets into various formats and manipulate configurations to visualize them in AWIPS. With the advent of the next generation of DSS, AWIPS II, developers will be able to develop their own plugins to handle any type of data. Raytheon is developing AWIPS II to be a more extensible package written mainly in Java, and built around a Service Oriented Architecture. A plugin architecture will allow users to install their own code modules, and (if all the rules have been properly followed) they will work hand-in-hand with AWIPS II as if it were originally built in. Users can bring in new datasets with existing plugins, tweak plugins to handle a nuance or desired new functionality, or create an entirely new visualization layout for a new dataset. SPoRT is developing plugins to ensure its existing NASA data will be ready for AWIPS II when it is delivered, and to prepare for the future of new instruments on upcoming satellites.

Point-of-care diagnostic assay for the detection of Zika virus using the recombinase polymerase amplification method.

PubMed

Vasileva Wand, Nadina I; Bonney, Laura C; Watson, Robert J; Graham, Victoria; Hewson, Roger

2018-06-13

The sudden and explosive expansion of Zika virus (ZIKV) from the African continent through Oceania and culminating in the outbreak in South America has highlighted the importance of new rapid point-of-care diagnostic tools for the control and prevention of transmission. ZIKV infection has devastating consequences, such as neurological congenital malformations in infants born to infected mothers and Guillain-Barré syndrome in adults. Additionally, its potential for transmission through vector bites, as well as from person to person through blood transfusions and sexual contact, are important considerations for prompt diagnosis. Recombinase polymerase amplification (RPA), an isothermal method, was developed as an alternative field-applicable assay to PCR. Here we report the development of a novel ZIKV real-time reverse transcriptase RPA (RT-RPA) assay capable of detecting a range of different ZIKV strains from a variety of geographical locations. The ZIKV RT-RPA was shown to be highly sensitive, being capable of detecting as few as five copies of target nucleic acid per reaction, and suitable for use with a battery-operated portable device. The ZIKV RT-RPA demonstrated 100 % specificity and 83 % sensitivity in clinical samples. Furthermore, we determined that the ZIKV RT-RPA is a versatile assay that can be applied to crude samples, such as saliva and serum, and can be used as a vector surveillance tool on crude mosquito homogenates. Therefore, the developed ZIKV RT-RPA is a useful diagnostic tool that can be transferred to a resource-limited location, eliminating the need for a specialized and sophisticated laboratory environment and highly trained staff.

Microhard MHX2420 Orbital Performance Evaluation Using RT Logic T400CS

NASA Technical Reports Server (NTRS)

TintoreGazulla, Oriol; Lombardi, Mark

2012-01-01

RT Logic allows simulation of Ground Station - satellite communications: Static tests have been successful. Dynamic tests have been performed for simple passes. Future dynamic tests are needed to simulate real orbit communications. Satellite attitude changes antenna gain. Atmospheric and rain losses need to be added. STK Plug-in will be the next step to improve the dynamic tests. There is a possibility of running longer simulations. Simulation of different losses available in the STK Plug-in. Microhard optimization: Effect of Microhard settings on the data throughput have been understood. Optimized settings improve data throughput for LEO communications. Longer hop intervals make transfer of larger packets more efficient (more time between hops in frequency). Use of FEC (Reed-Solomon) reduces the number of retransmissions for long-range or noisy communications.

Characterisation and optimisation of flexible transfer lines for liquid helium. Part II: Thermohydraulic modelling

NASA Astrophysics Data System (ADS)

Dittmar, N.; Haberstroh, Ch.; Hesse, U.; Krzyzowski, M.

2016-10-01

In part one of this publication experimental results for a single-channel transfer line used at liquid helium (LHe) decant stations are presented. The transfer of LHe into mobile dewars is an unavoidable process since the places of storage and usage are generally located apart from each other. The experimental results have shown that reasonable amounts of LHe evaporate due to heat leak and pressure drop. Thus, generated helium cold gas has to be collected and reliquefied, demanding a huge amount of electrical energy. Although this transfer process is common in cryogenic laboratories, no existing code could be found to model it. Therefore, a thermohydraulic model has been developed to model the LHe flow at operating conditions using published heat transfer and pressure drop correlations. This paper covers the basic equations used to calculate heat transfer and pressure drop, as well as the validation of the thermohydraulic code, and its application within the optimisation process. The final transfer line design features reduced heat leak and pressure drop values based on a combined measurement and modelling campaign in the range of 0.112 < pin < 0.148 MPa, 190 < G < 450 kg/(m2 s), and 0.04 < xout < 0.12.

Coupling Legacy and Contemporary Deterministic Codes to Goldsim for Probabilistic Assessments of Potential Low-Level Waste Repository Sites

NASA Astrophysics Data System (ADS)

Mattie, P. D.; Knowlton, R. G.; Arnold, B. W.; Tien, N.; Kuo, M.

2006-12-01

Sandia National Laboratories (Sandia), a U.S. Department of Energy National Laboratory, has over 30 years experience in radioactive waste disposal and is providing assistance internationally in a number of areas relevant to the safety assessment of radioactive waste disposal systems. International technology transfer efforts are often hampered by small budgets, time schedule constraints, and a lack of experienced personnel in countries with small radioactive waste disposal programs. In an effort to surmount these difficulties, Sandia has developed a system that utilizes a combination of commercially available codes and existing legacy codes for probabilistic safety assessment modeling that facilitates the technology transfer and maximizes limited available funding. Numerous codes developed and endorsed by the United States Nuclear Regulatory Commission and codes developed and maintained by United States Department of Energy are generally available to foreign countries after addressing import/export control and copyright requirements. From a programmatic view, it is easier to utilize existing codes than to develop new codes. From an economic perspective, it is not possible for most countries with small radioactive waste disposal programs to maintain complex software, which meets the rigors of both domestic regulatory requirements and international peer review. Therefore, re-vitalization of deterministic legacy codes, as well as an adaptation of contemporary deterministic codes, provides a creditable and solid computational platform for constructing probabilistic safety assessment models. External model linkage capabilities in Goldsim and the techniques applied to facilitate this process will be presented using example applications, including Breach, Leach, and Transport-Multiple Species (BLT-MS), a U.S. NRC sponsored code simulating release and transport of contaminants from a subsurface low-level waste disposal facility used in a cooperative technology transfer project between Sandia National Laboratories and Taiwan's Institute of Nuclear Energy Research (INER) for the preliminary assessment of several candidate low-level waste repository sites. Sandia National Laboratories is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy under Contract DE AC04 94AL85000.

MINIVER: Miniature version of real/ideal gas aero-heating and ablation computer program

NASA Technical Reports Server (NTRS)

Hendler, D. R.

1976-01-01

Computer code is used to determine heat transfer multiplication factors, special flow field simulation techniques, different heat transfer methods, different transition criteria, crossflow simulation, and more efficient thin skin thickness optimization procedure.

The application of nonlinear programming and collocation to optimal aeroassisted orbital transfers

NASA Astrophysics Data System (ADS)

Shi, Y. Y.; Nelson, R. L.; Young, D. H.; Gill, P. E.; Murray, W.; Saunders, M. A.

1992-01-01

Sequential quadratic programming (SQP) and collocation of the differential equations of motion were applied to optimal aeroassisted orbital transfers. The Optimal Trajectory by Implicit Simulation (OTIS) computer program codes with updated nonlinear programming code (NZSOL) were used as a testbed for the SQP nonlinear programming (NLP) algorithms. The state-of-the-art sparse SQP method is considered to be effective for solving large problems with a sparse matrix. Sparse optimizers are characterized in terms of memory requirements and computational efficiency. For the OTIS problems, less than 10 percent of the Jacobian matrix elements are nonzero. The SQP method encompasses two phases: finding an initial feasible point by minimizing the sum of infeasibilities and minimizing the quadratic objective function within the feasible region. The orbital transfer problem under consideration involves the transfer from a high energy orbit to a low energy orbit.

Experiences on p-Version Time-Discontinuous Galerkin's Method for Nonlinear Heat Transfer Analysis and Sensitivity Analysis

NASA Technical Reports Server (NTRS)

Hou, Gene

2004-01-01

The focus of this research is on the development of analysis and sensitivity analysis equations for nonlinear, transient heat transfer problems modeled by p-version, time discontinuous finite element approximation. The resulting matrix equation of the state equation is simply in the form ofA(x)x = c, representing a single step, time marching scheme. The Newton-Raphson's method is used to solve the nonlinear equation. Examples are first provided to demonstrate the accuracy characteristics of the resultant finite element approximation. A direct differentiation approach is then used to compute the thermal sensitivities of a nonlinear heat transfer problem. The report shows that only minimal coding effort is required to enhance the analysis code with the sensitivity analysis capability.

Grid orthogonality effects on predicted turbine midspan heat transfer and performance

NASA Technical Reports Server (NTRS)

Boyle, R. J.; Ameri, A. A.

1995-01-01

The effect of five different C type grid geometries on the predicted heat transfer and aerodynamic performance of a turbine stator is examined. Predictions were obtained using two flow analysis codes. One was a finite difference analysis, and the other was a finite volume analysis. Differences among the grids in terms of heat transfer and overall performance were small. The most significant difference among the five grids occurred in the prediction of pitchwise variation in total pressure. There was consistency between results obtained with each of the flow analysis codes when the same grid was used. A grid generating procedure in which the viscous grid is embedded within an inviscid type grid resulted in the best overall performance.

A novel TaqMan® assay for Nosema ceranae quantification in honey bee, based on the protein coding gene Hsp70.

PubMed

Cilia, Giovanni; Cabbri, Riccardo; Maiorana, Giacomo; Cardaio, Ilaria; Dall'Olio, Raffaele; Nanetti, Antonio

2018-04-01

Nosema ceranae is now a widespread honey bee pathogen with high incidence in apiculture. Rapid and reliable detection and quantification methods are a matter of concern for research community, nowadays mainly relying on the use of biomolecular techniques such as PCR, RT-PCR or HRMA. The aim of this technical paper is to provide a new qPCR assay, based on the highly-conserved protein coding gene Hsp70, to detect and quantify the microsporidian Nosema ceranae affecting the western honey bee Apis mellifera. The validation steps to assess efficiency, sensitivity, specificity and robustness of the assay are described also. Copyright © 2018 Elsevier GmbH. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stevens, D.L.; Simonen, F.A.; Strosnider, J. Jr.

The VISA (Vessel Integrity Simulation Analysis) code was developed as part of the NRC staff evaluation of pressurized thermal shock. VISA uses Monte Carlo simulation to evaluate the failure probability of a pressurized water reactor (PWR) pressure vessel subjected to a pressure and thermal transient specified by the user. Linear elastic fracture mechanics are used to model crack initiation and propagation. parameters for initial crack size, copper content, initial RT/sub NDT/, fluence, crack-initiation fracture toughness, and arrest fracture toughness are treated as random variables. This report documents the version of VISA used in the NRC staff report (Policy Issue frommore » J.W. Dircks to NRC Commissioners, Enclosure A: NRC Staff Evaluation of Pressurized Thermal Shock, November 1982, SECY-82-465) and includes a user's guide for the code.« less

GFSSP Training Course Lectures

NASA Technical Reports Server (NTRS)

Majumdar, Alok K.

2008-01-01

GFSSP has been extended to model conjugate heat transfer Fluid Solid Network Elements include: a) Fluid nodes and Flow Branches; b) Solid Nodes and Ambient Nodes; c) Conductors connecting Fluid-Solid, Solid-Solid and Solid-Ambient Nodes. Heat Conduction Equations are solved simultaneously with Fluid Conservation Equations for Mass, Momentum, Energy and Equation of State. The extended code was verified by comparing with analytical solution for simple conduction-convection problem The code was applied to model: a) Pressurization of Cryogenic Tank; b) Freezing and Thawing of Metal; c) Chilldown of Cryogenic Transfer Line; d) Boil-off from Cryogenic Tank.

Thermal radiation heat transfer in participating media by finite volume discretization using collimated beam incidence

NASA Astrophysics Data System (ADS)

Harijishnu, R.; Jayakumar, J. S.

2017-09-01

The main objective of this paper is to study the heat transfer rate of thermal radiation in participating media. For that, a generated collimated beam has been passed through a two dimensional slab model of flint glass with a refractive index 2. Both Polar and azimuthal angle have been varied to generate such a beam. The Temperature of the slab and Snells law has been validated by Radiation Transfer Equation (RTE) in OpenFOAM (Open Field Operation and Manipulation), a CFD software which is the major computational tool used in Industry and research applications where the source code is modified in which radiation heat transfer equation is added to the case and different radiation heat transfer models are utilized. This work concentrates on the numerical strategies involving both transparent and participating media. Since Radiation Transfer Equation (RTE) is difficult to solve, the purpose of this paper is to use existing solver buoyantSimlpeFoam to solve radiation model in the participating media by compiling the source code to obtain the heat transfer rate inside the slab by varying the Intensity of radiation. The Finite Volume Method (FVM) is applied to solve the Radiation Transfer Equation (RTE) governing the above said physical phenomena.

Higher-order Brain Areas Associated with Real-time Functional MRI Neurofeedback Training of the Somato-motor Cortex.

PubMed

Auer, Tibor; Dewiputri, Wan Ilma; Frahm, Jens; Schweizer, Renate

2018-05-15

Neurofeedback (NFB) allows subjects to learn self-regulation of neuronal brain activation based on information about the ongoing activation. The implementation of real-time functional magnetic resonance imaging (rt-fMRI) for NFB training now facilitates the investigation into underlying processes. Our study involved 16 control and 16 training right-handed subjects, the latter performing an extensive rt-fMRI NFB training using motor imagery. A previous analysis focused on the targeted primary somato-motor cortex (SMC). The present study extends the analysis to the supplementary motor area (SMA), the next higher brain area within the hierarchy of the motor system. We also examined transfer-related functional connectivity using a whole-volume psycho-physiological interaction (PPI) analysis to reveal brain areas associated with learning. The ROI analysis of the pre- and post-training fMRI data for motor imagery without NFB (transfer) resulted in a significant training-specific increase in the SMA. It could also be shown that the contralateral SMA exhibited a larger increase than the ipsilateral SMA in the training and the transfer runs, and that the right-hand training elicited a larger increase in the transfer runs than the left-hand training. The PPI analysis revealed a training-specific increase in transfer-related functional connectivity between the left SMA and frontal areas as well as the anterior midcingulate cortex (aMCC) for right- and left-hand trainings. Moreover, the transfer success was related with training-specific increase in functional connectivity between the left SMA and the target area SMC. Our study demonstrates that NFB training increases functional connectivity with non-targeted brain areas. These are associated with the training strategy (i.e., SMA) as well as with learning the NFB skill (i.e., aMCC and frontal areas). This detailed description of both the system to be trained and the areas involved in learning can provide valuable information for further optimization of NFB trainings. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Sensitivity Analysis of Cf-252 (sf) Neutron and Gamma Observables in CGMF

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carter, Austin Lewis; Talou, Patrick; Stetcu, Ionel

CGMF is a Monte Carlo code that simulates the decay of primary fission fragments by emission of neutrons and gamma rays, according to the Hauser-Feshbach equations. As the CGMF code was recently integrated into the MCNP6.2 transport code, great emphasis has been placed on providing optimal parameters to CGMF such that many different observables are accurately represented. Of these observables, the prompt neutron spectrum, prompt neutron multiplicity, prompt gamma spectrum, and prompt gamma multiplicity are crucial for accurate transport simulations of criticality and nonproliferation applications. This contribution to the ongoing efforts to improve CGMF presents a study of the sensitivitymore » of various neutron and gamma observables to several input parameters for Californium-252 spontaneous fission. Among the most influential parameters are those that affect the input yield distributions in fragment mass and total kinetic energy (TKE). A new scheme for representing Y(A,TKE) was implemented in CGMF using three fission modes, S1, S2 and SL. The sensitivity profiles were calculated for 17 total parameters, which show that the neutron multiplicity distribution is strongly affected by the TKE distribution of the fragments. The total excitation energy (TXE) of the fragments is shared according to a parameter RT, which is defined as the ratio of the light to heavy initial temperatures. The sensitivity profile of the neutron multiplicity shows a second order effect of RT on the mean neutron multiplicity. A final sensitivity profile was produced for the parameter alpha, which affects the spin of the fragments. Higher values of alpha lead to higher fragment spins, which inhibit the emission of neutrons. Understanding the sensitivity of the prompt neutron and gamma observables to the many CGMF input parameters provides a platform for the optimization of these parameters.« less

The Long Noncoding RNA Landscape of the Mouse Eye.

PubMed

Chen, Weiwei; Yang, Shuai; Zhou, Zhonglou; Zhao, Xiaoting; Zhong, Jiayun; Reinach, Peter S; Yan, Dongsheng

2017-12-01

Long noncoding RNAs (lncRNAs) are important regulators of diverse biological functions. However, an extensive in-depth analysis of their expression profile and function in mammalian eyes is still lacking. Here we describe comprehensive landscapes of stage-dependent and tissue-specific lncRNA expression in the mouse eye. Affymetrix transcriptome array profiled lncRNA signatures from six different ocular tissue subsets (i.e., cornea, lens, retina, RPE, choroid, and sclera) in newborn and 8-week-old mice. Quantitative RT-PCR analysis validated array findings. Cis analyses and Gene Ontology (GO) annotation of protein-coding genes adjacent to signature lncRNA loci clarified potential lncRNA roles in maintaining tissue identity and regulating eye maturation during the aforementioned phase. In newborn and 8-week-old mice, we identified 47,332 protein-coding and noncoding gene transcripts. LncRNAs comprise 19,313 of these transcripts annotated in public data banks. During this maturation phase of these six different tissue subsets, more than 1000 lncRNAs expression levels underwent ≥2-fold changes. qRT-PCR analysis confirmed part of the gene microarray analysis results. K-means clustering identified 910 lncRNAs in the P0 groups and 686 lncRNAs in the postnatal 8-week-old groups, suggesting distinct tissue-specific lncRNA clusters. GO analysis of protein-coding genes proximal to lncRNA signatures resolved close correlations with their tissue-specific functional maturation between P0 and 8 weeks of age in the 6 tissue subsets. Characterizating maturational changes in lncRNA expression patterns as well as tissue-specific lncRNA signatures in six ocular tissues suggest important contributions made by lncRNA to the control of developmental processes in the mouse eye.

Molecular cloning and functional analysis of MRLC2 in Tianfu, Boer, and Chengdu Ma goats.

PubMed

Xu, H G; Xu, G Y; Wan, L; Ma, J

2013-03-15

To determine the molecular basis of heterosis in goats, fluorescence quantitative polymerase chain reaction (PCR) was performed to investigate myosin-regulatory light chain 2 (MRLC2) gene expression in the longissimus dorsi muscle tissues of the Tianfu goat and its parents, the Boer and Chengdu Ma goats. The goat MRLC2 gene was differentially expressed in the crossbreed, and the purebred mRNA were isolated and identified using fluorescence quantitative reverse transcription-PCR (RT-PCR). The complete coding sequence of MRLC2 was obtained using the cDNA method, and the full-length coding sequence consisted of 513 bp encoding 172 amino acids. The EF-hand superfamily domain of the MRLC2 protein is well conserved in caprine and other animals. The deduced amino acid sequence of MRLC2 shared significant identity with MRLC2 from other mammals. Phylogenetic tree analysis revealed that the MRLC2 protein was closely related to MRLC2 in other mammals. Several predicted miRNA target sites were found in the coding sequence of caprine MRLC2 mRNA. Analysis by RT-PCR showed that MRLC2 mRNA was present in the heart, stomach, liver, spleen, lung, small intestine, kidney, leg muscle, abdominal muscle, and longissimus dorsi muscles. In particular, the high expression of MRLC2 mRNA was detected in the longissimus dorsi, leg muscle, abdominal muscle, stomach, and heart, but low levels of expression were also observed in the liver, spleen, lung, small intestine, and kidney. The expression of the MRLC2 gene was upregulated in the longissimus dorsi muscle of Boer and Tianfu goats, and it was moderately upregulated in Chengdu Ma goats.

MiR-22 is frequently downregulated in medulloblastomas and inhibits cell proliferation via the novel target PAPST1.

PubMed

Xu, Qing-Fu; Pan, Ya-Wen; Li, Li-Chao; Zhou, Zheng; Huang, Qi-Lin; Pang, Jesse Chung-Sean; Zhu, Xiao-Peng; Ren, Yong; Yang, Hui; Ohgaki, Hiroko; Lv, Sheng-Qing

2014-11-01

Medulloblastoma is the most frequent malignant central nervous system tumor in children. MicroRNAs (miRs) are small, non-coding RNAs that target protein-coding and non-coding RNAs, and play roles in a variety of cellular processes through regulation of multiple targets. In the present study, we analyzed miR-22 expression and its effect in cell proliferation and apoptosis in medulloblastomas. Quantitative reverse transcription PCR (RT-PCR) revealed significantly lower expression of miR-22 in 19 out of 27 (70%) medulloblastomas, D341, DAOY, ONS-76 medulloblastoma cell lines, compared with normal cerebellum. Forced expression of miR-22 by lentiviral vector transfection reduced cell proliferation and induced apoptosis, while knockdown of miR-22 increased proliferative activity in DAOY and ONS-76 cells. DAOY cells with miR-22 overexpression in nude mice yielded tumors smaller than those originated from control DAOY cells. Microarray analysis in DAOY cells with forced miR-22 expression showed significant changes in expression profiles, PAPST1 being the most significantly (10 folds) downregulated gene. Quantitative RT-PCR revealed PAPST1 mRNA upregulation in 18 out of 27 (67%) medulloblastomas. In addition, a luciferase reporter assay in ONS-76 and DAOY cells suggested that miR-22 directly targets the PAPST1 gene, and lentivirus-mediated knockdown of PAPST1 suppressed proliferation of DAOY and ONS-76 medulloblastoma cells. These results suggest that frequently downregulated miR-22 expression is associated with cell proliferation in medulloblastomas, and this may be at least in part via PAPST1, which is a novel target of miR-22. © 2014 International Society of Neuropathology.

Genome-wide identification of long non-coding RNA and mRNA profiling using RNA sequencing in subjects with sensitive skin

PubMed Central

Tu, Ying; Xu, Dan; Feng, Jiaqi; He, Li

2017-01-01

Sensitive skin (SS) is a condition of subjective cutaneous hyper-reactivity. The role of long non-coding RNAs (lncRNAs) in subjects with SS is unclear. Therefore, the aim of the present study was to provide a comprehensive profile of the mRNAs and lncRNAs in subjects with SS. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis presented the characteristics of associated protein-coding genes. In addition, a co-expression network of lncRNA and mRNA was constructed to identify potential underlying regulation targets; the results were verified by quantitative real-time PCR (qRT-PCR) and RNA-seq analyses in patients with SS and normal samples. Compared with the normal skin group, 266 novel lncRNAs and 6750 annotated lncRNAs were identified in the SS group. A total of 71 lncRNA transcripts and 2615 mRNA transcripts were differentially expressed (P < 0.05). The heat signature of the SS samples could be distinguished from the normal skin samples, whereas the majority of the genes that were present in enriched pathways were those that participated in focal adhesion, PI3K-Akt signaling, and cancer-related pathways. Five transcripts were selected for qRT-PCR analysis and the results were consistent with RNA-seq. The results suggested that LNC_000265 may play a role in the epidermal barrier structure of patient with SS. The data suggest novel genes and pathways that may be involved in the pathogenesis of SS and highlight potential targets that could be used for individualized treatment applications. PMID:29383128

Comparison of numerical techniques for integration of stiff ordinary differential equations arising in combustion chemistry

NASA Technical Reports Server (NTRS)

Radhakrishnan, K.

1984-01-01

The efficiency and accuracy of several algorithms recently developed for the efficient numerical integration of stiff ordinary differential equations are compared. The methods examined include two general-purpose codes, EPISODE and LSODE, and three codes (CHEMEQ, CREK1D, and GCKP84) developed specifically to integrate chemical kinetic rate equations. The codes are applied to two test problems drawn from combustion kinetics. The comparisons show that LSODE is the fastest code currently available for the integration of combustion kinetic rate equations. An important finding is that an interactive solution of the algebraic energy conservation equation to compute the temperature does not result in significant errors. In addition, this method is more efficient than evaluating the temperature by integrating its time derivative. Significant reductions in computational work are realized by updating the rate constants (k = at(supra N) N exp(-E/RT) only when the temperature change exceeds an amount delta T that is problem dependent. An approximate expression for the automatic evaluation of delta T is derived and is shown to result in increased efficiency.

Predicting skin sensitization potential and inter-laboratory reproducibility of a human Cell Line Activation Test (h-CLAT) in the European Cosmetics Association (COLIPA) ring trials.

PubMed

Sakaguchi, Hitoshi; Ryan, Cindy; Ovigne, Jean-Marc; Schroeder, Klaus R; Ashikaga, Takao

2010-09-01

Regulatory policies in Europe prohibited the testing of cosmetic ingredients in animals for a number of toxicological endpoints. Currently no validated non-animal test methods exist for skin sensitization. Evaluation of changes in cell surface marker expression in dendritic cell (DC)-surrogate cell lines represents one non-animal approach. The human Cell Line Activation Test (h-CLAT) examines the level of CD86 and CD54 expression on the surface of THP-1 cells, a human monocytic leukemia cell line, following 24h of chemical exposure. To examine protocol transferability, between-lab reproducibility, and predictive capacity, the h-CLAT has been evaluated by five independent laboratories in several ring trials (RTs) coordinated by the European Cosmetics Association (COLIPA). The results of the first and second RTs demonstrated that the protocol was transferable and basically had good between-lab reproducibility and predictivity, but there were some false negative data. To improve performance, protocol and prediction model were modified. Using the modified prediction model in the first and second RT, accuracy was improved. However, about 15% of the outcomes were not correctly identified, which exposes some of the limitations of the assay. For the chemicals evaluated, the limitation may due to chemical being a weak allergen or having low solubility (ex. alpha-hexylcinnamaldehyde). The third RT evaluated the modified prediction model and satisfactory results were obtained. From the RT data, the feasibility of utilizing cell lines as surrogate DC in development of in vitro skin sensitization methods shows promise. The data also support initiating formal pre-validation of the h-CLAT in order to fully understand the capabilities and limitations of the assay. Copyright 2010 Elsevier Ltd. All rights reserved.

LuAG:Pr3+-porphyrin based nanohybrid system for singlet oxygen production: Toward the next generation of PDTX drugs.

PubMed

Popovich, Kseniya; Tomanová, Kateřina; Čuba, Václav; Procházková, Lenka; Pelikánová, Iveta Terezie; Jakubec, Ivo; Mihóková, Eva; Nikl, Martin

2018-02-01

A highly prospective drug for the X-ray induced photodynamic therapy (PDTX), LuAG:Pr 3+ @SiO 2 -PpIX nanocomposite, was successfully prepared by a three step process: photo-induced precipitation of the Lu 3 Al 5 O 12 :Pr 3+ (LuAG:Pr 3+ ) core, sol-gel technique for amorphous silica coating, and a biofunctionalization by attaching the protoporphyrin IX (PpIX) molecules. The synthesis procedure provides three-layer nanocomposite with uniform shells covering an intensely luminescent core. Room temperature radioluminescence (RT RL) spectra as well as photoluminescence (RT PL) steady-state and time resolved spectra of the material confirm the non-radiative energy transfer from the core Pr 3+ ions to the PpIX outer layer. First, excitation of Pr 3+ ions results in the red luminescence of PpIX. Second, the decay measurements exhibit clear evidence of mentioned non-radiative energy transfer (ET). The singlet oxygen generation in the system was demonstrated by the 3'-(p-aminophenyl) fluorescein (APF) chemical probe sensitive to the singlet oxygen presence. The RT PL spectra of an X-ray irradiated material with the APF probe manifest the formation of singlet oxygen due to which enhanced luminescence around 530 nm is observed. Quenching studies, using NaN 3 as an 1 O 2 inhibitor, also confirm the presence of 1 O 2 in the system and rule out the parasitic reaction with OH radicals. To summarize, presented features of LuAG:Pr 3+ @SiO 2 -PpIX nanocomposite indicate its considerable potential for PDTX application. Copyright © 2018 Elsevier B.V. All rights reserved.

Shared acoustic codes underlie emotional communication in music and speech—Evidence from deep transfer learning

PubMed Central

Schuller, Björn

2017-01-01

Music and speech exhibit striking similarities in the communication of emotions in the acoustic domain, in such a way that the communication of specific emotions is achieved, at least to a certain extent, by means of shared acoustic patterns. From an Affective Sciences points of view, determining the degree of overlap between both domains is fundamental to understand the shared mechanisms underlying such phenomenon. From a Machine learning perspective, the overlap between acoustic codes for emotional expression in music and speech opens new possibilities to enlarge the amount of data available to develop music and speech emotion recognition systems. In this article, we investigate time-continuous predictions of emotion (Arousal and Valence) in music and speech, and the Transfer Learning between these domains. We establish a comparative framework including intra- (i.e., models trained and tested on the same modality, either music or speech) and cross-domain experiments (i.e., models trained in one modality and tested on the other). In the cross-domain context, we evaluated two strategies—the direct transfer between domains, and the contribution of Transfer Learning techniques (feature-representation-transfer based on Denoising Auto Encoders) for reducing the gap in the feature space distributions. Our results demonstrate an excellent cross-domain generalisation performance with and without feature representation transfer in both directions. In the case of music, cross-domain approaches outperformed intra-domain models for Valence estimation, whereas for Speech intra-domain models achieve the best performance. This is the first demonstration of shared acoustic codes for emotional expression in music and speech in the time-continuous domain. PMID:28658285

Shared acoustic codes underlie emotional communication in music and speech-Evidence from deep transfer learning.

PubMed

Coutinho, Eduardo; Schuller, Björn

2017-01-01

Music and speech exhibit striking similarities in the communication of emotions in the acoustic domain, in such a way that the communication of specific emotions is achieved, at least to a certain extent, by means of shared acoustic patterns. From an Affective Sciences points of view, determining the degree of overlap between both domains is fundamental to understand the shared mechanisms underlying such phenomenon. From a Machine learning perspective, the overlap between acoustic codes for emotional expression in music and speech opens new possibilities to enlarge the amount of data available to develop music and speech emotion recognition systems. In this article, we investigate time-continuous predictions of emotion (Arousal and Valence) in music and speech, and the Transfer Learning between these domains. We establish a comparative framework including intra- (i.e., models trained and tested on the same modality, either music or speech) and cross-domain experiments (i.e., models trained in one modality and tested on the other). In the cross-domain context, we evaluated two strategies-the direct transfer between domains, and the contribution of Transfer Learning techniques (feature-representation-transfer based on Denoising Auto Encoders) for reducing the gap in the feature space distributions. Our results demonstrate an excellent cross-domain generalisation performance with and without feature representation transfer in both directions. In the case of music, cross-domain approaches outperformed intra-domain models for Valence estimation, whereas for Speech intra-domain models achieve the best performance. This is the first demonstration of shared acoustic codes for emotional expression in music and speech in the time-continuous domain.

Transient PVT measurements and model predictions for vessel heat transfer. Part II.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Felver, Todd G.; Paradiso, Nicholas Joseph; Winters, William S., Jr.

2010-07-01

Part I of this report focused on the acquisition and presentation of transient PVT data sets that can be used to validate gas transfer models. Here in Part II we focus primarily on describing models and validating these models using the data sets. Our models are intended to describe the high speed transport of compressible gases in arbitrary arrangements of vessels, tubing, valving and flow branches. Our models fall into three categories: (1) network flow models in which flow paths are modeled as one-dimensional flow and vessels are modeled as single control volumes, (2) CFD (Computational Fluid Dynamics) models inmore » which flow in and between vessels is modeled in three dimensions and (3) coupled network/CFD models in which vessels are modeled using CFD and flows between vessels are modeled using a network flow code. In our work we utilized NETFLOW as our network flow code and FUEGO for our CFD code. Since network flow models lack three-dimensional resolution, correlations for heat transfer and tube frictional pressure drop are required to resolve important physics not being captured by the model. Here we describe how vessel heat transfer correlations were improved using the data and present direct model-data comparisons for all tests documented in Part I. Our results show that our network flow models have been substantially improved. The CFD modeling presented here describes the complex nature of vessel heat transfer and for the first time demonstrates that flow and heat transfer in vessels can be modeled directly without the need for correlations.« less

Kinetic: A system code for analyzing nuclear thermal propulsion rocket engine transients

NASA Astrophysics Data System (ADS)

Schmidt, Eldon; Lazareth, Otto; Ludewig, Hans

The topics are presented in viewgraph form and include the following: outline of kinetic code; a kinetic information flow diagram; kinetic neutronic equations; turbopump/nozzle algorithm; kinetic heat transfer equations per node; and test problem diagram.

3D-radiative transfer in terrestrial atmosphere: An efficient parallel numerical procedure

NASA Astrophysics Data System (ADS)

Bass, L. P.; Germogenova, T. A.; Nikolaeva, O. V.; Kokhanovsky, A. A.; Kuznetsov, V. S.

2003-04-01

Light propagation and scattering in terrestrial atmosphere is usually studied in the framework of the 1D radiative transfer theory [1]. However, in reality particles (e.g., ice crystals, solid and liquid aerosols, cloud droplets) are randomly distributed in 3D space. In particular, their concentrations vary both in vertical and horizontal directions. Therefore, 3D effects influence modern cloud and aerosol retrieval procedures, which are currently based on the 1D radiative transfer theory. It should be pointed out that the standard radiative transfer equation allows to study these more complex situations as well [2]. In recent year the parallel version of the 2D and 3D RADUGA code has been developed. This version is successfully used in gammas and neutrons transport problems [3]. Applications of this code to radiative transfer in atmosphere problems are contained in [4]. Possibilities of code RADUGA are presented in [5]. The RADUGA code system is an universal solver of radiative transfer problems for complicated models, including 2D and 3D aerosol and cloud fields with arbitrary scattering anisotropy, light absorption, inhomogeneous underlying surface and topography. Both delta type and distributed light sources can be accounted for in the framework of the algorithm developed. The accurate numerical procedure is based on the new discrete ordinate SWDD scheme [6]. The algorithm is specifically designed for parallel supercomputers. The version RADUGA 5.1(P) can run on MBC1000M [7] (768 processors with 10 Gb of hard disc memory for each processor). The peak productivity is equal 1 Tfl. Corresponding scalar version RADUGA 5.1 is working on PC. As a first example of application of the algorithm developed, we have studied the shadowing effects of clouds on neighboring cloudless atmosphere, depending on the cloud optical thickness, surface albedo, and illumination conditions. This is of importance for modern satellite aerosol retrieval algorithms development. [1] Sobolev, V. V., 1972: Light scattering in planetary atmosphere, M.:Nauka. [2] Evans, K. F., 1998: The spherical harmonic discrete ordinate method for three dimensional atmospheric radiative transfer, J. Atmos. Sci., 55, 429 446. [3] L.P. Bass, T.A. Germogenova, V.S. Kuznetsov, O.V. Nikolaeva. RADUGA 5.1 and RADUGA 5.1(P) codes for stationary transport equation solution in 2D and 3D geometries on one and multiprocessors computers. Report on seminar “Algorithms and Codes for neutron physical of nuclear reactor calculations” (Neutronica 2001), Obninsk, Russia, 30 October 2 November 2001. [4] T.A. Germogenova, L.P. Bass, V.S. Kuznetsov, O.V. Nikolaeva. Mathematical modeling on parallel computers solar and laser radiation transport in 3D atmosphere. Report on International Symposium CIS countries “Atmosphere radiation”, 18 21 June 2002, St. Peterburg, Russia, p. 15 16. [5] L.P. Bass, T.A. Germogenova, O.V. Nikolaeva, V.S. Kuznetsov. Radiative Transfer Universal 2D 3D Code RADUGA 5.1(P) for Multiprocessor Computer. Abstract. Poster report on this Meeting. [6] L.P. Bass, O.V. Nikolaeva. Correct calculation of Angular Flux Distribution in Strongly Heterogeneous Media and Voids. Proc. of Joint International Conference on Mathematical Methods and Supercomputing for Nuclear Applications, Saratoga Springs, New York, October 5 9, 1997, p. 995 1004. [7] http://www/jscc.ru

Optical, electrical, and magnetic field studies of organic materials for light emitting diodes and photovoltaic applications

NASA Astrophysics Data System (ADS)

Basel, Tek Prasad

We studied optical, electrical, and magnetic field responses of films and devices based on organic semiconductors that are used for organic light emitting diodes (OLEDs) and photovoltaic (OPV) solar cell applications. Our studies show that the hyperfine interaction (HFI)-mediated spin mixing is the key process underlying various magnetic field effects (MFE) and spin transport in aluminum tris(8-hydroxyquinoline)[Alq3]-based OLEDs and organic spin-valve (OSV). Conductivity-detected magnetic resonance in OLEDs and magneto-resistance (MR) in OSVs show substantial isotope dependence. In contrast, isotope-insensitive behavior in the magneto-conductance (MC) of same devices is explained by the collision of spin ½ carriers with triplet polaron pairs. We used steady state optical spectroscopy for studying the energy transfer dynamics in films and OLEDs based on host-guest blends of the fluorescent polymer and phosphorescent molecule. We have also studied the magnetic-field controlled color manipulation in these devices, which provide a strong proof for the `polaron-pair' mechanism underlying the MFE in organic devices. The critical issue that hampers organic spintronics device applications is significant magneto-electroluminescence (MEL) at room temperature (RT). Whereas inorganic spin valves (ISVs) show RT magneto-resistance, MR>80%, however, the devices do not exhibit electroluminescence (EL). In contrast, OLEDs show substantive EL emission, and are particularly attractive because of their flexibility, low cost, and potential for multicolor display. We report a conceptual novel hybrid organic/inorganic spintronics device (h-OLED), where we employ both ISV with large MR at RT, and OLED that has efficient EL emission. We investigated the charge transfer process in an OPV solar cell through optical, electrical, and magnetic field measurements of thin films and devices based on a low bandgap polymer, PTB7 (fluorinated poly-thienothiophene-benzodithiophene). We found that one of the major losses that limit the power conversion efficiency of OPV devices is the formation of triplet excitons in the polymer through recombination of charge-transfer (CT) excitons at the interface, and presented a method to suppress the dissociation of CT states by incorporating the spin ½ additive, galvinoxyl in the bulk heterojunction architecture of the active organic blend layer.

A Novel Iterative Scheme for the Very Fast and Accurate Solution of Non-LTE Radiative Transfer Problems

NASA Astrophysics Data System (ADS)

Trujillo Bueno, J.; Fabiani Bendicho, P.

1995-12-01

Iterative schemes based on Gauss-Seidel (G-S) and optimal successive over-relaxation (SOR) iteration are shown to provide a dramatic increase in the speed with which non-LTE radiation transfer (RT) problems can be solved. The convergence rates of these new RT methods are identical to those of upper triangular nonlocal approximate operator splitting techniques, but the computing time per iteration and the memory requirements are similar to those of a local operator splitting method. In addition to these properties, both methods are particularly suitable for multidimensional geometry, since they neither require the actual construction of nonlocal approximate operators nor the application of any matrix inversion procedure. Compared with the currently used Jacobi technique, which is based on the optimal local approximate operator (see Olson, Auer, & Buchler 1986), the G-S method presented here is faster by a factor 2. It gives excellent smoothing of the high-frequency error components, which makes it the iterative scheme of choice for multigrid radiative transfer. This G-S method can also be suitably combined with standard acceleration techniques to achieve even higher performance. Although the convergence rate of the optimal SOR scheme developed here for solving non-LTE RT problems is much higher than G-S, the computing time per iteration is also minimal, i.e., virtually identical to that of a local operator splitting method. While the conventional optimal local operator scheme provides the converged solution after a total CPU time (measured in arbitrary units) approximately equal to the number n of points per decade of optical depth, the time needed by this new method based on the optimal SOR iterations is only √n/2√2. This method is competitive with those that result from combining the above-mentioned Jacobi and G-S schemes with the best acceleration techniques. Contrary to what happens with the local operator splitting strategy currently in use, these novel methods remain effective even under extreme non-LTE conditions in very fine grids.

An Open-Source Bayesian Atmospheric Radiative Transfer (BART) Code, with Application to WASP-12b

NASA Astrophysics Data System (ADS)

Harrington, Joseph; Blecic, Jasmina; Cubillos, Patricio; Rojo, Patricio; Loredo, Thomas J.; Bowman, M. Oliver; Foster, Andrew S. D.; Stemm, Madison M.; Lust, Nate B.

2015-01-01

Atmospheric retrievals for solar-system planets typically fit, either with a minimizer or by eye, a synthetic spectrum to high-resolution (Δλ/λ ~ 1000-100,000) data with S/N > 100 per point. In contrast, exoplanet data often have S/N ~ 10 per point, and may have just a few points representing bandpasses larger than 1 um. To derive atmospheric constraints and robust parameter uncertainty estimates from such data requires a Bayesian approach. To date there are few investigators with the relevant codes, none of which are publicly available. We are therefore pleased to announce the open-source Bayesian Atmospheric Radiative Transfer (BART) code. BART uses a Bayesian phase-space explorer to drive a radiative-transfer model through the parameter phase space, producing the most robust estimates available for the thermal profile and chemical abundances in the atmosphere. We present an overview of the code and an initial application to Spitzer eclipse data for WASP-12b. We invite the community to use and improve BART via the open-source development site GitHub.com. This work was supported by NASA Planetary Atmospheres grant NNX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G. JB holds a NASA Earth and Space Science Fellowship.

An Open-Source Bayesian Atmospheric Radiative Transfer (BART) Code, and Application to WASP-12b

NASA Astrophysics Data System (ADS)

Harrington, Joseph; Blecic, Jasmina; Cubillos, Patricio; Rojo, Patricio M.; Loredo, Thomas J.; Bowman, Matthew O.; Foster, Andrew S.; Stemm, Madison M.; Lust, Nate B.

2014-11-01

Atmospheric retrievals for solar-system planets typically fit, either with a minimizer or by eye, a synthetic spectrum to high-resolution (Δλ/λ ~ 1000-100,000) data with S/N > 100 per point. In contrast, exoplanet data often have S/N ~ 10 per point, and may have just a few points representing bandpasses larger than 1 um. To derive atmospheric constraints and robust parameter uncertainty estimates from such data requires a Bayesian approach. To date there are few investigators with the relevant codes, none of which are publicly available. We are therefore pleased to announce the open-source Bayesian Atmospheric Radiative Transfer (BART) code. BART uses a Bayesian phase-space explorer to drive a radiative-transfer model through the parameter phase space, producing the most robust estimates available for the thermal profile and chemical abundances in the atmosphere. We present an overview of the code and an initial application to Spitzer eclipse data for WASP-12b. We invite the community to use and improve BART via the open-source development site GitHub.com. This work was supported by NASA Planetary Atmospheres grant NNX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G. JB holds a NASA Earth and Space Science Fellowship.

Simultaneous Semi-Distributed Model Calibration Guided by ...

EPA Pesticide Factsheets

Modelling approaches to transfer hydrologically-relevant information from locations with streamflow measurements to locations without such measurements continues to be an active field of research for hydrologists. The Pacific Northwest Hydrologic Landscapes (PNW HL) provide a solid conceptual classification framework based on our understanding of dominant processes. A Hydrologic Landscape code (5 letter descriptor based on physical and climatic properties) describes each assessment unit area, and these units average area 60km2. The core function of these HL codes is to relate and transfer hydrologically meaningful information between watersheds without the need for streamflow time series. We present a novel approach based on the HL framework to answer the question “How can we calibrate models across separate watersheds simultaneously, guided by our understanding of dominant processes?“. We should be able to apply the same parameterizations to assessment units of common HL codes if 1) the Hydrologic Landscapes contain hydrologic information transferable between watersheds at a sub-watershed-scale and 2) we use a conceptual hydrologic model and parameters that reflect the hydrologic behavior of a watershed. In this study, This work specifically tests the ability or inability to use HL-codes to inform and share model parameters across watersheds in the Pacific Northwest. EPA’s Western Ecology Division has published and is refining a framework for defining la

Biodegradation of paint stripper solvents in a modified gas lift loop bioreactor.

PubMed

Vanderberg-Twary, L; Steenhoudt, K; Travis, B J; Hanners, J L; Foreman, T M; Brainard, J R

1997-07-05

Paint stripping wastes generated during the decontamination and decommissioning of former nuclear facilities contain paint stripping organics (dichloromethane, 2-propanol, and methanol) and bulk materials containing paint pigments. It is desirable to degrade the organic residues as part of an integrated chemical-biological treatment system. We have developed a modified gas lift loop bioreactor employing a defined consortium of Rhodococcus rhodochrous strain OFS and Hyphomicrobium sp. DM-2 that degrades paint stripper organics. Mass transfer coefficients and kinetic constants for biodegradation in the system were determined. It was found that transfer of organic substrates from surrogate waste into the air and further into the liquid medium in the bioreactor were rapid processes, occurring within minutes. Monod kinetics was employed to model the biodegradation of paint stripping organics. Analysis of the bioreactor process was accomplished with BIOLAB, a mathematical code that simulates coupled mass transfer and biodegradation processes. This code was used to fit experimental data to Monod kinetics and to determine kinetic parameters. The BIOLAB code was also employed to compare activities in the bioreactor of individual microbial cultures to the activities of combined cultures in the bioreactor. This code is of benefit for further optimization and scale-up of the bioreactor for treatment of paint stripping and other volatile organic wastes in bulk materials.

Detection and partial molecular characterization of atypical plum pox virus isolates from naturally infected sour cherry.

PubMed

Chirkov, Sergei; Ivanov, Peter; Sheveleva, Anna

2013-06-01

Atypical isolates of plum pox virus (PPV) were discovered in naturally infected sour cherry in urban ornamental plantings in Moscow, Russia. The isolates were detected by polyclonal double antibody sandwich ELISA and RT-PCR using universal primers specific for the 3'-non-coding and coat protein (CP) regions of the genome but failed to be recognized by triple antibody sandwich ELISA with the universal monoclonal antibody 5B and by RT-PCR using primers specific to for PPV strains D, M, C and W. Sequence analysis of the CP genes of nine isolates revealed 99.2-100 % within-group identity and 62-85 % identity to conventional PPV strains. Phylogenetic analysis showed that the atypical isolates represent a group that is distinct from the known PPV strains. Alignment of the N-terminal amino acid sequences of CP demonstrated their close similarity to those of a new tentative PPV strain, CR.

Numerical investigation of roughness effects in aircraft icing calculations

NASA Astrophysics Data System (ADS)

Matheis, Brian Daniel

2008-10-01

Icing codes are playing a role of increasing significance in the design and certification of ice protected aircraft surfaces. However, in the interest of computational efficiency certain small scale physics of the icing problem are grossly approximated by the codes. One such small scale phenomena is the effect of ice roughness on the development of the surface water film and on the convective heat transfer. This study uses computational methods to study the potential effect of ice roughness on both of these small scale phenomena. First, a two-dimensional condensed layer code is used to examine the effect of roughness on surface water development. It is found that the Couette approximation within the film breaks down as the wall shear goes to zero, depending on the film thickness. Roughness elements with initial flow separation in the air induce flow separation in the water layer at steady state, causing a trapping of the film. The amount of trapping for different roughness configurations is examined. Second, a three-dimensional incompressible Navier-Stokes code is developed to examine large scale ice roughness on the leading edge. The effect on the convective heat transfer and potential effect on the surface water dynamics is examined for a number of distributed roughness parameters including Reynolds number, roughness height, streamwise extent, roughness spacing and roughness shape. In most cases the roughness field increases the net average convective heat transfer on the leading edge while narrowing surface shear lines, indicating a choking of the surface water flow. Both effects show significant variation on the scale of the ice roughness. Both the change in heat transfer as well as the potential change in surface water dynamics are presented in terms of the development of singularities in the surface shear pattern. Of particular interest is the effect of the smooth zone upstream of the roughness which shows both a relatively large increase in convective heat transfer as well as excessive choking of the surface shear lines at the upstream end of the roughness field. A summary of the heat transfer results is presented for both the averaged heat transfer as well as the maximum heat transfer over each roughness element, indicating that the roughness Reynolds number is the primary parameter which characterizes the behavior of the roughness for the problem of interest.

An Overview of Plume Tracker: Mapping Volcanic Emissions with Interactive Radiative Transfer Modeling

NASA Astrophysics Data System (ADS)

Realmuto, V. J.; Berk, A.; Guiang, C.

2014-12-01

Infrared remote sensing is a vital tool for the study of volcanic plumes, and radiative transfer (RT) modeling is required to derive quantitative estimation of the sulfur dioxide (SO2), sulfate aerosol (SO4), and silicate ash (pulverized rock) content of these plumes. In the thermal infrared, we must account for the temperature, emissivity, and elevation of the surface beneath the plume, plume altitude and thickness, and local atmospheric temperature and humidity. Our knowledge of these parameters is never perfect, and interactive mapping allows us to evaluate the impact of these uncertainties on our estimates of plume composition. To enable interactive mapping, the Jet Propulsion Laboratory is collaborating with Spectral Sciences, Inc., (SSI) to develop the Plume Tracker toolkit. This project is funded by a NASA AIST Program Grant (AIST-11-0053) to SSI. Plume Tracker integrates (1) retrieval procedures for surface temperature and emissivity, SO2, NH3, or CH4 column abundance, and scaling factors for H2O vapor and O3 profiles, (2) a RT modeling engine based on MODTRAN, and (3) interactive visualization and analysis utilities under a single graphics user interface. The principal obstacle to interactive mapping is the computational overhead of the RT modeling engine. Under AIST-11-0053 we have achieved a 300-fold increase in the performance of the retrieval procedures through the use of indexed caches of model spectra, optimization of the minimization procedures, and scaling of the effects of surface temperature and emissivity on model radiance spectra. In the final year of AIST-11-0053 we will implement parallel processing to exploit multi-core CPUs and cluster computing, and optimize the RT engine to eliminate redundant calculations when iterating over a range of gas concentrations. These enhancements will result in an additional 8 - 12X increase in performance. In addition to the improvements in performance, we have improved the accuracy of the Plume Tracker retrievals through refinements in the description of surface emissivity and use of vector projection to define the misfit between model and observed spectra. Portions of this research were conducted at the Jet Propulsion Laboratory, California Institute of Technology, under contract to the National Aeronautics and Space Administration.

Transcriptome interrogation of human myometrium identifies differentially expressed sense-antisense pairs of protein-coding and long non-coding RNA genes in spontaneous labor at term.

PubMed

Romero, Roberto; Tarca, Adi L; Chaemsaithong, Piya; Miranda, Jezid; Chaiworapongsa, Tinnakorn; Jia, Hui; Hassan, Sonia S; Kalita, Cynthia A; Cai, Juan; Yeo, Lami; Lipovich, Leonard

2014-09-01

To identify differentially expressed long non-coding RNA (lncRNA) genes in human myometrium in women with spontaneous labor at term. Myometrium was obtained from women undergoing cesarean deliveries who were not in labor (n = 19) and women in spontaneous labor at term (n = 20). RNA was extracted and profiled using an Illumina® microarray platform. We have used computational approaches to bound the extent of long non-coding RNA representation on this platform, and to identify co-differentially expressed and correlated pairs of long non-coding RNA genes and protein-coding genes sharing the same genomic loci. We identified co-differential expression and correlation at two genomic loci that contain coding-lncRNA gene pairs: SOCS2-AK054607 and LMCD1-NR_024065 in women in spontaneous labor at term. This co-differential expression and correlation was validated by qRT-PCR, an experimental method completely independent of the microarray analysis. Intriguingly, one of the two lncRNA genes differentially expressed in term labor had a key genomic structure element, a splice site, that lacked evolutionary conservation beyond primates. We provide, for the first time, evidence for coordinated differential expression and correlation of cis-encoded antisense lncRNAs and protein-coding genes with known as well as novel roles in pregnancy in the myometrium of women in spontaneous labor at term.

Validation of Heat Transfer and Film Cooling Capabilities of the 3-D RANS Code TURBO

NASA Technical Reports Server (NTRS)

Shyam, Vikram; Ameri, Ali; Chen, Jen-Ping

2010-01-01

The capabilities of the 3-D unsteady RANS code TURBO have been extended to include heat transfer and film cooling applications. The results of simulations performed with the modified code are compared to experiment and to theory, where applicable. Wilcox s k-turbulence model has been implemented to close the RANS equations. Two simulations are conducted: (1) flow over a flat plate and (2) flow over an adiabatic flat plate cooled by one hole inclined at 35 to the free stream. For (1) agreement with theory is found to be excellent for heat transfer, represented by local Nusselt number, and quite good for momentum, as represented by the local skin friction coefficient. This report compares the local skin friction coefficients and Nusselt numbers on a flat plate obtained using Wilcox's k-model with the theory of Blasius. The study looks at laminar and turbulent flows over an adiabatic flat plate and over an isothermal flat plate for two different wall temperatures. It is shown that TURBO is able to accurately predict heat transfer on a flat plate. For (2) TURBO shows good qualitative agreement with film cooling experiments performed on a flat plate with one cooling hole. Quantitatively, film effectiveness is under predicted downstream of the hole.

Optimization of lightweight structure and supporting bipod flexure for a space mirror.

PubMed

Chen, Yi-Cheng; Huang, Bo-Kai; You, Zhen-Ting; Chan, Chia-Yen; Huang, Ting-Ming

2016-12-20

This article presents an optimization process for integrated optomechanical design. The proposed optimization process for integrated optomechanical design comprises computer-aided drafting, finite element analysis (FEA), optomechanical transfer codes, and an optimization solver. The FEA was conducted to determine mirror surface deformation; then, deformed surface nodal data were transferred into Zernike polynomials through MATLAB optomechanical transfer codes to calculate the resulting optical path difference (OPD) and optical aberrations. To achieve an optimum design, the optimization iterations of the FEA, optomechanical transfer codes, and optimization solver were automatically connected through a self-developed Tcl script. Two examples of optimization design were illustrated in this research, namely, an optimum lightweight design of a Zerodur primary mirror with an outer diameter of 566 mm that is used in a spaceborne telescope and an optimum bipod flexure design that supports the optimum lightweight primary mirror. Finally, optimum designs were successfully accomplished in both examples, achieving a minimum peak-to-valley (PV) value for the OPD of the deformed optical surface. The simulated optimization results showed that (1) the lightweight ratio of the primary mirror increased from 56% to 66%; and (2) the PV value of the mirror supported by optimum bipod flexures in the horizontal position effectively decreased from 228 to 61 nm.

Understanding Stellar Light Spatial Inhomogeneities and Time Variability

NASA Technical Reports Server (NTRS)

Uitenbroek, Han; Sasselov, Dimitar D.

2000-01-01

We would like the opportunity to thank NASA for supporting our efforts to construct tools to analyze the spectra of spatially inhomogeneous and temporally varying stellar atmospheres. This financial support has allowed us to a versatile radiative transfer code that can be used for many different applications. With this numerical code we have written a point-and-click analysis package written in IDL that can be used to look extensively at the generated output data. Below we describe the most recent results obtained with our transfer code and list papers that have appeared with these results. Although we have not been able to produce as many time-dependent calculations as we had hoped (mainly because of programmatic reasons; Sasselov took another position halfway through the grant), we believe we have

Interfacing a General Purpose Fluid Network Flow Program with the SINDA/G Thermal Analysis Program

NASA Technical Reports Server (NTRS)

Schallhorn, Paul; Popok, Daniel

1999-01-01

A general purpose, one dimensional fluid flow code is currently being interfaced with the thermal analysis program Systems Improved Numerical Differencing Analyzer/Gaski (SINDA/G). The flow code, Generalized Fluid System Simulation Program (GFSSP), is capable of analyzing steady state and transient flow in a complex network. The flow code is capable of modeling several physical phenomena including compressibility effects, phase changes, body forces (such as gravity and centrifugal) and mixture thermodynamics for multiple species. The addition of GFSSP to SINDA/G provides a significant improvement in convective heat transfer modeling for SINDA/G. The interface development is conducted in multiple phases. This paper describes the first phase of the interface which allows for steady and quasi-steady (unsteady solid, steady fluid) conjugate heat transfer modeling.

Ozone retrievals from MAGEAQ GEO TIR+VIS for air quality

NASA Astrophysics Data System (ADS)

Quesada-Ruiz, Samuel; Attié, Jean-Luc; Lahoz, William A.; Abida, Rachid; El-Amraoui, Laaziz; Ricaud, Philippe; Zbinden, Regina; Spurr, Robert; da Silva, Arlindo M.

2016-04-01

Nowadays, air quality monitoring is based on the use of ground-based stations (GBS) or satellite measurements. GBS provide accurate measurements of pollutant concentrations, especially in the planetary boundary layer (PBL), but usually the spatial coverage is sparse. Polar-orbiting satellites provide good spatial resolution but low temporal coverage -this is insufficient for tracking pollutants exhibiting a diurnal cycle (Lahoz et al., 2012). However, pollutant concentrations can be measured by instruments placed on board a geostationary satellite, which can provide sufficiently high temporal and spatial resolutions (e.g. Hache et al., 2014). In this work, we investigate the potentiality of a possible future geostationary instrument, MAGEAQ (Monitoring the Atmosphere from Geostationary orbit for European Air Quality), for retrieving ozone measurements over Europe. In particular, MAGEAQ can provide 1-hour temporal sampling at 10x10km pixel resolution for measurements in both visible (VIS) and thermal infrared (TIR) bands -thus, we will be able to measure during the day and at night. MAGEAQ synthetic radiance observations are obtained through radiative transfer (RT) simulations using the VLIDORT discrete ordinate RT model (Spurr, 2006) based on output from the GEOS-5 Nature Run (Gelaro et al., 2015) providing optical information, plus a suitable instrument model. Ozone is retrieved from these synthetic measurements using the optimal estimation inversion scheme of Levenberg-Marquardt. Finally, we examine an application of the air quality concept based on these ozone retrievals during the heatwave event of July 2006 over Europe. REFERENCES Gelaro, R., Putman, W. M., Pawson, S., Draper, C., Molod, A., Norris, P. M., Ott, L., Privé, N., Reale, O., Achuthavarier, D., Bosilovich, M., Buchard, V., Chao, W., Coy, L., Cullather, R., da Silva, A., Darmenov, A., Errico, R. M., Fuentes, M., Kim, M-J., Koster, R., McCarty, W., Nattala, J., Partyka, G., Schubert, S., Vernieres, G., Vikhliaev, Y., and Wargan, K.. Evaluation of the 7-km GEOS-5 Nature Run. NASA/TM-2014-104606, Vol. 36., 2015. Hache, E., Attié, J.L., Tourneur, C., Ricaud, P., Coret, L., Lahoz, W.A., El Amraoui, L., Josse, B., Hamer, P., Warner, J., Liu, X., Chance, K., Höpfner, M., Spurr, R., Natraj, V., Kulawik, S., Eldering, A. and Orphal, J.. The added value of a visible channel to a geostationary thermal infrared instrument to monitor ozone for air quality. Atmos. Meas. Tech., 7, 2185-2201, 2014. Lahoz, W. A., Peuch, V. H., Orphal, J., Attie, J.L., Chance, K., Liu, X., Edwards, D., Elbern, H., Flaud, J. M., Claeyman, M., and El Amraoui, L.. Monitoring Air Quality from Space: The Case for the Geostationay Platform. Bulletin of the American Meteorological Society, 93, 221-233, 2012. Spurr, R. J. D.. VLIDORT: A Linearized Pseudo-Spherical Vector Discrete Ordinate Radiative Transfer Code for Forward Model and Retrieval Studies in Multilayer Multiple Scattering Media. Journal of Quantitative Spectroscopy & Radiative Transfer, 102, 316-342, 2006.

Effective Bayesian Transfer Learning

DTIC Science & Technology

2010-03-01

reasonable value of k , defined by the task B training set size. Transfer Regret 1 Regret = 100 * G AB B No Transfer With Transfer AB...a. REPORT U b . ABSTRACT U c. THIS PAGE U 19b. TELEPHONE NUMBER (Include area code) N/A Standard Form 298 (Rev. 8-98) Prescribed...rule set given the prior and developed staged approximate inference strategy, in which data from observed tasks 1 to k are used to infer general rule

Tert-butylalumoxanes: Synthetic Analogs for Methylalumoxane (MAO) and New Catalytic Routes to Polyolefins and Polyketones

DTIC Science & Technology

1994-06-15

91-J-1934 R&T Code 4132060 Tert-butylalumoxanes: synthetic analogs for methylalumoxane (MAO) and new catalytic routes to polyolef’ms and polyketones ...and Principal Investigator: new catalytic routes to polyolefins and polyketones A. R. Barron Mailing Address: Dept. of.Chemistry Harvard University...catalyst complex,[CP2Zr(Me)] [(t~u)6,Al6(O)6(Me)]. Our studies with Pd/alumoxane polyketone synthesis have now demonstrated that high molecular weight

Charge-Coupled Devices for Analog Signal Processing -- A Circuit Study

DTIC Science & Technology

1976-03-01

FNG( T+H/2) ) /H (X2»Y3»Z2) 1*2*K2-^2*K3*’ɜ) /o.3 ECK TO SEE IF IT’S TIME TO PRINT OUT. SGN(L)*1.’.5E-9>=i^«𔃽 THEN 1120 80 ^^^^ LEI rt=b 113^ LEI a...DISTRIBUTION LIST No. Copies 1. Defense Docmnentation Center 2 Cameron Station Alexandria, Virginia 22314 2. Library, Code 0212 2 Naval Postgraduate School

Trapped Electron Model 2 (TEM-2)

DTIC Science & Technology

2010-04-25

density and computes sample correlations : 9t = ft-{ft)T, («6) £T = (stsf)T, («7) RT = {9t9j+i)r- (88) We have made the very safe...such as solar wind correlation studies, initial and boundary conditions for numerical simulations, and principal component analysis. We...O’Brien 19b. TELEPHONE NUMBER (include area code ) 571-307-3978 Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std. 239.18 Ackmowledgments This work

Incorporating Non-Linear Sorption into High Fidelity Subsurface Reactive Transport Models

NASA Astrophysics Data System (ADS)

Matott, L. S.; Rabideau, A. J.; Allen-King, R. M.

2014-12-01

A variety of studies, including multiple NRC (National Research Council) reports, have stressed the need for simulation models that can provide realistic predictions of contaminant behavior during the groundwater remediation process, most recently highlighting the specific technical challenges of "back diffusion and desorption in plume models". For a typically-sized remediation site, a minimum of about 70 million grid cells are required to achieve desired cm-level thickness among low-permeability lenses responsible for driving the back-diffusion phenomena. Such discretization is nearly three orders of magnitude more than is typically seen in modeling practice using public domain codes like RT3D (Reactive Transport in Three Dimensions). Consequently, various extensions have been made to the RT3D code to support efficient modeling of recently proposed dual-mode non-linear sorption processes (e.g. Polanyi with linear partitioning) at high-fidelity scales of grid resolution. These extensions have facilitated development of exploratory models in which contaminants are introduced into an aquifer via an extended multi-decade "release period" and allowed to migrate under natural conditions for centuries. These realistic simulations of contaminant loading and migration provide high fidelity representation of the underlying diffusion and sorption processes that control remediation. Coupling such models with decision support processes is expected to facilitate improved long-term management of complex remediation sites that have proven intractable to conventional remediation strategies.

[Construction of the superantigen SEA transfected laryngocarcinoma cells].

PubMed

Ji, Xiaobin; Jingli, J V; Liu, Qicai; Xie, Jinghua

2013-04-01

To construct an eukaryotic expression vectors containing superantigen staphylococcal enterotoxin A (SEA) gene, and to identify its expression in laryngeal squamous carcinoma cells. SEA full-length gene fragment was obtained from ATCC13565 genome of the staphylococcus, referencing standard strains producing SEA. Coding sequence of SEA was artificially synthetized. Than, SEA gene fragments was subcloned into eukaryotic expression vector pIRES-EGFP. The recombinant plasmid pSEA-IRES-EGFP was constructed and was transfected to laryngocarcinoma Hep-2 cells. Resistant clones were screened by G418. The expression of SEA in laryngocarcinoma cells was identified with ELISA and RT-PCR method. The subclone of artificially synthetized SEA gene was subclone to eukaryotic expression vector pires-EGFP. Flanking sequence confirmed that SEA sequence was fully identical to the coding sequence of standard staphylococcus strains ATCC13565 in Genbank. After recombinant plasmid transfected to laryngocarcinoma cells, the resistant clones was obtained after screening for two weeks. The clones were selected. The specific gene fragment was obtained by RT-PCR amplification. ELISA assay confirmed that the content of SEA protein in supernatant fluid of cell culture had reached about Pg level. The recombinant eukaryotic expression vector containing superantigen SEA gene is successfully constructed, and is capable of effective expression and continued secretion of SEA protein in laryngochrcinoma Hep-2 cells after recombinant plasmid transfected to laryngocarcinoma cells.

Comparing Split and Unsplit Numerical Methods for Simulating Low and High Mach Number Turbulent Flows in Xrage

NASA Astrophysics Data System (ADS)

Saenz, Juan; Grinstein, Fernando; Dolence, Joshua; Rauenzahn, Rick; Masser, Thomas; Francois, Marianne; LANL Team

2017-11-01

We report progress in evaluating an unsplit hydrodynamic solver being implemented in the radiation adaptive grid Eulerian (xRAGE) code, and compare to a split scheme. xRage is a Eulerian hydrodynamics code used for implicit large eddy simulations (ILES) of multi-material, multi-physics flows where low and high Mach number (Ma) processes and instabilities interact and co-exist. The hydrodynamic solver in xRAGE uses a directionally split, second order Godunov, finite volume (FV) scheme. However, a standard, unsplit, Godunov-type FV scheme with 2nd and 3rd order reconstruction options, low Ma correction and a variety of Riemann solvers has recently become available. To evaluate the hydrodynamic solvers for turbulent low Ma flows, we use simulations of the Taylor Green Vortex (TGV), where there is a transition to turbulence via vortex stretching and production of small-scale eddies. We also simulate a high-low Ma shock-tube flow, where a shock passing over a perturbed surface generates a baroclinic Richtmyer-Meshkov instability (RMI); after the shock has passed, the turbulence in the accelerated interface region resembles Rayleigh Taylor (RT) instability. We compare turbulence spectra and decay in simulated TGV flows, and we present progress in simulating the high-low Ma RMI-RT flow. LANL is operated by LANS LLC for the U.S. DOE NNSA under Contract No. DE-AC52-06NA25396.

RELAP5 Model of the First Wall/Blanket Primary Heat Transfer System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Popov, Emilian L; Yoder Jr, Graydon L; Kim, Seokho H

2010-06-01

ITER inductive power operation is modeled and simulated using a system level computer code to evaluate the behavior of the Primary Heat Transfer System (PHTS) and predict parameter operational ranges. The control algorithm strategy and derivation are summarized in this report as well. A major feature of ITER is pulsed operation. The plasma does not burn continuously, but the power is pulsed with large periods of zero power between pulses. This feature requires active temperature control to maintain a constant blanket inlet temperature and requires accommodation of coolant thermal expansion during the pulse. In view of the transient nature ofmore » the power (plasma) operation state a transient system thermal-hydraulics code was selected: RELAP5. The code has a well-documented history for nuclear reactor transient analyses, it has been benchmarked against numerous experiments, and a large user database of commonly accepted modeling practices exists. The process of heat deposition and transfer in the blanket modules is multi-dimensional and cannot be accurately captured by a one-dimensional code such as RELAP5. To resolve this, a separate CFD calculation of blanket thermal power evolution was performed using the 3-D SC/Tetra thermofluid code. A 1D-3D co-simulation more realistically models FW/blanket internal time-dependent thermal inertia while eliminating uncertainties in the time constant assumed in a 1-D system code. Blanket water outlet temperature and heat release histories for any given ITER pulse operation scenario are calculated. These results provide the basis for developing time dependent power forcing functions which are used as input in the RELAP5 calculations.« less

HT-FRTC: a fast radiative transfer code using kernel regression

NASA Astrophysics Data System (ADS)

Thelen, Jean-Claude; Havemann, Stephan; Lewis, Warren

2016-09-01

The HT-FRTC is a principal component based fast radiative transfer code that can be used across the electromagnetic spectrum from the microwave through to the ultraviolet to calculate transmittance, radiance and flux spectra. The principal components cover the spectrum at a very high spectral resolution, which allows very fast line-by-line, hyperspectral and broadband simulations for satellite-based, airborne and ground-based sensors. The principal components are derived during a code training phase from line-by-line simulations for a diverse set of atmosphere and surface conditions. The derived principal components are sensor independent, i.e. no extra training is required to include additional sensors. During the training phase we also derive the predictors which are required by the fast radiative transfer code to determine the principal component scores from the monochromatic radiances (or fluxes, transmittances). These predictors are calculated for each training profile at a small number of frequencies, which are selected by a k-means cluster algorithm during the training phase. Until recently the predictors were calculated using a linear regression. However, during a recent rewrite of the code the linear regression was replaced by a Gaussian Process (GP) regression which resulted in a significant increase in accuracy when compared to the linear regression. The HT-FRTC has been trained with a large variety of gases, surface properties and scatterers. Rayleigh scattering as well as scattering by frozen/liquid clouds, hydrometeors and aerosols have all been included. The scattering phase function can be fully accounted for by an integrated line-by-line version of the Edwards-Slingo spherical harmonics radiation code or approximately by a modification to the extinction (Chou scaling).

Implementation of a Blowing Boundary Condition in the LAURA Code

NASA Technical Reports Server (NTRS)

Thompson, Richard a.; Gnoffo, Peter A.

2008-01-01

Preliminary steps toward modeling a coupled ablation problem using a finite-volume Navier-Stokes code (LAURA) are presented in this paper. Implementation of a surface boundary condition with mass transfer (blowing) is described followed by verification and validation through comparisons with analytic results and experimental data. Application of the code to a carbon-nosetip ablation problem is demonstrated and the results are compared with previously published data. It is concluded that the code and coupled procedure are suitable to support further ablation analyses and studies.

Simplified diagnostic coding sheet for computerized data storage and analysis in ophthalmology.

PubMed

Tauber, J; Lahav, M

1987-11-01

A review of currently-available diagnostic coding systems revealed that most are either too abbreviated or too detailed. We have compiled a simplified diagnostic coding sheet based on the International Coding and Diagnosis (ICD-9), which is both complete and easy to use in a general practice. The information is transferred to a computer, which uses the relevant (ICD-9) diagnoses as database and can be retrieved later for display of patients' problems or analysis of clinical data.

High-precision two-way optic-fiber time transfer using an improved time code.

PubMed

Wu, Guiling; Hu, Liang; Zhang, Hao; Chen, Jianping

2014-11-01

We present a novel high-precision two-way optic-fiber time transfer scheme. The Inter-Range Instrumentation Group (IRIG-B) time code is modified by increasing bit rate and defining new fields. The modified time code can be transmitted directly using commercial optical transceivers and is able to efficiently suppress the effect of the Rayleigh backscattering in the optical fiber. A dedicated codec (encoder and decoder) with low delay fluctuation is developed. The synchronization issue is addressed by adopting a mask technique and combinational logic circuit. Its delay fluctuation is less than 27 ps in terms of the standard deviation. The two-way optic-fiber time transfer using the improved codec scheme is verified experimentally over 2 m to100 km fiber links. The results show that the stability over 100 km fiber link is always less than 35 ps with the minimum value of about 2 ps at the averaging time around 1000 s. The uncertainty of time difference induced by the chromatic dispersion over 100 km is less than 22 ps.

Radiation Coupling with the FUN3D Unstructured-Grid CFD Code

NASA Technical Reports Server (NTRS)

Wood, William A.

2012-01-01

The HARA radiation code is fully-coupled to the FUN3D unstructured-grid CFD code for the purpose of simulating high-energy hypersonic flows. The radiation energy source terms and surface heat transfer, under the tangent slab approximation, are included within the fluid dynamic ow solver. The Fire II flight test, at the Mach-31 1643-second trajectory point, is used as a demonstration case. Comparisons are made with an existing structured-grid capability, the LAURA/HARA coupling. The radiative surface heat transfer rates from the present approach match the benchmark values within 6%. Although radiation coupling is the focus of the present work, convective surface heat transfer rates are also reported, and are seen to vary depending upon the choice of mesh connectivity and FUN3D ux reconstruction algorithm. On a tetrahedral-element mesh the convective heating matches the benchmark at the stagnation point, but under-predicts by 15% on the Fire II shoulder. Conversely, on a mixed-element mesh the convective heating over-predicts at the stagnation point by 20%, but matches the benchmark away from the stagnation region.

Interfacing the Generalized Fluid System Simulation Program with the SINDA/G Thermal Program

NASA Technical Reports Server (NTRS)

Schallhorn, Paul; Palmiter, Christopher; Farmer, Jeffery; Lycans, Randall; Tiller, Bruce

2000-01-01

A general purpose, one dimensional fluid flow code has been interfaced with the thermal analysis program SINDA/G. The flow code, GFSSP, is capable of analyzing steady state and transient flow in a complex network. The flow code is capable of modeling several physical phenomena including compressibility effects, phase changes, body forces (such as gravity and centrifugal) and mixture thermodynamics for multiple species. The addition of GFSSP to SINDA/G provides a significant improvement in convective heat transfer modeling for SINDA/G. The interface development was conducted in two phases. This paper describes the first (which allows for steady and quasi-steady - unsteady solid, steady fluid - conjugate heat transfer modeling). The second (full transient conjugate heat transfer modeling) phase of the interface development will be addressed in a later paper. Phase 1 development has been benchmarked to an analytical solution with excellent agreement. Additional test cases for each development phase demonstrate desired features of the interface. The results of the benchmark case, three additional test cases and a practical application are presented herein.

Computing Temperatures in Optically Thick Protoplanetary Disks

NASA Technical Reports Server (NTRS)

Capuder, Lawrence F.. Jr.

2011-01-01

We worked with a Monte Carlo radiative transfer code to simulate the transfer of energy through protoplanetary disks, where planet formation occurs. The code tracks photons from the star into the disk, through scattering, absorption and re-emission, until they escape to infinity. High optical depths in the disk interior dominate the computation time because it takes the photon packet many interactions to get out of the region. High optical depths also receive few photons and therefore do not have well-estimated temperatures. We applied a modified random walk (MRW) approximation for treating high optical depths and to speed up the Monte Carlo calculations. The MRW is implemented by calculating the average number of interactions the photon packet will undergo in diffusing within a single cell of the spatial grid and then updating the packet position, packet frequencies, and local radiation absorption rate appropriately. The MRW approximation was then tested for accuracy and speed compared to the original code. We determined that MRW provides accurate answers to Monte Carlo Radiative transfer simulations. The speed gained from using MRW is shown to be proportional to the disk mass.

Real Time Polymerase Chain Reaction (rt-PCR): A New Patent to Diagnostic Purposes for Paracoccidioidomycosis.

PubMed

Rocha-Silva, Fabiana; Gomes, Luciana I; Gracielle-Melo, Cidiane; Goes, Alfredo M; Caligiorne, Rachel B

2017-01-01

Paracoccidioidomycosis (PCM) is a systemic mycosis caused by dimorphic fungi Paracoccidioides brasiliensis and Paracoccidioides lutzii. It is prevalent in Latin American, mainly in Brazil. Therefore, PCM has fundamental impact on the Brazilian global economy, especially in public health system, since it is affecting economical active population in different country regions. The present study aimed to standardize the Real Time-Polymerase Chain Reaction (rt-PCR) for an efficient and safe PCM diagnosis amplifying the recombinant protein PB27 gene, only expressed by specimens of Paracoccidioides genus. To standardize a methodology of rt-PCR using species-specific primers and probe designed for annealing in this specific region of the fungi´s genome, amplifying the recombinant protein PB27 gene, only expressed by specimens of Paracoccidioides genus. Followed by design in silico, experiments were performed in vitro to determine rt-PCR specificity, efficiency and genome detection limit. The primers and probe sequences were deposited in Brazilian Coordination of Technological Innovation and Transfer (CTIT), under patent reference number BR1020160078830. The present study demonstrated the rt-PCR applicability for support on diagnosis of paracoccidioidomycosis, presenting low cost, which makes it affordable for public health services in developing countries as Brazil. It is noteworthy that it is necessary to validate this methodology using clinical samples before to use as a safe method of diagnosis. A review of all patents related to this topic was performed and it was shown that, to date, there are no records of patent on kits for paracoccidioidomycosis´s diagnostic. Indeed, there is still a lot to go to reach this goal. The reaction developed was standardized and patented, opening perspectives to molecular diagnosis development for paracoccidioidomycosis, since rt-PCR can be applied to a broad spectrum of infectious diseases. It would need to be tested in biological samples in order to validate this method and then generate a diagnostic kit for Paracoccidioidomycosis. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Site-specific crosslinking of 4-thiouridine-modified human tRNA(3Lys) to reverse transcriptase from human immunodeficiency virus type I.

PubMed Central

Mishima, Y; Steitz, J A

1995-01-01

We have mapped specific RNA-protein contacts between human immunodeficiency virus (HIV) type I reverse transcriptase (RT) and its natural primer, human tRNA(3Lys), using a site-specific crosslinking strategy. Four different tRNA(3Lys) constructs with a single 32P-labeled 4-thiouridine (4-thioU) residue at positions -1, 16, 36 or 41 were synthesized. After incubation with RT followed by irradiation, crosslinks were localized to either the p66 or p51 subunit of RT by digestion with nuclease and SDS gel fractionation. 4-thioU at position -1 or 16 transferred label to the p66 subunit almost exclusively (> 90%), whereas position 36 labeled both p66 and p51 (3:1). Position 41 yielded no detectable crosslinks. The region of p66 contacted by position -1 of tRNA(3Lys) was localized to the 203 C-terminal amino acids of RT by CNBr cleavage, whereas a 127 amino acid-CNBr peptide (residues 230-357) from both p66 and p51 was labeled by position 36. Functionality of the 4-thioU-modified tRNA(3Lys)(-1) crosslinked to RT in the presence of an RNA but not a DNA template was demonstrated by the ability of the tRNA to be extended. These results localize the 5' half of the tRNA on the interface between the two RT subunits, closer to the RNase H domain than to the polymerase active site, in accord with previous suggestions. They argue further that a specific binding site for the 5' end of the primer tRNA(3Lys) may exist within the C-terminal portion of the p66 subunit, which could be important for the initiation of reverse transcription. Images PMID:7540137

TH-E-BRF-10: Interim Esophageal Cancer Response Assessment Via 18FDG-PET Scanning During Radiation Therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Higgins, K; Wu, Q; Perez, B

2014-06-15

Purpose: Local failure occurs in a large proportion of esophageal cancer patients treated with chemoradiation. The treatment strategy for non-responders could potentially be modified if they are identified during therapy. This work investigates the utility of an interim 18FDG-PET scan acquired during the course of therapy as a predictor of pathological response post-therapy. Methods: Fifteen patients underwent 18FDG-PET scanning prior to radiation therapy (RT) and once during RT, after delivery of ∼32 Gy. The physician-contoured GTV on the planning CT scan was used to automatically segment a PET-based GTV on the pre-RT PET (GTV-pre-PET) as the volume with >40% ofmore » the maximum GTV PET SUV value. The pre- and intra-RT CTs were deformably registered to each other to transfer the GTV-pre-PET to the intra-RT PET (GTV-intra-PET). The fractional decrease in the maximum SUV, mean SUV and the SUV to the highest intensity 10% – 90% volumes from GTV-pre-PET to GTV-intra-PET were compared to pathological response assessed at the time of post-RT surgery. Results: Based on post-treatment pathology of 15 patients, 7 were classified as achieving favorable response (treatment effect grade ≤ 1) and 8 as unfavorable response (treatment effect grade > 1). Neither fractional decrease in maximum SUV nor mean SUV were significant between the favorable and unfavorable groups. However, the fractional decrease in SUV20% (SUV to the highest 20% volume) was significant (p = 0.02), with an area under the Receiver Operating Characteristics (ROC) curve of 0.84. An optimal cutoff value of 0.46 for this metric was able to distinguish between the two groups with 71% sensitivity (favorable) and 88% specificity (unfavorable). Conclusion: The fractional decrease in SUV to the volume with highest 20% intensity from pre- to intra-RT 18FDG-PET imaging may be used to distinguish between favorable and unfavorable responders with high sensitivity and specificity.« less

Py4CAtS - Python tools for line-by-line modelling of infrared atmospheric radiative transfer

NASA Astrophysics Data System (ADS)

Schreier, Franz; García, Sebastián Gimeno

2013-05-01

Py4CAtS — Python scripts for Computational ATmospheric Spectroscopy is a Python re-implementation of the Fortran infrared radiative transfer code GARLIC, where compute-intensive code sections utilize the Numeric/Scientific Python modules for highly optimized array-processing. The individual steps of an infrared or microwave radiative transfer computation are implemented in separate scripts to extract lines of relevant molecules in the spectral range of interest, to compute line-by-line cross sections for given pressure(s) and temperature(s), to combine cross sections to absorption coefficients and optical depths, and to integrate along the line-of-sight to transmission and radiance/intensity. The basic design of the package, numerical and computational aspects relevant for optimization, and a sketch of the typical workflow are presented.

Long non-coding RNA ZEB1-AS1 is associated with poor prognosis in gastric cancer and promotes cancer cell metastasis.

PubMed

Liu, X-J; Li, S-L; Li, J-S; Lu, H; Yin, L-L; Zheng, W-F; Wang, W-C

2018-05-01

To investigate the expression of long non-coding RNA zinc-finger E-box binding homeobox 1-AS1 (lncRNA ZEB1-AS1) in gastric cancer cells and tissues, to study its effect on the gastric cancer cell metastasis capacity, and analyze its clinical significance. The relative expression level of lncRNA ZEB1-AS1 in gastric cancer cells was detected via quantitative reverse transcription polymerase chain reaction (qRT-PCR). Transwell assay was used to detect the effects of lncRNA ZEB1-AS1 on the invasion and metastasis capacities of gastric cancer cells. qRT-PCR was used to detect the relative expression level of lncRNA ZEB1-AS1 in 75 pairs of gastric cancer tissues, and the correlations of its expression with the pathological characteristics and prognosis of patients were statistically analyzed. qRT-PCR showed that compared with that in the normal gastric epithelial cell (GES-1), the expression level of lncRNA ZEB1-AS1 was up-regulated in gastric cancer cells (MKN28, MKN45, BGC823, MGC803, KATOIII, and SGC7901). LncRNA ZEB1-AS1 interfering sequence was transfected into model cells, and Transwell assay showed that the cell invasion and migration capacities were significantly inhibited. qRT-PCR also revealed that the expression of lncRNA ZEB1-AS1 was up-regulated in 55 out of 75 cases of gastric cancer and para-carcinoma tissues (fold change > 1). Statistical analysis showed that the high expression of lncRNA ZEB1-AS1 was positively correlated with TNM staging (p = 0.002), lymph node metastasis (p = 0.002), and invasion degree (p = 0.004). The survival time of patients with high expression of lncRNA ZEB1-AS1 in gastric cancer tissues was shorter than that of patients with low expression (p = 0.004). LncRNA ZEB1-AS1 is highly expressed in gastric cancer tissues and cells, and it is expected to be a new prognostic marker of gastric cancer used for the clinical diagnosis and prognostic evaluation. After intervention in lncRNA ZEB1-AS1 expression, the cell invasion and migration are inhibited, and lncRNA ZEB1-AS1 may be an important target to reverse the malignant phenotype of gastric cancer.

Assessing 1D Atmospheric Solar Radiative Transfer Models: Interpretation and Handling of Unresolved Clouds.

NASA Astrophysics Data System (ADS)

Barker, H. W.; Stephens, G. L.; Partain, P. T.; Bergman, J. W.; Bonnel, B.; Campana, K.; Clothiaux, E. E.; Clough, S.; Cusack, S.; Delamere, J.; Edwards, J.; Evans, K. F.; Fouquart, Y.; Freidenreich, S.; Galin, V.; Hou, Y.; Kato, S.; Li, J.;  Mlawer, E.;  Morcrette, J.-J.;  O'Hirok, W.;  Räisänen, P.;  Ramaswamy, V.;  Ritter, B.;  Rozanov, E.;  Schlesinger, M.;  Shibata, K.;  Sporyshev, P.;  Sun, Z.;  Wendisch, M.;  Wood, N.;  Yang, F.

2003-08-01

The primary purpose of this study is to assess the performance of 1D solar radiative transfer codes that are used currently both for research and in weather and climate models. Emphasis is on interpretation and handling of unresolved clouds. Answers are sought to the following questions: (i) How well do 1D solar codes interpret and handle columns of information pertaining to partly cloudy atmospheres? (ii) Regardless of the adequacy of their assumptions about unresolved clouds, do 1D solar codes perform as intended?One clear-sky and two plane-parallel, homogeneous (PPH) overcast cloud cases serve to elucidate 1D model differences due to varying treatments of gaseous transmittances, cloud optical properties, and basic radiative transfer. The remaining four cases involve 3D distributions of cloud water and water vapor as simulated by cloud-resolving models. Results for 25 1D codes, which included two line-by-line (LBL) models (clear and overcast only) and four 3D Monte Carlo (MC) photon transport algorithms, were submitted by 22 groups. Benchmark, domain-averaged irradiance profiles were computed by the MC codes. For the clear and overcast cases, all MC estimates of top-of-atmosphere albedo, atmospheric absorptance, and surface absorptance agree with one of the LBL codes to within ±2%. Most 1D codes underestimate atmospheric absorptance by typically 15-25 W m-2 at overhead sun for the standard tropical atmosphere regardless of clouds.Depending on assumptions about unresolved clouds, the 1D codes were partitioned into four genres: (i) horizontal variability, (ii) exact overlap of PPH clouds, (iii) maximum/random overlap of PPH clouds, and (iv) random overlap of PPH clouds. A single MC code was used to establish conditional benchmarks applicable to each genre, and all MC codes were used to establish the full 3D benchmarks. There is a tendency for 1D codes to cluster near their respective conditional benchmarks, though intragenre variances typically exceed those for the clear and overcast cases. The majority of 1D codes fall into the extreme category of maximum/random overlap of PPH clouds and thus generally disagree with full 3D benchmark values. Given the fairly limited scope of these tests and the inability of any one code to perform extremely well for all cases begs the question that a paradigm shift is due for modeling 1D solar fluxes for cloudy atmospheres.

15 CFR 740.7 - Computers (APP).

Code of Federal Regulations, 2010 CFR

2010-01-01

... 4A003. (2) Technology and software. License Exception APP authorizes exports of technology and software... programmability. (ii) Technology and source code. Technology and source code eligible for License Exception APP..., reexports and transfers (in-country) for nuclear, chemical, biological, or missile end-users and end-uses...

A proposed study of multiple scattering through clouds up to 1 THz

NASA Technical Reports Server (NTRS)

Gerace, G. C.; Smith, E. K.

1992-01-01

A rigorous computation of the electromagnetic field scattered from an atmospheric liquid water cloud is proposed. The recent development of a fast recursive algorithm (Chew algorithm) for computing the fields scattered from numerous scatterers now makes a rigorous computation feasible. A method is presented for adapting this algorithm to a general case where there are an extremely large number of scatterers. It is also proposed to extend a new binary PAM channel coding technique (El-Khamy coding) to multiple levels with non-square pulse shapes. The Chew algorithm can be used to compute the transfer function of a cloud channel. Then the transfer function can be used to design an optimum El-Khamy code. In principle, these concepts can be applied directly to the realistic case of a time-varying cloud (adaptive channel coding and adaptive equalization). A brief review is included of some preliminary work on cloud dispersive effects on digital communication signals and on cloud liquid water spectra and correlations.

Exosomes and microvesicles: extracellular vesicles for genetic information transfer and gene therapy.

PubMed

Lee, Yi; El Andaloussi, Samir; Wood, Matthew J A

2012-10-15

Exosomes and microvesicles are extracellular nanovesicles released by most but not all cells. They are specifically equipped to mediate intercellular communication via the transfer of genetic information, including the transfer of both coding and non-coding RNAs, to recipient cells. As a result, both exosomes and microvesicles play a fundamental biological role in the regulation of normal physiological as well as aberrant pathological processes, via altered gene regulatory networks and/or via epigenetic programming. For example, microvesicle-mediated genetic transfer can regulate the maintenance of stem cell plasticity and induce beneficial cell phenotype modulation. Alternatively, such vesicles play a role in tumor pathogenesis and the spread of neurodegenerative diseases via the transfer of specific microRNAs and pathogenic proteins. Given this natural property for genetic information transfer, the possibility of exploiting these vesicles for therapeutic purposes is now being investigated. Stem cell-derived microvesicles appear to be naturally equipped to mediate tissue regeneration under certain conditions, while recent evidence suggests that exosomes might be harnessed for the targeted delivery of human genetic therapies via the introduction of exogenous genetic cargoes such as siRNA. Thus, extracellular vesicles are emerging as potent genetic information transfer agents underpinning a range of biological processes and with therapeutic potential.

Analysis of correlation structures in the Synechocystis PCC6803 genome.

PubMed

Wu, Zuo-Bing

2014-12-01

Transfer of nucleotide strings in the Synechocystis sp. PCC6803 genome is investigated to exhibit periodic and non-periodic correlation structures by using the recurrence plot method and the phase space reconstruction technique. The periodic correlation structures are generated by periodic transfer of several substrings in long periodic or non-periodic nucleotide strings embedded in the coding regions of genes. The non-periodic correlation structures are generated by non-periodic transfer of several substrings covering or overlapping with the coding regions of genes. In the periodic and non-periodic transfer, some gaps divide the long nucleotide strings into the substrings and prevent their global transfer. Most of the gaps are either the replacement of one base or the insertion/reduction of one base. In the reconstructed phase space, the points generated from two or three steps for the continuous iterative transfer via the second maximal distance can be fitted by two lines. It partly reveals an intrinsic dynamics in the transfer of nucleotide strings. Due to the comparison of the relative positions and lengths, the substrings concerned with the non-periodic correlation structures are almost identical to the mobile elements annotated in the genome. The mobile elements are thus endowed with the basic results on the correlation structures. Copyright © 2014 Elsevier Ltd. All rights reserved.

Heat Transfer and Fluid Dynamics Measurements in the Expansion Space of a Stirling Cycle Engine

NASA Technical Reports Server (NTRS)

Jiang, Nan; Simon, Terrence W.

2006-01-01

The heater (or acceptor) of a Stirling engine, where most of the thermal energy is accepted into the engine by heat transfer, is the hottest part of the engine. Almost as hot is the adjacent expansion space of the engine. In the expansion space, the flow is oscillatory, impinging on a two-dimensional concavely-curved surface. Knowing the heat transfer on the inside surface of the engine head is critical to the engine design for efficiency and reliability. However, the flow in this region is not well understood and support is required to develop the CFD codes needed to design modern Stirling engines of high efficiency and power output. The present project is to experimentally investigate the flow and heat transfer in the heater head region. Flow fields and heat transfer coefficients are measured to characterize the oscillatory flow as well as to supply experimental validation for the CFD Stirling engine design codes. Presented also is a discussion of how these results might be used for heater head and acceptor region design calculations.

Influence of aerosols on surface reaching spectral irradiance and introduction to a new technique of estimating aerosol radiative forcing from high resolution spectral flux measurements

NASA Astrophysics Data System (ADS)

Rao, Roshan

2016-04-01

Aerosol radiative forcing estimates with high certainty are required in climate change studies. The approach in estimating the aerosol radiative forcing by using the chemical composition of aerosols is not effective as the chemical composition data with radiative properties are not widely available. We look into the approach where ground based spectral radiation flux measurement is made and along with an Radtiative transfer (RT) model, radiative forcing is estimated. Measurements of spectral flux were made using an ASD spectroradiometer with 350 - 1050 nm wavelength range and a 3nm resolution during around 54 clear-sky days during which AOD range was around 0.01 to 0.7. Simultaneous measurements of black carbon were also made using Aethalometer (Magee Scientific) which ranged from around 1.5 ug/m3 to 8 ug/m3. The primary study involved in understanding the sensitivity of spectral flux due to change in individual aerosol species (Optical properties of Aerosols and Clouds (OPAC) classified aerosol species) using the SBDART RT model. This made us clearly distinguish the influence of different aerosol species on the spectral flux. Following this, a new technique has been introduced to estimate an optically equivalent mixture of aerosol species for the given location. The new method involves matching different combinations of aerosol species in OPAC model and RT model as long as the combination which gives the minimum root mean squared deviation from measured spectral flux is obtained. Using the optically equivalent aerosol mixture and RT model, aerosol radiative forcing is estimated. Also an alternate method to estimate the spectral SSA is discussed. Here, the RT model, the observed spectral flux and spectral AOD is used. Spectral AOD is input to RT model and SSA is varied till the minimum root mean squared difference between observed and simulated spectral flux from RT model is obtained. The methods discussed are limited to clear sky scenes and its accuracy to derive an optically equivalent aerosol mixture reduces when diffuse component of flux increases. In our analysis, RT model clearly shows that direct component of spectral flux is more sensitive to different aerosol species than total spectral flux which is also supported by our observed data.

On the probability of cure for heavy-ion radiotherapy

NASA Astrophysics Data System (ADS)

Hanin, Leonid; Zaider, Marco

2014-07-01

The probability of a cure in radiation therapy (RT)—viewed as the probability of eventual extinction of all cancer cells—is unobservable, and the only way to compute it is through modeling the dynamics of cancer cell population during and post-treatment. The conundrum at the heart of biophysical models aimed at such prospective calculations is the absence of information on the initial size of the subpopulation of clonogenic cancer cells (also called stem-like cancer cells), that largely determines the outcome of RT, both in an individual and population settings. Other relevant parameters (e.g. potential doubling time, cell loss factor and survival probability as a function of dose) are, at least in principle, amenable to empirical determination. In this article we demonstrate that, for heavy-ion RT, microdosimetric considerations (justifiably ignored in conventional RT) combined with an expression for the clone extinction probability obtained from a mechanistic model of radiation cell survival lead to useful upper bounds on the size of the pre-treatment population of clonogenic cancer cells as well as upper and lower bounds on the cure probability. The main practical impact of these limiting values is the ability to make predictions about the probability of a cure for a given population of patients treated to newer, still unexplored treatment modalities from the empirically determined probability of a cure for the same or similar population resulting from conventional low linear energy transfer (typically photon/electron) RT. We also propose that the current trend to deliver a lower total dose in a smaller number of fractions with larger-than-conventional doses per fraction has physical limits that must be understood before embarking on a particular treatment schedule.

Pennsylvania comprehensive stroke center collaborative: Statement on the recently updated IV rt-PA prescriber information for acute ischemic stroke.

PubMed

Daou, Badih; Deprince, Maureen; D'Ambrosio, Robin; Tjoumakaris, Stavropoula; Rosenwasser, Robert H; Ackerman, Daniel J; Bell, Rodney; Tzeng, Diana L; Ghobrial, Michelle; Fernandez, Andres; Shah, Qaisar; Gzesh, Dan J; Murphy, Deborah; Castaldo, John E; Mathiesen, Claranne; Pineda, Maria Carissa; Jabbour, Pascal

2015-12-01

Recently, the FDA guidelines regarding the eligibility of patients with acute ischemic stroke to receive IV rt-PA have been modified and are not in complete accord with the latest AHA/ASA guidelines. The resultant differences may result in discrepancies in patient selection for intravenous thrombolysis. Several comprehensive stroke centers in the state of Pennsylvania have undertaken a collaborative effort to clarify and unify our own recommendations regarding how to reconcile these different guidelines. Seizure at onset of stroke, small previous strokes that are subacute or chronic, multilobar infarct involving more than one third of the middle cerebral artery territory on CT scan, hypoglycemia, minor or rapidly improving symptoms should not be considered as contraindications for intravenous thrombolysis. It is recommended to follow the AHA/ASA guidelines regarding blood pressure management and bleeding diathesis. Patients receiving factor Xa inhibitors and direct thrombin inhibitors within the preceding 48 h should be excluded from receiving IV rt-PA. CT angiography is effective in identifying candidates for endovascular therapy. Consultation with and/or transfer to a comprehensive stroke center should be an option where indicated. Patients should receive IV rt-PA up to 4.5h after the onset of stroke. The process of identifying patients who will benefit the most from IV rt-PA is still evolving. Considering the rapidity with which patients need to be evaluated and treated, it remains imperative that systems of care adopt protocols to quickly gather the necessary data and have access to expert consultation as necessary to facilitate best practices. Copyright © 2015 Elsevier B.V. All rights reserved.

How-To-Do-It: Recombinant DNA Made Easy: I. "Jumping Genes."

ERIC Educational Resources Information Center

Thomson, Robert G.

1988-01-01

Presents as part I of a two-part series a study involving the intercellular transfer of bacterial DNA that codes for the resistance to antibiotics. Demonstrates to students that such transfers occur. Discusses laboratory procedures, materials and results. (CW)

Overexpression of wheat lipid transfer protein gene TaLTP5 increases resistances to Cochliobolus sativus and Fusarium graminearum in transgenic wheat.

PubMed

Zhu, Xiuliang; Li, Zhao; Xu, Huijun; Zhou, Miaoping; Du, Lipu; Zhang, Zengyan

2012-08-01

The fungus Cochliobolus sativus is the main pathogen of common root rot, a serious soil-borne disease of wheat (Triticum aestivum L.). The fungus Fusarium graminearum is the primary pathogen of Fusarium head blight, a devastating disease of wheat worldwide. In this study, the wheat lipid transfer protein gene, TaLTP5, was cloned and evaluated for its ability to suppress disease development in transgenic wheat. TaLTP5 expression was induced after C. sativus infection. The TaLTP5 expression vector, pA25-TaLTP5, was constructed and bombarded into Chinese wheat variety Yangmai 18. Six TaLTP5 transgenic wheat lines were established and characterized. PCR and Southern blot analyses indicated that the introduced TaLTP5 gene was integrated into the genomes of six transgenic wheat lines by distinct patterns, and heritable. RT-PCR and real-time quantitative RT-PCR revealed that the TaLTP5 gene was over-expressed in the transgenic wheat lines compared to segregants lacking the transgene and wild-type wheat plants. Following challenge with C. sativus or F. graminearum, all six transgenic lines overexpressing TaLTP5 exhibited significantly enhanced resistance to both common root rot and Fusarium head blight compared to the untransformed wheat Yangmai 18.

The CCSDS Next Generation Space Data Link Protocol (NGSLP)

NASA Technical Reports Server (NTRS)

Kazz, Greg J.; Greenberg, Edward

2014-01-01

The CCSDS space link protocols i.e., Telemetry (TM), Telecommand (TC), Advanced Orbiting Systems (AOS) were developed in the early growth period of the space program. They were designed to meet the needs of the early missions, be compatible with the available technology and focused on the specific link environments. Digital technology was in its infancy and spacecraft power and mass issues enforced severe constraints on flight implementations. Therefore the Telecommand protocol was designed around a simple Bose, Hocquenghem, Chaudhuri (BCH) code that provided little coding gain and limited error detection but was relatively simple to decode on board. The infusion of the concatenated Convolutional and Reed-Solomon codes5 for telemetry was a major milestone and transformed telemetry applications by providing them the ability to more efficiently utilize the telemetry link and its ability to deliver user data. The ability to significantly lower the error rates on the telemetry links enabled the use of packet telemetry and data compression. The infusion of the high performance codes for telemetry was enabled by the advent of digital processing, but it was limited to earth based systems supporting telemetry. The latest CCSDS space link protocol, Proximity-1 was developed in early 2000 to meet the needs of short-range, bi-directional, fixed or mobile radio links characterized by short time delays, moderate but not weak signals, and short independent sessions. Proximity-1 has been successfully deployed on both NASA and ESA missions at Mars and is planned to be utilized by all Mars missions in development. A new age has arisen, one that now provides the means to perform advanced digital processing in spacecraft systems enabling the use of improved transponders, digital correlators, and high performance forward error correcting codes for all communications links. Flight transponders utilizing digital technology have emerged and can efficiently provide the means to make the next leap in performance for space link communications. Field Programmable Gate Arrays (FPGAs) provide the capability to incorporate high performance forward error correcting codes implemented within software transponders providing improved performance in data transfer, ranging, link security, and time correlation. Given these synergistic technological breakthroughs, the time has come to take advantage of them in applying them to both on going (e.g., command, telemetry) and emerging (e.g., space link security, optical communication) space link applications. However one of the constraining factors within the Data Link Layer in realizing these performance gains is the lack of a generic transfer frame format and common supporting services amongst the existing CCSDS link layer protocols. Currently each of the four CCSDS link layer protocols (TM, TC, AOS, and Proximity-1) have unique formats and services which prohibits their reuse across the totality of all space link applications of CCSDS member space agencies. For example, Mars missions. These missions implement their proximity data link layer using the Proximity-1 frame format and the services it supports but is still required to support the direct from Earth (TC) protocols and the Direct To Earth (AOS/TM) protocols. The prime purpose of this paper, is to describe a new general purpose CCSDS Data Link layer protocol, the NGSLP that will provide the required services along with a common transfer frame format for all the CCSDS space links (ground to/from space and space to space links) targeted for emerging missions after a CCSDS agency-wide coordinated date. This paper will also describe related options that can be included for the Coding and Synchronization sub-layer of the Data Link layer to extend the capacities of the link and additionally provide an independence of the transfer frame sub-layer from the coding sublayer. This feature will provide missions the option of running either the currently performed synchronous coding and transfer frame data link or an asynchronous coding/frame data link, in which the transfer frame length is independent of the block size of the code. The benefits from the elimination of this constraint (frame synchronized to the code block) will simplify the interface between the transponder and the data handling equipment and reduce implementation costs and complexities. The benefits include: inclusion of encoders/decoders into transmitters and receivers without regard to data link protocols, providing the ability to insert latency sensitive messages into the link to support launch, landing/docking, telerobotics. and Variable Coded Modulation (VCM). In addition the ability to transfer different sized frames can provide a backup for delivering stored anomaly engineering data simultaneously with real time data, or relaying of frames from various sources onto a trunk line for delivery to Earth.

Investigation of Advanced Counterrotation Blade Configuration Concepts for High Speed Turboprop Systems. Task 8: Cooling Flow/heat Transfer Analysis

NASA Technical Reports Server (NTRS)

Hall, Edward J.; Topp, David A.; Heidegger, Nathan J.; Delaney, Robert A.

1994-01-01

The focus of this task was to validate the ADPAC code for heat transfer calculations. To accomplish this goal, the ADPAC code was modified to allow for a Cartesian coordinate system capability and to add boundary conditions to handle spanwise periodicity and transpiration boundaries. The primary validation case was the film cooled C3X vane. The cooling hole modeling included both a porous region and grid in each discrete hold. Predictions for these models as well as smooth wall compared well with the experimental data.

Stakeholder analysis for adopting a personal health record standard in Korea.

PubMed

Kang, Min-Jeoung; Jung, Chai Young; Kim, Soyoun; Boo, Yookyung; Lee, Yuri; Kim, Sundo

Interest in health information exchanges (HIEs) is increasing. Several countries have adopted core health data standards with appropriate strategies. This study was conducted to determine the feasibility of a continuity of care record (CCR) as the standard for an electronic version of the official transfer note and the HIE in Korean healthcare. A technical review of the CCR standard and analysis of stakeholders' views were undertaken. Transfer notes were reviewed and matched with CCR standard categories. The standard for the Korean coding system was selected. Stakeholder analysis included an online survey of members of the Korean Society of Medical Informatics, a public hearing to derive opinions of consumers, doctors, vendors, academic societies and policy makers about the policy process, and a focus group meeting with EMR vendors to determine which HIE objects were technically applicable. Data objects in the official transfer note form matched CCR standards. Korean Classification of Diseases, Korean Standard Terminology of Medicine, Electronic Data Interchange code (EDI code), Logical Observation Identifiers Names and Codes, and Korean drug codes (KD code) were recommended as the Korean coding standard.'Social history', 'payers', and 'encounters' were mostly marked as optional or unnecessary sections, and 'allergies', 'alerts', 'medication list', 'problems/diagnoses', 'results',and 'procedures' as mandatory. Unlike the US, 'social history' was considered optional and 'advance directives' mandatory.At the public hearing there was some objection from the Korean Medical Association to the HIE on legal grounds in termsof intellectual property and patients' personal information. Other groups showed positive or neutral responses. Focus group members divided CCR data objects into three phases based onpredicted adoption time in CCR: (i) immediate adoption; (ii) short-term adoption ('alerts', 'family history'); and (iii) long-term adoption ('results', 'advanced directives', 'functional status', 'medical equipment', 'vital signs', 'plan of care', 'social history'). There were no technical problems in generating the CCR standard document from EMRs. Matters of concern that arose from study results should be resolved with time and consultation.

Some Problems and Solutions in Transferring Ecosystem Simulation Codes to Supercomputers

NASA Technical Reports Server (NTRS)

Skiles, J. W.; Schulbach, C. H.

1994-01-01

Many computer codes for the simulation of ecological systems have been developed in the last twenty-five years. This development took place initially on main-frame computers, then mini-computers, and more recently, on micro-computers and workstations. Recent recognition of ecosystem science as a High Performance Computing and Communications Program Grand Challenge area emphasizes supercomputers (both parallel and distributed systems) as the next set of tools for ecological simulation. Transferring ecosystem simulation codes to such systems is not a matter of simply compiling and executing existing code on the supercomputer since there are significant differences in the system architectures of sequential, scalar computers and parallel and/or vector supercomputers. To more appropriately match the application to the architecture (necessary to achieve reasonable performance), the parallelism (if it exists) of the original application must be exploited. We discuss our work in transferring a general grassland simulation model (developed on a VAX in the FORTRAN computer programming language) to a Cray Y-MP. We show the Cray shared-memory vector-architecture, and discuss our rationale for selecting the Cray. We describe porting the model to the Cray and executing and verifying a baseline version, and we discuss the changes we made to exploit the parallelism in the application and to improve code execution. As a result, the Cray executed the model 30 times faster than the VAX 11/785 and 10 times faster than a Sun 4 workstation. We achieved an additional speed-up of approximately 30 percent over the original Cray run by using the compiler's vectorizing capabilities and the machine's ability to put subroutines and functions "in-line" in the code. With the modifications, the code still runs at only about 5% of the Cray's peak speed because it makes ineffective use of the vector processing capabilities of the Cray. We conclude with a discussion and future plans.

The physics of volume rendering

NASA Astrophysics Data System (ADS)

Peters, Thomas

2014-11-01

Radiation transfer is an important topic in several physical disciplines, probably most prominently in astrophysics. Computer scientists use radiation transfer, among other things, for the visualization of complex data sets with direct volume rendering. In this article, I point out the connection between physical radiation transfer and volume rendering, and I describe an implementation of direct volume rendering in the astrophysical radiation transfer code RADMC-3D. I show examples for the use of this module on analytical models and simulation data.

Evaluation of the Time and Frequency Transfer Capabilities of a Network of GNSS Receivers Located in Timing Laboratories

DTIC Science & Technology

2009-11-01

metrology, different techniques are used for time and frequency transfer, basically TWSTFT (Two-Way Satellite Time and Frequency Transfer), GPS CV (Common...traditional GPS/GLONASS CV/AV receivers and TWSTFT equipment. Time and frequency transfer using GPS code and carrier-phase is an important...or mixing GPS geodetic results with other independent techniques, such as the TWSTFT . 41 st Annual Precise Time and Time Interval (PTTI

Implementation of radiation shielding calculation methods. Volume 1: Synopsis of methods and summary of results

NASA Technical Reports Server (NTRS)

Capo, M. A.; Disney, R. K.

1971-01-01

The work performed in the following areas is summarized: (1) Analysis of Realistic nuclear-propelled vehicle was analyzed using the Marshall Space Flight Center computer code package. This code package includes one and two dimensional discrete ordinate transport, point kernel, and single scatter techniques, as well as cross section preparation and data processing codes, (2) Techniques were developed to improve the automated data transfer in the coupled computation method of the computer code package and improve the utilization of this code package on the Univac-1108 computer system. (3) The MSFC master data libraries were updated.

Radiation from advanced solid rocket motor plumes

NASA Technical Reports Server (NTRS)

Farmer, Richard C.; Smith, Sheldon D.; Myruski, Brian L.

1994-01-01

The overall objective of this study was to develop an understanding of solid rocket motor (SRM) plumes in sufficient detail to accurately explain the majority of plume radiation test data. Improved flowfield and radiation analysis codes were developed to accurately and efficiently account for all the factors which effect radiation heating from rocket plumes. These codes were verified by comparing predicted plume behavior with measured NASA/MSFC ASRM test data. Upon conducting a thorough review of the current state-of-the-art of SRM plume flowfield and radiation prediction methodology and the pertinent data base, the following analyses were developed for future design use. The NOZZRAD code was developed for preliminary base heating design and Al2O3 particle optical property data evaluation using a generalized two-flux solution to the radiative transfer equation. The IDARAD code was developed for rapid evaluation of plume radiation effects using the spherical harmonics method of differential approximation to the radiative transfer equation. The FDNS CFD code with fully coupled Euler-Lagrange particle tracking was validated by comparison to predictions made with the industry standard RAMP code for SRM nozzle flowfield analysis. The FDNS code provides the ability to analyze not only rocket nozzle flow, but also axisymmetric and three-dimensional plume flowfields with state-of-the-art CFD methodology. Procedures for conducting meaningful thermo-vision camera studies were developed.

USAF Hyperbaric Animal Transfer Chamber System.

DTIC Science & Technology

1988-01-01

in full accordance with the requirements of the ASME Boiler and Pressure Vessel Code , Section VIII, Division 2, including provisions for lethal and...possible application to military and aviation medicine. REFERENCES 1. ASME Boiler and Pressure Vessel Code , Sec III, Div 2, para AD-160, AF-402, . and

Probabilistic Structural Analysis Methods (PSAM) for select space propulsion systems components

NASA Technical Reports Server (NTRS)

1991-01-01

Summarized here is the technical effort and computer code developed during the five year duration of the program for probabilistic structural analysis methods. The summary includes a brief description of the computer code manuals and a detailed description of code validation demonstration cases for random vibrations of a discharge duct, probabilistic material nonlinearities of a liquid oxygen post, and probabilistic buckling of a transfer tube liner.

Evaluation of Multi-Vessel Ship Motion Prediction Codes

DTIC Science & Technology

2008-09-01

each other, and accounting for the hydrodynamic effects between the hulls. The major differences in the capabilities of the codes were in the non...Figure 28. Effects of irregular frequency smoothing has on the resultant pitch transfer function for three meter separation, 135 degree heading, and...and accounting for the hydrodynamic effects between the hulls. The major differences in the capabilities of the codes were in the non-hydrodynamic

Development of a Real-Time, TaqMan Reverse Transcription-PCR Assay for Detection and Differentiation of Lyssavirus Genotypes 1, 5, and 6

PubMed Central

Wakeley, P. R.; Johnson, N.; McElhinney, L. M.; Marston, D.; Sawyer, J.; Fooks, A. R.

2005-01-01

Several reverse transcription-PCR (RT-PCR) methods have been reported for the detection of rabies and rabies-related viruses. These methods invariably involve multiple transfers of nucleic acids between different tubes, with the risk of contamination leading to the production of false-positive results. Here we describe a single, closed-tube, nonnested RT-PCR with TaqMan technology that distinguishes between classical rabies virus (genotype 1) and European bat lyssaviruses 1 and 2 (genotypes 5 and 6) in real time. The TaqMan assay is rapid, sensitive, and specific and allows for the genotyping of unknown isolates concomitant with the RT-PCR. The assay can be applied quantitatively and the use of an internal control enables the quality of the isolated template to be assessed. Despite sequence heterogeneity in the N gene between the different genotypes, a universal forward and reverse primer set has been designed, allowing for the simplification of previously described assays. We propose that within a geographically constrained area, this assay will be a useful tool for the detection and differentiation of members of the Lyssavirus genus. PMID:15956398

Isoflurane modulates neuronal excitability of the nucleus reticularis thalami in vitro.

PubMed

Joksovic, Pavle M; Todorovic, Slobodan M

2010-06-01

The thalamus has a key function in processing sensory information, sleep, and cognition. We examined the effects of a common volatile anesthetic, isoflurane, on modulation of neuronal excitability in reticular thalamic nucleus (nRT) in intact brain slices from immature rats. In current-clamp recordings, isoflurane (300-600 micromol/L) consistently depolarized membrane potential, decreased input resistance, and inhibited both rebound burst firing and tonic spike firing modes of nRT neurons. The isoflurane-induced depolarization persisted not only in the presence of tetrodotoxin, but after replacement of Ca(2+) with Ba(2+) ions in external solution; it was abolished by partial replacement of extracellular Na(+) ions with N-methyl-D-glucamine. In voltage-clamp recordings, we found that isoflurane slowed recovery from inactivation of T-type Ca(2+) current. Thus, at clinically relevant concentrations, isoflurane inhibits neuronal excitability of nRT neurons in developing brain via multiple ion channels. Inhibition of the neuronal excitability of thalamic cells may contribute to impairment of sensory information transfer in the thalamocortical network by general anesthetics. The findings may be important for understanding cellular mechanisms of anesthesia, such as loss of consciousness and potentially damaging consequences of general anesthetics on developing mammalian brains.

Construction and Operation of an Internal Coil Device, RT-1, with a High-Temperature Superconductor

NASA Astrophysics Data System (ADS)

Ogawa, Yuichi; Yoshida, Zensho; Morikawa, Junji; Saito, Haruhiko; Watanabe, Sho; Yano, Yoshihisa; Mizumaki, Shoichi; Tosaka, Taizo

An internal coil device called Ring Trap-1 (RT-1) has been constructed to explore an innovative concept for a high-beta plasma based on a new relaxation theory. A high-temperature superconductor (HTS) Bi-2223 tape is employed for the internal coil of RT-1. The coil is cooled to 20 K with helium gas supplied by G-M refrigerators, and charged to a magnetomotive force of 250 kA using an external power supply. For these cooling and charging methods, we have developed several innovative techniques such as a demountable transfer tube system, persistent current switch, detachable electrode, and others. In addition, we have paid much attention to the deterioration of the HTS tape during the fabrication of the internal coil. As a result, we have demonstrated that the decay of the persistent current of the internal coil is ˜1% during 8 h. The internal coil is lifted with a levitation coil located at the upper region of the vacuum vessel. The coil position monitored with laser sensors is feedback controlled through the regulation of the levitation coil current. Stable levitation for a few hours has been demonstrated for various plasma experiments.

Long non-coding RNA expression patterns in lung tissues of chronic cigarette smoke induced COPD mouse model.

PubMed

Zhang, Haiyun; Sun, Dejun; Li, Defu; Zheng, Zeguang; Xu, Jingyi; Liang, Xue; Zhang, Chenting; Wang, Sheng; Wang, Jian; Lu, Wenju

2018-05-15

Long non-coding RNAs (lncRNAs) have critical regulatory roles in protein-coding gene expression. Aberrant expression profiles of lncRNAs have been observed in various human diseases. In this study, we investigated transcriptome profiles in lung tissues of chronic cigarette smoke (CS)-induced COPD mouse model. We found that 109 lncRNAs and 260 mRNAs were significantly differential expressed in lungs of chronic CS-induced COPD mouse model compared with control animals. GO and KEGG analyses indicated that differentially expressed lncRNAs associated protein-coding genes were mainly involved in protein processing of endoplasmic reticulum pathway, and taurine and hypotaurine metabolism pathway. The combination of high throughput data analysis and the results of qRT-PCR validation in lungs of chronic CS-induced COPD mouse model, 16HBE cells with CSE treatment and PBMC from patients with COPD revealed that NR_102714 and its associated protein-coding gene UCHL1 might be involved in the development of COPD both in mouse and human. In conclusion, our study demonstrated that aberrant expression profiles of lncRNAs and mRNAs existed in lungs of chronic CS-induced COPD mouse model. From animal models perspective, these results might provide further clues to investigate biological functions of lncRNAs and their potential target protein-coding genes in the pathogenesis of COPD.

Scalar collapse in AdS with an OpenCL open source code

NASA Astrophysics Data System (ADS)

Liebling, Steven L.; Khanna, Gaurav

2017-10-01

We study the spherically symmetric collapse of a scalar field in anti-de Sitter spacetime using a newly constructed, open-source code which parallelizes over heterogeneous architectures using the open standard OpenCL. An open question for this scenario concerns how to tell, a priori, whether some form of initial data will be stable or will instead develop under the turbulent instability into a black hole in the limit of vanishing amplitude. Previous work suggested the existence of islands of stability around quasi-periodic solutions, and we use this new code to examine the stability properties of approximately quasi-periodic solutions which balance energy transfer to higher modes with energy transfer to lower modes. The evolutions provide some evidence, though not conclusively, for stability of initial data sufficiently close to quasiperiodic solutions.

WINCOF-I code for prediction of fan compressor unit with water ingestion

NASA Technical Reports Server (NTRS)

Murthy, S. N. B.; Mullican, A.

1990-01-01

The PURDUE-WINCOF code, which provides a numerical method of obtaining the performance of a fan-compressor unit of a jet engine with water ingestion into the inlet, was modified to take into account: (1) the scoop factor, (2) the time required for the setting-in of a quasi-steady distribution of water, and (3) the heat and mass transfer processes over the time calculated under 2. The modified code, named WINCOF-I was utilized to obtain the performance of a fan-compressor unit of a generic jet engine. The results illustrate the manner in which quasi-equilibrium conditions become established in the machine and the redistribution of ingested water in various stages in the form of a film out of the casing wall, droplets across the span, and vapor due to mass transfer.

Design of Instrument Approach Procedure Charts Comprehension Speed of Missed Approach Instructions Coded in Text or Icons

DOT National Transportation Integrated Search

1992-02-01

Instrument approach procedure (IAP) charts are often cluttered and confusing. The quantified effects of chart design : changes on information transfer are needed by chart manufacturers to make changes uhich will enhance information transfer : and hum...

Progress towards understanding and predicting convection heat transfer in the turbine gas path

NASA Technical Reports Server (NTRS)

Simoneau, Robert J.; Simon, Frederick F.

1992-01-01

A new era is drawing in the ability to predict convection heat transfer in the turbine gas path. We feel that the technical community now has the capability to mount a major assault on this problem, which has eluded significant progress for a long time. We hope to make a case for this bold statement by reviewing the state of the art in three major heat transfer, configuration-specific experiments, whose data have provided the big picture and guided both the fundamental modeling research and the code development. Following that, we review progress and directions in the development of computer codes to predict turbine gas path heat transfer. Finally, we cite examples and make observations on the more recent efforts to do all this work in a simultaneous, interactive, and more synergistic manner. We conclude with an assessment of progress, suggestions for how to use the current state of the art, and recommendations for the future.

A Comparison of Grid-based and SPH Binary Mass-transfer and Merger Simulations

DOE PAGES

Motl, Patrick M.; Frank, Juhan; Staff, Jan; ...

2017-03-29

There is currently a great amount of interest in the outcomes and astrophysical implications of mergers of double degenerate binaries. In a commonly adopted approximation, the components of such binaries are represented by polytropes with an index of n = 3/2. We present detailed comparisons of stellar mass-transfer and merger simulations of polytropic binaries that have been carried out using two very different numerical algorithms—a finite-volume "grid" code and a smoothed-particle hydrodynamics (SPH) code. We find that there is agreement in both the ultimate outcomes of the evolutions and the intermediate stages if the initial conditions for each code aremore » chosen to match as closely as possible. We find that even with closely matching initial setups, the time it takes to reach a concordant evolution differs between the two codes because the initial depth of contact cannot be matched exactly. There is a general tendency for SPH to yield higher mass transfer rates and faster evolution to the final outcome. Here, we also present comparisons of simulations calculated from two different energy equations: in one series, we assume a polytropic equation of state and in the other series an ideal gas equation of state. In the latter series of simulations, an atmosphere forms around the accretor, which can exchange angular momentum and cause a more rapid loss of orbital angular momentum. In the simulations presented here, the effect of the ideal equation of state is to de-stabilize the binary in both SPH and grid simulations, but the effect is more pronounced in the grid code.« less

Bayesian Atmospheric Radiative Transfer (BART): Model, Statistics Driver, and Application to HD 209458b

NASA Astrophysics Data System (ADS)

Cubillos, Patricio; Harrington, Joseph; Blecic, Jasmina; Stemm, Madison M.; Lust, Nate B.; Foster, Andrew S.; Rojo, Patricio M.; Loredo, Thomas J.

2014-11-01

Multi-wavelength secondary-eclipse and transit depths probe the thermo-chemical properties of exoplanets. In recent years, several research groups have developed retrieval codes to analyze the existing data and study the prospects of future facilities. However, the scientific community has limited access to these packages. Here we premiere the open-source Bayesian Atmospheric Radiative Transfer (BART) code. We discuss the key aspects of the radiative-transfer algorithm and the statistical package. The radiation code includes line databases for all HITRAN molecules, high-temperature H2O, TiO, and VO, and includes a preprocessor for adding additional line databases without recompiling the radiation code. Collision-induced absorption lines are available for H2-H2 and H2-He. The parameterized thermal and molecular abundance profiles can be modified arbitrarily without recompilation. The generated spectra are integrated over arbitrary bandpasses for comparison to data. BART's statistical package, Multi-core Markov-chain Monte Carlo (MC3), is a general-purpose MCMC module. MC3 implements the Differental-evolution Markov-chain Monte Carlo algorithm (ter Braak 2006, 2009). MC3 converges 20-400 times faster than the usual Metropolis-Hastings MCMC algorithm, and in addition uses the Message Passing Interface (MPI) to parallelize the MCMC chains. We apply the BART retrieval code to the HD 209458b data set to estimate the planet's temperature profile and molecular abundances. This work was supported by NASA Planetary Atmospheres grant NNX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G. JB holds a NASA Earth and Space Science Fellowship.

Critical Contribution of Tyr15 in the HIV-1 Integrase (IN) in Facilitating IN Assembly and Nonenzymatic Function through the IN Precursor Form with Reverse Transcriptase.

PubMed

Takahata, Tatsuro; Takeda, Eri; Tobiume, Minoru; Tokunaga, Kenzo; Yokoyama, Masaru; Huang, Yu-Lun; Hasegawa, Atsuhiko; Shioda, Tatsuo; Sato, Hironori; Kannagi, Mari; Masuda, Takao

2017-01-01

Nonenzymatic roles for HIV-1 integrase (IN) at steps prior to the enzymatic integration step have been reported. To obtain structural and functional insights into the nonenzymatic roles of IN, we performed genetic analyses of HIV-1 IN, focusing on a highly conserved Tyr15 in the N-terminal domain (NTD), which has previously been shown to regulate an equilibrium state between two NTD dimer conformations. Replacement of Tyr15 with alanine, histidine, or tryptophan prevented HIV-1 infection and caused severe impairment of reverse transcription without apparent defects in reverse transcriptase (RT) or in capsid disassembly kinetics after entry into cells. Cross-link analyses of recombinant IN proteins demonstrated that lethal mutations of Tyr15 severely impaired IN structure for assembly. Notably, replacement of Tyr15 with phenylalanine was tolerated for all IN functions, demonstrating that a benzene ring of the aromatic side chain is a key moiety for IN assembly and functions. Additional mutagenic analyses based on previously proposed tetramer models for IN assembly suggested a key role of Tyr15 in facilitating the hydrophobic interaction among IN subunits, together with other proximal residues within the subunit interface. A rescue experiment with a mutated HIV-1 with RT and IN deleted (ΔRT ΔIN) and IN and RT supplied in trans revealed that the nonenzymatic IN function might be exerted through the IN precursor conjugated with RT (RT-IN). Importantly, the lethal mutations of Tyr15 significantly reduced the RT-IN function and assembly. Taken together, Tyr15 seems to play a key role in facilitating the proper assembly of IN and RT on viral RNA through the RT-IN precursor form. Inhibitors of the IN enzymatic strand transfer function (INSTI) have been applied in combination antiretroviral therapies to treat HIV-1-infected patients. Recently, allosteric IN inhibitors (ALLINIs) that interact with HIV-1 IN residues, the locations of which are distinct from the catalytic sites targeted by INSTI, have been discovered. Importantly, ALLINIs affect the nonenzymatic role(s) of HIV-1 IN, providing a rationale for the development of next-generation IN inhibitors with a mechanism that is distinct from that of INSTI. Here, we demonstrate that Tyr15 in the HIV-1 IN NTD plays a critical role during IN assembly by facilitating the hydrophobic interaction of the NTD with the other domains of IN. Importantly, we found that the functional assembly of IN through its fusion form with RT is critical for IN to exert its nonenzymatic function. Our results provide a novel mechanistic insight into the nonenzymatic function of HIV-1 IN and its prevention. Copyright © 2016 American Society for Microbiology.

Upregulation of long non-coding RNA M26317 correlates with tumor progression and poor prognosis in gastric cancer.

PubMed

Li, Li; Wang, Yuan-Yu; Mou, Xiao Zhou; Ye, Zai-Yuan; Zhao, Zhong-Sheng

2018-04-23

To investigate the expression and clinical significance of long non-coding RNA (lnc RNA) in gastric cancer, we applied microarray analysis to obtain expression profiles of protein coding genes and lncRNAs in tumor and paired adjacent non-tumor tissues. We found that 41 lncRNAs were upregulated and 31 lncRNAs were downregulated more than 2-fold in gastric cancer versus noncancerous tissues (ratio>2.0, P<.01). We established a co-expression network of the differentially expressed lncRNAs and targeted coding genes that included 17 lncRNAs and 16 coding genes. As the results of microarray analysis showed that lncRNA M26317 was upregulated in gastric cancer tissues we examined the expression level of M26317 in 103 gastric cancer tissues by RT-PCR and 436 gastric cancer tissues by in situ hybridization. Our data confirmed that M26317 was upregulated in gastric cancer tissues. Moreover, expression of M26317 correlated with patient age, size of tumor, Lauren's classification, depth of invasion, lymph node and distant metastasis, TNM stage and poor prognosis (P<.05), but was not associated with gender, location of tumor, and differentiation (P>.05). M26317 may have an important role in malignant transformation and metastasis of gastric cancer. Copyright © 2018. Published by Elsevier Inc.

Development of a duplex real-time RT-qPCR assay to monitor genome replication, gene expression and gene insert stability during in vivo replication of a prototype live attenuated canine distemper virus vector encoding SIV gag.

PubMed

Coleman, John W; Wright, Kevin J; Wallace, Olivia L; Sharma, Palka; Arendt, Heather; Martinez, Jennifer; DeStefano, Joanne; Zamb, Timothy P; Zhang, Xinsheng; Parks, Christopher L

2015-03-01

Advancement of new vaccines based on live viral vectors requires sensitive assays to analyze in vivo replication, gene expression and genetic stability. In this study, attenuated canine distemper virus (CDV) was used as a vaccine delivery vector and duplex 2-step quantitative real-time RT-PCR (RT-qPCR) assays specific for genomic RNA (gRNA) or mRNA have been developed that concurrently quantify coding sequences for the CDV nucleocapsid protein (N) and a foreign vaccine antigen (SIV Gag). These amplicons, which had detection limits of about 10 copies per PCR reaction, were used to show that abdominal cavity lymphoid tissues were a primary site of CDV vector replication in infected ferrets, and importantly, CDV gRNA or mRNA was undetectable in brain tissue. In addition, the gRNA duplex assay was adapted for monitoring foreign gene insert genetic stability during in vivo replication by analyzing the ratio of CDV N and SIV gag genomic RNA copies over the course of vector infection. This measurement was found to be a sensitive probe for assessing the in vivo genetic stability of the foreign gene insert. Copyright © 2014 Elsevier B.V. All rights reserved.

Computer Code For Turbocompounded Adiabatic Diesel Engine

NASA Technical Reports Server (NTRS)

Assanis, D. N.; Heywood, J. B.

1988-01-01

Computer simulation developed to study advantages of increased exhaust enthalpy in adiabatic turbocompounded diesel engine. Subsytems of conceptual engine include compressor, reciprocator, turbocharger turbine, compounded turbine, ducting, and heat exchangers. Focus of simulation of total system is to define transfers of mass and energy, including release and transfer of heat and transfer of work in each subsystem, and relationship among subsystems. Written in FORTRAN IV.

A Qualitative Study of Multidisciplinary Providers' Experiences With the Transfer Process for Injured Children and Ideas for Improvement.

PubMed

Gawel, Marcie; Emerson, Beth; Giuliano, John S; Rosenberg, Alana; Minges, Karl E; Feder, Shelli; Violano, Pina; Morrell, Patricia; Petersen, Judy; Christison-Lagay, Emily; Auerbach, Marc

2018-02-01

Most injured children initially present to a community hospital, and many will require transfer to a regional pediatric trauma center. The purpose of this study was 1) to explore multidisciplinary providers' experiences with the process of transferring injured children and 2) to describe proposed ideas for process improvement. This qualitative study involved 26 semistructured interviews. Subjects were recruited from 6 community hospital emergency departments and the trauma and transport teams of a level I pediatric trauma center in New Haven, Conn. Participants (n = 34) included interprofessional providers from sending facilities, transport teams, and receiving facilities. Using the constant comparative method, a multidisciplinary team coded transcripts and collectively refined codes to generate recurrent themes across interviews until theoretical saturation was achieved. Participants reported that the transfer process for injured children is complex, stressful, and necessitates collaboration. The transfer process was perceived to involve numerous interrelated components, including professions, disciplines, and institutions. The 5 themes identified as areas to improve this transfer process included 1) Creation of a unified standard operating procedure that crosses institutions/teams, 2) Enhancing 'shared sense making' of all providers, 3) Improving provider confidence, expertise, and skills in caring for pediatric trauma transfer cases, 4) Addressing organization and environmental factors that may impede/delay transfer, and 5) Fostering institutional and personal relationships. Efforts to improve the transfer process for injured children should be guided by the experiences of and input from multidisciplinary frontline emergency providers.

Development and validation of MCNPX-based Monte Carlo treatment plan verification system

PubMed Central

Jabbari, Iraj; Monadi, Shahram

2015-01-01

A Monte Carlo treatment plan verification (MCTPV) system was developed for clinical treatment plan verification (TPV), especially for the conformal and intensity-modulated radiotherapy (IMRT) plans. In the MCTPV, the MCNPX code was used for particle transport through the accelerator head and the patient body. MCTPV has an interface with TiGRT planning system and reads the information which is needed for Monte Carlo calculation transferred in digital image communications in medicine-radiation therapy (DICOM-RT) format. In MCTPV several methods were applied in order to reduce the simulation time. The relative dose distribution of a clinical prostate conformal plan calculated by the MCTPV was compared with that of TiGRT planning system. The results showed well implementation of the beams configuration and patient information in this system. For quantitative evaluation of MCTPV a two-dimensional (2D) diode array (MapCHECK2) and gamma index analysis were used. The gamma passing rate (3%/3 mm) of an IMRT plan was found to be 98.5% for total beams. Also, comparison of the measured and Monte Carlo calculated doses at several points inside an inhomogeneous phantom for 6- and 18-MV photon beams showed a good agreement (within 1.5%). The accuracy and timing results of MCTPV showed that MCTPV could be used very efficiently for additional assessment of complicated plans such as IMRT plan. PMID:26170554

Image Processing, Coding, and Compression with Multiple-Point Impulse Response Functions.

NASA Astrophysics Data System (ADS)

Stossel, Bryan Joseph

1995-01-01

Aspects of image processing, coding, and compression with multiple-point impulse response functions are investigated. Topics considered include characterization of the corresponding random-walk transfer function, image recovery for images degraded by the multiple-point impulse response, and the application of the blur function to image coding and compression. It is found that although the zeros of the real and imaginary parts of the random-walk transfer function occur in continuous, closed contours, the zeros of the transfer function occur at isolated spatial frequencies. Theoretical calculations of the average number of zeros per area are in excellent agreement with experimental results obtained from computer counts of the zeros. The average number of zeros per area is proportional to the standard deviations of the real part of the transfer function as well as the first partial derivatives. Statistical parameters of the transfer function are calculated including the mean, variance, and correlation functions for the real and imaginary parts of the transfer function and their corresponding first partial derivatives. These calculations verify the assumptions required in the derivation of the expression for the average number of zeros. Interesting results are found for the correlations of the real and imaginary parts of the transfer function and their first partial derivatives. The isolated nature of the zeros in the transfer function and its characteristics at high spatial frequencies result in largely reduced reconstruction artifacts and excellent reconstructions are obtained for distributions of impulses consisting of 25 to 150 impulses. The multiple-point impulse response obscures original scenes beyond recognition. This property is important for secure transmission of data on many communication systems. The multiple-point impulse response enables the decoding and restoration of the original scene with very little distortion. Images prefiltered by the random-walk transfer function yield greater compression ratios than are obtained for the original scene. The multiple-point impulse response decreases the bit rate approximately 40-70% and affords near distortion-free reconstructions. Due to the lossy nature of transform-based compression algorithms, noise reduction measures must be incorporated to yield acceptable reconstructions after decompression.

Development of a High Resolution Weather Forecast Model for Mesoamerica Using the NASA Ames Code I Private Cloud Computing Environment

NASA Technical Reports Server (NTRS)

Molthan, Andrew; Case, Jonathan; Venner, Jason; Moreno-Madrinan, Max J.; Delgado, Francisco

2012-01-01

Two projects at NASA Marshall Space Flight Center have collaborated to develop a high resolution weather forecast model for Mesoamerica: The NASA Short-term Prediction Research and Transition (SPoRT) Center, which integrates unique NASA satellite and weather forecast modeling capabilities into the operational weather forecasting community. NASA's SERVIR Program, which integrates satellite observations, ground-based data, and forecast models to improve disaster response in Central America, the Caribbean, Africa, and the Himalayas.

Transition Organometallic Heterobimettalic Microns-Carbon Dioxide and Microns-Format Complexes in Homogeneous Carbon Dioxide Fixation

DTIC Science & Technology

1992-08-12

AD-A254 538 OFFICE OF NAVAL RESEARCH FINAL REPORT FCR Contract N00014-87-K-0465 R&T Code 413j006 "Transition Organometallic Heterobimetallic ix...ransition Organometallic Heterobimetallic P-Carbon Dioxide and p-FormateComplexes in Homogeneous Carbon Dioxide Fixation 12. PERSONAL AUTHOR(S) Alan R...J. L. Shibley, and A. R. Cutler, J. Organomet. Chem. 1989,378, 421.* "Characterization of the Heterobimetallic ±(r011-C: T12 -O,O’) Carbon Dioxide

Characterization of Robotic Tail Orientation as a Function of Platform Position for Surf-Zone Robots

DTIC Science & Technology

2009-06-01

components. The basic components for Robster’s power supply and distribution system were taken from the Bigfoot robot developed by John Herkamp [5...18MAR2009 Changes: Eliminated all references to Bigfoot Arm and Thermopile Commented out sonar II. AGBOT Code v2.1 - 20MAR2009 Changes: Added...anaOutVolts(rt_ch, PW_STOP); anaOutVolts(lt_ch, PW_STOP); //Stops Bigfoot for (i = 0; i < 10; i++) 69

Electrical Microengineering of Redox Enzymes

DTIC Science & Technology

1994-03-31

coating applied to the electrode 41 to prevent lose of mediator graphite foil potassium -~0.02a 0.03  electrolyte wus dioxane with 15% 42...hexacyanoferrats(ll)d aqueous buffer carbon fiber’ none h 40-5000 biotin/avidin complex used to obtain a 43 surface layer of HRP Pt organic metal, potassium ...OFFICE OF NAVAL RESEARCH AD-A279 015 FINAL REPORT FOR CONTRACT NOOO 14-91 -J- 1656 R&T CODE 413h007---05 ELECTRICAL MICROENGINEERING OF REDOX ENZYMES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liebetrau, A.M.

Work is underway at Pacific Northwest Laboratory (PNL) to improve the probabilistic analysis used to model pressurized thermal shock (PTS) incidents in reactor pressure vessels, and, further, to incorporate these improvements into the existing Vessel Integrity Simulation Analysis (VISA) code. Two topics related to work on input distributions in VISA are discussed in this paper. The first involves the treatment of flaw size distributions and the second concerns errors in the parameters in the (Guthrie) equation which is used to compute ..delta..RT/sub NDT/, the shift in reference temperature for nil ductility transition.

Software for pre-processing Illumina next-generation sequencing short read sequences

PubMed Central

2014-01-01

Background When compared to Sanger sequencing technology, next-generation sequencing (NGS) technologies are hindered by shorter sequence read length, higher base-call error rate, non-uniform coverage, and platform-specific sequencing artifacts. These characteristics lower the quality of their downstream analyses, e.g. de novo and reference-based assembly, by introducing sequencing artifacts and errors that may contribute to incorrect interpretation of data. Although many tools have been developed for quality control and pre-processing of NGS data, none of them provide flexible and comprehensive trimming options in conjunction with parallel processing to expedite pre-processing of large NGS datasets. Methods We developed ngsShoRT (next-generation sequencing Short Reads Trimmer), a flexible and comprehensive open-source software package written in Perl that provides a set of algorithms commonly used for pre-processing NGS short read sequences. We compared the features and performance of ngsShoRT with existing tools: CutAdapt, NGS QC Toolkit and Trimmomatic. We also compared the effects of using pre-processed short read sequences generated by different algorithms on de novo and reference-based assembly for three different genomes: Caenorhabditis elegans, Saccharomyces cerevisiae S288c, and Escherichia coli O157 H7. Results Several combinations of ngsShoRT algorithms were tested on publicly available Illumina GA II, HiSeq 2000, and MiSeq eukaryotic and bacteria genomic short read sequences with the focus on removing sequencing artifacts and low-quality reads and/or bases. Our results show that across three organisms and three sequencing platforms, trimming improved the mean quality scores of trimmed sequences. Using trimmed sequences for de novo and reference-based assembly improved assembly quality as well as assembler performance. In general, ngsShoRT outperformed comparable trimming tools in terms of trimming speed and improvement of de novo and reference-based assembly as measured by assembly contiguity and correctness. Conclusions Trimming of short read sequences can improve the quality of de novo and reference-based assembly and assembler performance. The parallel processing capability of ngsShoRT reduces trimming time and improves the memory efficiency when dealing with large datasets. We recommend combining sequencing artifacts removal, and quality score based read filtering and base trimming as the most consistent method for improving sequence quality and downstream assemblies. ngsShoRT source code, user guide and tutorial are available at http://research.bioinformatics.udel.edu/genomics/ngsShoRT/. ngsShoRT can be incorporated as a pre-processing step in genome and transcriptome assembly projects. PMID:24955109

Transversal Clifford gates on folded surface codes

DOE PAGES

Moussa, Jonathan E.

2016-10-12

Surface and color codes are two forms of topological quantum error correction in two spatial dimensions with complementary properties. Surface codes have lower-depth error detection circuits and well-developed decoders to interpret and correct errors, while color codes have transversal Clifford gates and better code efficiency in the number of physical qubits needed to achieve a given code distance. A formal equivalence exists between color codes and folded surface codes, but it does not guarantee the transferability of any of these favorable properties. However, the equivalence does imply the existence of constant-depth circuit implementations of logical Clifford gates on folded surfacemore » codes. We achieve and improve this result by constructing two families of folded surface codes with transversal Clifford gates. This construction is presented generally for qudits of any dimension. Lastly, the specific application of these codes to universal quantum computation based on qubit fusion is also discussed.« less

Summary of SMIRT20 Preconference Topical Workshop – Identifying Structural Issues in Advanced Reactors

DOE Office of Scientific and Technical Information (OSTI.GOV)

William Richins; Stephen Novascone; Cheryl O'Brien

Summary of SMIRT20 Preconference Topical Workshop – Identifying Structural Issues in Advanced Reactors William Richins1, Stephen Novascone1, and Cheryl O’Brien1 1Idaho National Laboratory, US Dept. of Energy, Idaho Falls, Idaho, USA, e-mail: William.Richins@inl.gov The Idaho National Laboratory (INL, USA) and IASMiRT sponsored an international forum Nov 5-6, 2008 in Porvoo, Finland for nuclear industry, academic, and regulatory representatives to identify structural issues in current and future advanced reactor design, especially for extreme conditions and external threats. The purpose of this Topical Workshop was to articulate research, engineering, and regulatory Code development needs. The topics addressed by the Workshop were selectedmore » to address critical industry needs specific to advanced reactor structures that have long lead times and can be the subject of future SMiRT technical sessions. The topics were; 1) structural/materials needs for extreme conditions and external threats in contemporary (Gen. III) and future (Gen. IV and NGNP) advanced reactors and 2) calibrating simulation software and methods that address topic 1 The workshop discussions and research needs identified are presented. The Workshop successfully produced interactive discussion on the two topics resulting in a list of research and technology needs. It is recommended that IASMiRT communicate the results of the discussion to industry and researchers to encourage new ideas and projects. In addition, opportunities exist to retrieve research reports and information that currently exists, and encourage more international cooperation and collaboration. It is recommended that IASMiRT continue with an off-year workshop series on select topics.« less

Characterization of HIV-1 Resistance to Tenofovir Alafenamide In Vitro

PubMed Central

Johnson, Audun; Miller, Michael D.; Callebaut, Christian

2015-01-01

Tenofovir alafenamide (TAF) is an investigational prodrug of the HIV-1 nucleotide reverse transcriptase (RT) inhibitor (NtRTI) tenofovir (TFV), with improved potency and drug delivery properties over the current prodrug, tenofovir disoproxil fumarate (TDF). TAF is currently in phase 3 clinical studies for the treatment of HIV-1 infection, in combination with other antiretroviral agents. Phase 1 and 2 studies have shown that TAF was associated with increased peripheral blood mononuclear cell (PBMC) drug loading and increased suppression of HIV-1 replication compared to treatment with TDF. In this study, selection of in vitro resistance to both TAF and the parent compound, TFV, led to the emergence of HIV-1 with the K65R amino acid substitution in RT with 6.5-fold-reduced susceptibility to TAF. Although TAF is more potent than TFV in vitro, the antiviral susceptibilities to TAF and TFV of a large panel of nucleoside/nucleotide RT inhibitor (NRTI)-resistant mutants were highly correlated (R2 = 0.97), indicating that the two compounds have virtually the same resistance profile when assessed as fold change from the wild type. TAF showed full antiviral activity in PBMCs against primary HIV-1 isolates with protease inhibitor, nonnucleoside RT inhibitor (NNRTI), or integrase strand transfer inhibitor resistance but reduced activity against isolates with extensive NRTI resistance amino acid substitutions. However, the increased cell loading of TFV with TAF versus TDF observed in vivo suggests that TAF may retain activity against TDF-resistant mutant viruses. PMID:26149983

Decline of Tumor Vascular Function as Assessed by Dynamic Contrast-Enhanced Magnetic Resonance Imaging Is Associated With Poor Responses to Radiation Therapy and Chemotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Fang-Hsin; Wang, Chun-Chieh; Radiation Biology Research Center, Institute for Radiological Research, Chang Gung University/Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan

Purpose: To investigate whether changes in the volume transfer coefficient (K{sup trans}) in a growing tumor could be used as a surrogate marker for predicting tumor responses to radiation therapy (RT) and chemotherapy (CT). Methods and Materials: Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) was consecutively performed on tumor-bearing mice, and temporal and spatial changes of K{sup trans} values were measured along with tumor growth. Tumor responses to RT and CT were studied before and after observed changes in K{sup trans} values with time. Results: Dynamic changes with an initial increase and subsequent decline in K{sup trans} values were found tomore » be associated with tumor growth. When each tumor was divided into core and peripheral regions, the K{sup trans} decline was greater in core, although neither vascular structure or necrosis could be linked to this spatial difference. Tumor responses to RT were worse if applied after the decline of K{sup trans}, and there was less drug distribution and cell death in the tumor core after CT. Conclusion: The K{sup trans} value in growing tumors, reflecting the changes of tumor microenvironment and vascular function, is strongly associated with tumor responses to RT and CT and could be a potential surrogate marker for predicting the tumor response to these treatments.« less

Transferring ecosystem simulation codes to supercomputers

NASA Technical Reports Server (NTRS)

Skiles, J. W.; Schulbach, C. H.

1995-01-01

Many ecosystem simulation computer codes have been developed in the last twenty-five years. This development took place initially on main-frame computers, then mini-computers, and more recently, on micro-computers and workstations. Supercomputing platforms (both parallel and distributed systems) have been largely unused, however, because of the perceived difficulty in accessing and using the machines. Also, significant differences in the system architectures of sequential, scalar computers and parallel and/or vector supercomputers must be considered. We have transferred a grassland simulation model (developed on a VAX) to a Cray Y-MP/C90. We describe porting the model to the Cray and the changes we made to exploit the parallelism in the application and improve code execution. The Cray executed the model 30 times faster than the VAX and 10 times faster than a Unix workstation. We achieved an additional speedup of 30 percent by using the compiler's vectoring and 'in-line' capabilities. The code runs at only about 5 percent of the Cray's peak speed because it ineffectively uses the vector and parallel processing capabilities of the Cray. We expect that by restructuring the code, it could execute an additional six to ten times faster.

Design and Analysis of Boiler Pressure Vessels based on IBR codes

NASA Astrophysics Data System (ADS)

Balakrishnan, B.; Kanimozhi, B.

2017-05-01

Pressure vessels components are widely used in the thermal and nuclear power plants for generating steam using the philosophy of heat transfer. In Thermal power plant, Coal is burnt inside the boiler furnace for generating the heat. The amount of heat produced through the combustion of pulverized coal is used in changing the phase transfer (i.e. Water into Super-Heated Steam) in the Pressure Parts Component. Pressure vessels are designed as per the Standards and Codes of the country, where the boiler is to be installed. One of the Standards followed in designing Pressure Parts is ASME (American Society of Mechanical Engineers). The mandatory requirements of ASME code must be satisfied by the manufacturer. In our project case, A Shell/pipe which has been manufactured using ASME code has an issue during the drilling of hole. The Actual Size of the drilled holes must be, as per the drawing, but due to error, the size has been differentiate from approved design calculation (i.e. the diameter size has been exceeded). In order to rectify this error, we have included an additional reinforcement pad to the drilled and modified the design of header in accordance with the code requirements.

High Temperature Gas Energy Transfer.

DTIC Science & Technology

1980-08-12

Office of Naval Research 1 Code 260 Code AFRPL MKPAArlingon, VA 22217 Edwards AFB, CA 93523Attn: Mr. D. Siegel Attn: Dr. F. Roberto Office of Naval...ResearchOffice of Naval Research Directorate of Aero-San Francisco Area Office space SciencesOne allidie Plaza Suite 601 Bolling Air Force BaseSan Francisco, CA

Hypersonic CFD applications at NASA Langley using CFL3D and CFL3DE

NASA Technical Reports Server (NTRS)

Richardson, Pamela F.

1989-01-01

The CFL3D/CFL3DE CFD codes and the industrial use status of the codes are outlined. Comparison of grid density, pressure, heat transfer, and aerodynamic coefficience are presented. Future plans related to the National Aerospace Plane Program are briefly outlined.

75 FR 53019 - Proposed Collection; Comment Request for Regulation Project

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-30

... soliciting comments concerning an existing regulation, REG-147144-06, (TD 9446) Section 1.367(a)-8, Gain...: Gain Recognition Agreements With Respect to Certain Transfers of Stock or Securities by United States... Internal Revenue Code (Code) concerning gain recognition agreements filed by United States persons with...

Studies of Heat Transfer in Complex Internal Flows.

DTIC Science & Technology

1982-01-01

D.C. 20362 (Tel 202-692-6874) Mr. Richard S. Carlton Director, Engines Division, Code 523 NC #4 Naval Sea Systems Command Washington, D.C. 20362...Walter Ritz Code 033C Naval Ships Systems Engineering Station Philadelphia, Pennsylvania 19112 (Tel. 215-755-3841) Dr. Simion Kuo United Tech. Res

Comparative Dosimetric Estimates of a 25 keV Electron Micro-beam with three Monte Carlo Codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mainardi, Enrico; Donahue, Richard J.; Blakely, Eleanor A.

2002-09-11

The calculations presented compare the different performances of the three Monte Carlo codes PENELOPE-1999, MCNP-4C and PITS, for the evaluation of Dose profiles from a 25 keV electron micro-beam traversing individual cells. The overall model of a cell is a water cylinder equivalent for the three codes but with a different internal scoring geometry: hollow cylinders for PENELOPE and MCNP, whereas spheres are used for the PITS code. A cylindrical cell geometry with scoring volumes with the shape of hollow cylinders was initially selected for PENELOPE and MCNP because of its superior simulation of the actual shape and dimensions ofmore » a cell and for its improved computer-time efficiency if compared to spherical internal volumes. Some of the transfer points and energy transfer that constitute a radiation track may actually fall in the space between spheres, that would be outside the spherical scoring volume. This internal geometry, along with the PENELOPE algorithm, drastically reduced the computer time when using this code if comparing with event-by-event Monte Carlo codes like PITS. This preliminary work has been important to address dosimetric estimates at low electron energies. It demonstrates that codes like PENELOPE can be used for Dose evaluation, even with such small geometries and energies involved, which are far below the normal use for which the code was created. Further work (initiated in Summer 2002) is still needed however, to create a user-code for PENELOPE that allows uniform comparison of exact cell geometries, integral volumes and also microdosimetric scoring quantities, a field where track-structure codes like PITS, written for this purpose, are believed to be superior.« less

Characterization of circulating transfer RNA-Derived RNA fragments in cattle

USDA-ARS?s Scientific Manuscript database

The objective was to characterize naturally occurring circulating transfer RNA-derived RNA Fragments (tRFs) in cattle. Serum from eight clinically normal adult dairy cows was collected, and small non-coding RNAs were extracted immediately after collection and sequenced by Illumina MiSeq. Sequences a...

Promoting Transfer of Ecosystems Concepts

ERIC Educational Resources Information Center

Yu, Yawen; Hmelo-Silver, Cindy E.; Jordan, Rebecca; Eberbach, Catherine; Sinha, Suparna

2016-01-01

This study examines to what extent students transferred their knowledge from a familiar aquatic ecosystem to an unfamiliar rainforest ecosystem after participating in a technology-rich inquiry curriculum. We coded students' drawings for components of important ecosystems concepts at pre- and posttest. Our analysis examined the extent to which each…

Assessment of polarization effect on aerosol retrievals from MODIS

NASA Astrophysics Data System (ADS)

Korkin, S.; Lyapustin, A.

2010-12-01

Light polarization affects the total intensity of scattered radiation. In this work, we compare aerosol retrievals performed by code MAIAC [1] with and without taking polarization into account. The MAIAC retrievals are based on the look-up tables (LUT). For this work, MAIAC was run using two different LUTs, the first one generated using the scalar code SHARM [2], and the second one generated with the vector code Modified Vector Discrete Ordinates Method (MVDOM). MVDOM is a new code suitable for computations with highly anisotropic phase functions, including cirrus clouds and snow [3]. To this end, the solution of the vector radiative transfer equation (VRTE) is represented as a sum of anisotropic and regular components. The anisotropic component is evaluated in the Small Angle Modification of the Spherical Harmonics Method (MSH) [4]. The MSH is formulated in the frame of reference of the solar beam where z-axis lies along the solar beam direction. In this case, the MSH solution for anisotropic part is nearly symmetric in azimuth, and is computed analytically. In scalar case, this solution coincides with the Goudsmit-Saunderson small-angle approximation [5]. To correct for an analytical separation of the anisotropic part of the signal, the transfer equation for the regular part contains a correction source function term [6]. Several examples of polarization impact on aerosol retrievals over different surface types will be presented. 1. Lyapustin A., Wang Y., Laszlo I., Kahn R., Korkin S., Remer L., Levy R., and Reid J. S. Multi-Angle Implementation of Atmospheric Correction (MAIAC): Part 2. Aerosol Algorithm. J. Geophys. Res., submitted (2010). 2. Lyapustin A., Muldashev T., Wang Y. Code SHARM: fast and accurate radiative transfer over spatially variable anisotropic surfaces. In: Light Scattering Reviews 5. Chichester: Springer, 205 - 247 (2010). 3. Budak, V.P., Korkin S.V. On the solution of a vectorial radiative transfer equation in an arbitrary three-dimensional turbid medium with anisotropic scattering. JQSRT, 109, 220-234 (2008). 4. Budak V.P., Sarmin S.E. Solution of radiative transfer equation by the method of spherical harmonics in the small angle modification. Atmospheric and Oceanic Optics, 3, 898-903 (1990). 5. Goudsmit S., Saunderson J.L. Multiple scattering of electrons. Phys. Rev., 57, 24-29 (1940). 6. Budak V.P, Klyuykov D.A., Korkin S.V. Convergence acceleration of radiative transfer equation solution at strongly anisotropic scattering. In: Light Scattering Reviews 5. Chichester: Springer, 147 - 204 (2010).

Intermanual transfer effects in sequential tactuomotor learning: evidence for effector independent coding.

PubMed

van Mier, Hanneke I; Petersen, Steven E

2006-01-01

Results from our earlier brain imaging studies regarding motor learning have shown different areas activated during naive and practiced performance. When right handed participants moved a pen either with the dominant or non-dominant hand continuously through a cut-out maze as quickly and accurately as possible, practice resulted in decreased brain activity in right premotor and parietal areas as well as left cerebellum, while increased activity was found in the supplementary motor area (SMA). These lateralized practiced-related changes in brain activation suggest effector-independent abstract coding of information. To test this hypothesis more extensively, intermanual transfer of learning was examined in 24 male and female participants (12 right- and 12 left-handed) using the same maze-learning task. It was hypothesized that if an abstract representation of the movement is learned and stored, intermanual transfer effects should be more pronounced when participants transferred to a same maze as opposed to a mirror image of the maze. Errors and velocity were measured during the following conditions: initial naive performance (Naive); after practice on the maze (Prac); during intermanual transfer to the same maze (Transfer Identical); and to the mirror maze (Transfer Mirror). Transfer direction was tested from the dominant to non-dominant hand and vice versa. No significant differences were found between right- and left-handed participants, males and females, and transfer directions. However, intermanual transfer of learning was significantly greater to the identical maze as opposed to the mirror maze. These results showed that learning was indeed taking place at an abstract effector independent level.

Excitation wavelength dependence of the fluorescence kinetics in Photosystem I particles from Synechocystis PCC 6803 and Synechococcus elongatus.

PubMed

Gobets, Bas; van Stokkum, Ivo H M; van Mourik, Frank; Dekker, Jan P; van Grondelle, Rienk

2003-12-01

The excitation-wavelength dependence of the excited-state dynamics of monomeric and trimeric Photosystem I (PSI) particles from Synechocystis PCC 6803 as well as trimeric PSI particles from Synechococcus elongatus has been studied at room temperature using time-resolved fluorescence spectroscopy. For aselective (400 nm), carotenoid (505 nm), and bulk chlorophyll (approximately 650 nm) excitation in all species, a downhill energy-transfer component is observed, corresponding to a lifetime of 3.4-5.5 ps. For selective red excitation (702-719 nm) in all species, a significantly faster, an approximately 1-ps, uphill transfer component was recorded. In Synechococcus PSI, an additional approximately 10-ps downhill energy-transfer component is found for all wavelengths of excitation, except 719 nm. Each of the species exhibits its own characteristic trap spectrum, the shape of which is independent of the wavelength of excitation. This trap spectrum decays in approximately 23 ps in both monomeric and trimeric Synechocystis PSI and in approximately 35 ps in trimeric Synechococcus PSI. The data were simulated based on the 2.5 A structural model of PSI of Synechococcus elongatus using the Förster equation for energy transfer, and using the 0.6-1-ps charge-separation time and the value of 1.2-1.3 for the index of refraction that were obtained from the dynamics of a hypothetical PSI particle without red chls. The experimentally obtained lifetimes and spectra were reproduced well by assigning three of the chlorophyll-a (chla) dimers observed in the structure to the C708/C702RT pool of red chls present in PSI from both species. Essential for the simulation of the dynamics of Synechococcus PSI is the assignment of the single chla trimer in the structure to the C719/C708RT pool present in this species.

Persistence and transferability of noroviruses on and between common surfaces and foods.

PubMed

Escudero, B I; Rawsthorne, H; Gensel, C; Jaykus, L A

2012-05-01

Human noroviruses (HuNoV) are the leading cause of foodborne disease, and poor personal hygiene practices of infected workers are the most common mode of contamination. The purpose of this study was to characterize the persistence and transferability of representative noroviruses Norwalk virus (NV), Snow Mountain virus (SMV), and murine norovirus 1 (MNV-1) on and between solid surfaces and foods. Changes in virus concentration on artificially inoculated solid surfaces (stainless steel, ceramic, and Formica) or lettuce were monitored over a period of 14 to 42 days. Virus transfer was evaluated from donor (solid surface) to recipient (food, e.g., lettuce and sliced turkey deli meat) for up to 2 h postinoculation. Viruses were recovered by elution and titered with reverse transcription quantitative PCR (RT-qPCR) and/or infectivity assay, as appropriate. Based on RTqPCR, the concentration of NV and SMV on surfaces dropped gradually over time, with an average reduction of 1.5 to 2.0 and 1.8 to 2.3 log, respectively, after 42 days, with no statistically significant differences by surface. When inoculated onto lettuce stored for 2 weeks at 4°C and room temperature, the titers of NV and SMV dropped by approximately 1.0 and 1.2 to 1.8 log, respectively. Comparatively, the RT-qPCR signal associated with purified HuNoV RNA placed on the same surfaces was more rapidly lost to degradation. Transfer efficiency ranged from 0 to 26 % for lettuce and from 55 to 95 % for sliced turkey deli meat, with statistically significant differences (P ≤ 0.05) in transferability as a function of contact pressure (100 and 1,000 g/9 cm(2)) and inoculum drying time. When similar experiments were done with MNV-1, infectious virus failed to be detected on solid surfaces after storage day 21, although the virus did persist on lettuce. This study provides much needed quantitative data for use in risk assessment efforts intended to characterize the transmission of HuNoV during food preparation and handling.

The effects of potato virus Y-derived virus small interfering RNAs of three biologically distinct strains on potato (Solanum tuberosum) transcriptome.

PubMed

Moyo, Lindani; Ramesh, Shunmugiah V; Kappagantu, Madhu; Mitter, Neena; Sathuvalli, Vidyasagar; Pappu, Hanu R

2017-07-17

Potato virus Y (PVY) is one of the most economically important pathogen of potato that is present as biologically distinct strains. The virus-derived small interfering RNAs (vsiRNAs) from potato cv. Russet Burbank individually infected with PVY-N, PVY-NTN and PVY-O strains were recently characterized. Plant defense RNA-silencing mechanisms deployed against viruses produce vsiRNAs to degrade homologous viral transcripts. Based on sequence complementarity, the vsiRNAs can potentially degrade host RNA transcripts raising the prospect of vsiRNAs as pathogenicity determinants in virus-host interactions. This study investigated the global effects of PVY vsiRNAs on the host potato transcriptome. The strain-specific vsiRNAs of PVY, expressed in high copy number, were analyzed in silico for their proclivity to target potato coding and non-coding RNAs using psRobot and psRNATarget algorithms. Functional annotation of target coding transcripts was carried out to predict physiological effects of the vsiRNAs on the potato cv. Russet Burbank. The downregulation of selected target coding transcripts was further validated using qRT-PCR. The vsiRNAs derived from biologically distinct strains of PVY displayed diversity in terms of absolute number, copy number and hotspots for siRNAs on their respective genomes. The vsiRNAs populations were derived with a high frequency from 6 K1, P1 and Hc-Pro for PVY-N, P1, Hc-Pro and P3 for PVY-NTN, and P1, 3' UTR and NIa for PVY-O genomic regions. The number of vsiRNAs that displayed interaction with potato coding transcripts and number of putative coding target transcripts were comparable between PVY-N and PVY-O, and were relatively higher for PVY-NTN. The most abundant target non-coding RNA transcripts for the strain specific PVY-derived vsiRNAs were found to be MIR821, 28S rRNA,18S rRNA, snoR71, tRNA-Met and U5. Functional annotation and qRT-PCR validation suggested that the vsiRNAs target genes involved in plant hormone signaling, genetic information processing, plant-pathogen interactions, plant defense and stress response processes in potato. The findings suggested that the PVY-derived vsiRNAs could act as a pathogenicity determinant and as a counter-defense strategy to host RNA silencing in PVY-potato interactions. The broad range of host genes targeted by PVY vsiRNAs in infected potato suggests a diverse role for vsiRNAs that includes suppression of host stress responses and developmental processes. The interactome scenario is the first report on the interaction between one of the most important Potyvirus genome-derived siRNAs and the potato transcripts.

Development of tailored real-time RT-PCR assays for the detection and differentiation of serotype O, A and Asia-1 foot-and-mouth disease virus lineages circulating in the Middle East.

PubMed

Reid, Scott M; Mioulet, Valerie; Knowles, Nick J; Shirazi, Nazeem; Belsham, Graham J; King, Donald P

2014-10-01

Rapid and accurate diagnosis is essential for effective control of foot-and-mouth disease (FMD). In countries where FMD is endemic, identification of the serotypes of the causative virus strains is important for vaccine selection and tracing the source of outbreaks. In this study, real-time reverse transcription polymerase chain reaction (rRT-PCR) assays using primer/probe sets designed from the VP1 coding region of the virus genomes were developed for the specific detection of serotype O, A and Asia-1 FMD viruses (FMDVs) circulating in the Middle East. These assays were evaluated using representative field samples of serotype O strains belonging exclusively to the PanAsia-2 lineage, serotype A strains of the Iran-05 lineage and serotype Asia-1 viruses from three relevant sub-groups. When RNA extracted from archival and contemporary field strains was tested using one- or two-step rRT-PCR assays, all three primer/probe sets detected the RNA from homotypic viruses and no cross-reactivity was observed with heterotypic viruses. Similar results were obtained using both single- and multiplex assay formats. Using plasmid standards, the minimum detection level of these tests was found to be lower than two copies. The results illustrate the potential of tailored rRT-PCR tools for the detection and categorization of viruses circulating in the Middle East belonging to distinct subgroups of serotypes O, A and Asia-1. These assays can also overcome the problem of serotyping samples which are found positive by the generic rRT-PCR diagnostic assays but negative by virus isolation and antigen-detection ELISA which would otherwise have to be serotyped by nucleotide sequencing. A similar approach could be used to develop serotyping assays for FMDV strains circulating in other regions of the world. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

SU-F-J-72: A Clinical Usable Integrated Contouring Quality Evaluation Software for Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, S; Dolly, S; Cai, B

Purpose: To introduce the Auto Contour Evaluation (ACE) software, which is the clinical usable, user friendly, efficient and all-in-one toolbox for automatically identify common contouring errors in radiotherapy treatment planning using supervised machine learning techniques. Methods: ACE is developed with C# using Microsoft .Net framework and Windows Presentation Foundation (WPF) for elegant GUI design and smooth GUI transition animations through the integration of graphics engines and high dots per inch (DPI) settings on modern high resolution monitors. The industrial standard software design pattern, Model-View-ViewModel (MVVM) pattern, is chosen to be the major architecture of ACE for neat coding structure, deepmore » modularization, easy maintainability and seamless communication with other clinical software. ACE consists of 1) a patient data importing module integrated with clinical patient database server, 2) a 2D DICOM image and RT structure simultaneously displaying module, 3) a 3D RT structure visualization module using Visualization Toolkit or VTK library and 4) a contour evaluation module using supervised pattern recognition algorithms to detect contouring errors and display detection results. ACE relies on supervised learning algorithms to handle all image processing and data processing jobs. Implementations of related algorithms are powered by Accord.Net scientific computing library for better efficiency and effectiveness. Results: ACE can take patient’s CT images and RT structures from commercial treatment planning software via direct user input or from patients’ database. All functionalities including 2D and 3D image visualization and RT contours error detection have been demonstrated with real clinical patient cases. Conclusion: ACE implements supervised learning algorithms and combines image processing and graphical visualization modules for RT contours verification. ACE has great potential for automated radiotherapy contouring quality verification. Structured with MVVM pattern, it is highly maintainable and extensible, and support smooth connections with other clinical software tools.« less

MicroRNA markers for forensic body fluid identification obtained from microarray screening and quantitative RT-PCR confirmation

PubMed Central

Zubakov, Dmitry; Boersma, Anton W. M.; Choi, Ying; van Kuijk, Patricia F.; Wiemer, Erik A. C.

2010-01-01

MicroRNAs (miRNAs) are non-protein coding molecules with important regulatory functions; many have tissue-specific expression patterns. Their very small size in principle makes them less prone to degradation processes, unlike messenger RNAs (mRNAs), which were previously proposed as molecular tools for forensic body fluid identification. To identify suitable miRNA markers for forensic body fluid identification, we first screened total RNA samples derived from saliva, semen, vaginal secretion, and venous and menstrual blood for the expression of 718 human miRNAs using a microarray platform. All body fluids could be easily distinguished from each other on the basis of complete array-based miRNA expression profiles. Results from quantitative reverse transcription PCR (RT-PCR; TaqMan) assays for microarray candidate markers confirmed strong over-expression in the targeting body fluid of several miRNAs for venous blood and several others for semen. However, no candidate markers from array experiments for other body fluids such as saliva, vaginal secretion, or menstrual blood could be confirmed by RT-PCR. Time-wise degradation of venous blood and semen stains for at least 1 year under lab conditions did not significantly affect the detection sensitivity of the identified miRNA markers. The detection limit of the TaqMan assays tested for selected venous blood and semen miRNA markers required only subpicogram amounts of total RNA per single RT-PCR test, which is considerably less than usually needed for reliable mRNA RT-PCR detection. We therefore propose the application of several stable miRNA markers for the forensic identification of blood stains and several others for semen stain identification, using commercially available TaqMan assays. Additional work remains necessary in search for suitable miRNA markers for other forensically relevant body fluids. Electronic supplementary material The online version of this article (doi:10.1007/s00414-009-0402-3) contains supplementary material, which is available to authorized users. PMID:20145944

Subsystem real-time time dependent density functional theory.

PubMed

Krishtal, Alisa; Ceresoli, Davide; Pavanello, Michele

2015-04-21

We present the extension of Frozen Density Embedding (FDE) formulation of subsystem Density Functional Theory (DFT) to real-time Time Dependent Density Functional Theory (rt-TDDFT). FDE is a DFT-in-DFT embedding method that allows to partition a larger Kohn-Sham system into a set of smaller, coupled Kohn-Sham systems. Additional to the computational advantage, FDE provides physical insight into the properties of embedded systems and the coupling interactions between them. The extension to rt-TDDFT is done straightforwardly by evolving the Kohn-Sham subsystems in time simultaneously, while updating the embedding potential between the systems at every time step. Two main applications are presented: the explicit excitation energy transfer in real time between subsystems is demonstrated for the case of the Na4 cluster and the effect of the embedding on optical spectra of coupled chromophores. In particular, the importance of including the full dynamic response in the embedding potential is demonstrated.

Software Exploit Prevention and Remediation via Software Memory Protection

DTIC Science & Technology

2009-05-01

trampolines that are necessary. Trampolines are pieces of code emitted into the fragment cache to transfer con- trol back to Strata. Most control...transfer instructions (CTIs) are initially linked to trampolines (unless the transfer target already exists in the fragment cache). Once a CTI’s target...instruction becomes available in the fragment cache, the CTI is linked directly to the destination, avoiding future uses of the trampoline . This

Supporting Students' Knowledge Transfer in Modeling Activities

ERIC Educational Resources Information Center

Piksööt, Jaanika; Sarapuu, Tago

2014-01-01

This study investigates ways to enhance secondary school students' knowledge transfer in complex science domains by implementing question prompts. Two samples of students applied two web-based models to study molecular genetics--the model of genetic code (n = 258) and translation (n = 245). For each model, the samples were randomly divided into…

29 CFR 4043.28 - Plan merger, consolidation, or transfer.

Code of Federal Regulations, 2012 CFR

2012-07-01

... TERMINATIONS REPORTABLE EVENTS AND CERTAIN OTHER NOTIFICATION REQUIREMENTS Post-Event Notice of Reportable Events § 4043.28 Plan merger, consolidation, or transfer. (a) Reportable event. A reportable event occurs... section 414(1) of the Code. (b) Waivers. Notice is waived for this event. However, notice may be required...

29 CFR 4043.28 - Plan merger, consolidation, or transfer.

Code of Federal Regulations, 2011 CFR

2011-07-01

... TERMINATIONS REPORTABLE EVENTS AND CERTAIN OTHER NOTIFICATION REQUIREMENTS Post-Event Notice of Reportable Events § 4043.28 Plan merger, consolidation, or transfer. (a) Reportable event. A reportable event occurs... section 414(1) of the Code. (b) Waivers. Notice is waived for this event. However, notice may be required...

29 CFR 4043.28 - Plan merger, consolidation, or transfer.

Code of Federal Regulations, 2014 CFR

2014-07-01

... TERMINATIONS REPORTABLE EVENTS AND CERTAIN OTHER NOTIFICATION REQUIREMENTS Post-Event Notice of Reportable Events § 4043.28 Plan merger, consolidation, or transfer. (a) Reportable event. A reportable event occurs... section 414(1) of the Code. (b) Waivers. Notice is waived for this event. However, notice may be required...

29 CFR 4043.28 - Plan merger, consolidation, or transfer.

Code of Federal Regulations, 2013 CFR

2013-07-01

... TERMINATIONS REPORTABLE EVENTS AND CERTAIN OTHER NOTIFICATION REQUIREMENTS Post-Event Notice of Reportable Events § 4043.28 Plan merger, consolidation, or transfer. (a) Reportable event. A reportable event occurs... section 414(1) of the Code. (b) Waivers. Notice is waived for this event. However, notice may be required...

29 CFR 4043.28 - Plan merger, consolidation, or transfer.

Code of Federal Regulations, 2010 CFR

2010-07-01

... TERMINATIONS REPORTABLE EVENTS AND CERTAIN OTHER NOTIFICATION REQUIREMENTS Post-Event Notice of Reportable Events § 4043.28 Plan merger, consolidation, or transfer. (a) Reportable event. A reportable event occurs... section 414(1) of the Code. (b) Waivers. Notice is waived for this event. However, notice may be required...

Report of the Secretary of Defense Task Force on DoD Nuclear Weapons Management. Phase 1. The Air Force’s Nuclear Mission

DTIC Science & Technology

2008-09-01

under- resourced. • Missile transfer vans /warhead transfer vans require upgrades. • ICBM weapon system test sets under-funded; the coding system...Air Force’s Nuclear Mission D-1 Appendix D. Current B-52 Basing Status Barksdale AFB, LA 64 B-52Hs Minot AFB, ND 27 B-52Hs Edwards AFB, CA 3...Barksdale – 64 B-52s 2 BW (ACC) 15 TF; 24 CC; 7 BAI 53 WG (ACC) 2 Test Coded 917 WG (AFRC) 8 CC; 1 BAI 7 Unfunded AR Edwards - 3 B-52s 412 TW 2 Test

Thermal protection for hypervelocity flight in earth's atmosphere by use of radiation backscattering ablating materials

NASA Technical Reports Server (NTRS)

Howe, John T.; Yang, Lily

1991-01-01

A heat-shield-material response code predicting the transient performance of a material subject to the combined convective and radiative heating associated with the hypervelocity flight is developed. The code is dynamically interactive to the heating from a transient flow field, including the effects of material ablation on flow field behavior. It accomodates finite time variable material thickness, internal material phase change, wavelength-dependent radiative properties, and temperature-dependent thermal, physical, and radiative properties. The equations of radiative transfer are solved with the material and are coupled to the transfer energy equation containing the radiative flux divergence in addition to the usual energy terms.

TRUST. I. A 3D externally illuminated slab benchmark for dust radiative transfer

NASA Astrophysics Data System (ADS)

Gordon, K. D.; Baes, M.; Bianchi, S.; Camps, P.; Juvela, M.; Kuiper, R.; Lunttila, T.; Misselt, K. A.; Natale, G.; Robitaille, T.; Steinacker, J.

2017-07-01

Context. The radiative transport of photons through arbitrary three-dimensional (3D) structures of dust is a challenging problem due to the anisotropic scattering of dust grains and strong coupling between different spatial regions. The radiative transfer problem in 3D is solved using Monte Carlo or Ray Tracing techniques as no full analytic solution exists for the true 3D structures. Aims: We provide the first 3D dust radiative transfer benchmark composed of a slab of dust with uniform density externally illuminated by a star. This simple 3D benchmark is explicitly formulated to provide tests of the different components of the radiative transfer problem including dust absorption, scattering, and emission. Methods: The details of the external star, the slab itself, and the dust properties are provided. This benchmark includes models with a range of dust optical depths fully probing cases that are optically thin at all wavelengths to optically thick at most wavelengths. The dust properties adopted are characteristic of the diffuse Milky Way interstellar medium. This benchmark includes solutions for the full dust emission including single photon (stochastic) heating as well as two simplifying approximations: One where all grains are considered in equilibrium with the radiation field and one where the emission is from a single effective grain with size-distribution-averaged properties. A total of six Monte Carlo codes and one Ray Tracing code provide solutions to this benchmark. Results: The solution to this benchmark is given as global spectral energy distributions (SEDs) and images at select diagnostic wavelengths from the ultraviolet through the infrared. Comparison of the results revealed that the global SEDs are consistent on average to a few percent for all but the scattered stellar flux at very high optical depths. The image results are consistent within 10%, again except for the stellar scattered flux at very high optical depths. The lack of agreement between different codes of the scattered flux at high optical depths is quantified for the first time. Convergence tests using one of the Monte Carlo codes illustrate the sensitivity of the solutions to various model parameters. Conclusions: We provide the first 3D dust radiative transfer benchmark and validate the accuracy of this benchmark through comparisons between multiple independent codes and detailed convergence tests.

Carrier-phase time transfer.

PubMed

Larson, K M; Levine, J

1999-01-01

We have conducted several time-transfer experiments using the phase of the GPS carrier rather than the code, as is done in current GPS-based time-transfer systems. Atomic clocks were connected to geodetic GPS receivers; we then used the GPS carrier-phase observations to estimate relative clock behavior at 6-minute intervals. GPS carrier-phase time transfer is more than an order of magnitude more precise than GPS common view time transfer and agrees, within the experimental uncertainty, with two-way satellite time-transfer measurements for a 2400 km baseline. GPS carrier-phase time transfer has a stability of 100 ps, which translates into a frequency uncertainty of about two parts in 10(-15) for an average time of 1 day.

NOR-USA Scientific Traverse of East Antarctica: Science and Logistics on a Three-Month Expedition Across Antarctica's Farthest Frontier

NASA Technical Reports Server (NTRS)

Albert, Mary R.

2012-01-01

Dr. Albert's current research is centered on transfer processes in porous media, including air-snow exchange in the Polar Regions and in soils in temperate areas. Her research includes field measurements, laboratory experiments, and theoretical modeling. Mary conducts field and laboratory measurements of the physical properties of natural terrain surfaces, including permeability, microstructure, and thermal conductivity. Mary uses the measurements to examine the processes of diffusion and advection of heat, mass, and chemical transport through snow and other porous media. She has developed numerical models for investigation of a variety of problems, from interstitial transport to freezing of flowing liquids. These models include a two-dimensional finite element code for air flow with heat, water vapor, and chemical transport in porous media, several multidimensional codes for diffusive transfer, as well as a computational fluid dynamics code for analysis of turbulent water flow in moving-boundary phase change problems.

Exact first order scattering correction for vector radiative transfer in coupled atmosphere and ocean systems

NASA Astrophysics Data System (ADS)

Zhai, Peng-Wang; Hu, Yongxiang; Josset, Damien B.; Trepte, Charles R.; Lucker, Patricia L.; Lin, Bing

2012-06-01

We have developed a Vector Radiative Transfer (VRT) code for coupled atmosphere and ocean systems based on the successive order of scattering (SOS) method. In order to achieve efficiency and maintain accuracy, the scattering matrix is expanded in terms of the Wigner d functions and the delta fit or delta-M technique is used to truncate the commonly-present large forward scattering peak. To further improve the accuracy of the SOS code, we have implemented the analytical first order scattering treatment using the exact scattering matrix of the medium in the SOS code. The expansion and truncation techniques are kept for higher order scattering. The exact first order scattering correction was originally published by Nakajima and Takana.1 A new contribution of this work is to account for the exact secondary light scattering caused by the light reflected by and transmitted through the rough air-sea interface.

A Parallel Numerical Algorithm To Solve Linear Systems Of Equations Emerging From 3D Radiative Transfer

NASA Astrophysics Data System (ADS)

Wichert, Viktoria; Arkenberg, Mario; Hauschildt, Peter H.

2016-10-01

Highly resolved state-of-the-art 3D atmosphere simulations will remain computationally extremely expensive for years to come. In addition to the need for more computing power, rethinking coding practices is necessary. We take a dual approach by introducing especially adapted, parallel numerical methods and correspondingly parallelizing critical code passages. In the following, we present our respective work on PHOENIX/3D. With new parallel numerical algorithms, there is a big opportunity for improvement when iteratively solving the system of equations emerging from the operator splitting of the radiative transfer equation J = ΛS. The narrow-banded approximate Λ-operator Λ* , which is used in PHOENIX/3D, occurs in each iteration step. By implementing a numerical algorithm which takes advantage of its characteristic traits, the parallel code's efficiency is further increased and a speed-up in computational time can be achieved.

Development of a thermal and structural analysis procedure for cooled radial turbines

NASA Technical Reports Server (NTRS)

Kumar, Ganesh N.; Deanna, Russell G.

1988-01-01

A procedure for computing the rotor temperature and stress distributions in a cooled radial turbine are considered. Existing codes for modeling the external mainstream flow and the internal cooling flow are used to compute boundary conditions for the heat transfer and stress analysis. The inviscid, quasi three dimensional code computes the external free stream velocity. The external velocity is then used in a boundary layer analysis to compute the external heat transfer coefficients. Coolant temperatures are computed by a viscous three dimensional internal flow cade for the momentum and energy equation. These boundary conditions are input to a three dimensional heat conduction code for the calculation of rotor temperatures. The rotor stress distribution may be determined for the given thermal, pressure and centrifugal loading. The procedure is applied to a cooled radial turbine which will be tested at the NASA Lewis Research Center. Representative results are given.

Extracellular vesicle-mediated transfer of donor genomic DNA to recipient cells is a novel mechanism for genetic influence between cells

PubMed Central

Cai, Jin; Han, Yu; Ren, Hongmei; Chen, Caiyu; He, Duofen; Zhou, Lin; Eisner, Gilbert M.; Asico, Laureano D.; Jose, Pedro A.; Zeng, Chunyu

2013-01-01

Extracellular vesicles (EVs) carry signals within or at their limiting membranes, providing a mechanism by which cells can exchange more complex information than what was previously thought. In addition to mRNAs and microRNAs, there are DNA fragments in EVs. Solexa sequencing indicated the presence of at least 16434 genomic DNA (gDNA) fragments in the EVs from human plasma. Immunofluorescence study showed direct evidence that acridine orange-stained EV DNAs could be transferred into the cells and localize to and inside the nuclear membrane. However, whether the transferred EV DNAs are functional or not is not clear. We found that EV gDNAs could be homologously or heterologously transferred from donor cells to recipient cells, and increase gDNA-coding mRNA, protein expression, and function (e.g. AT1 receptor). An endogenous promoter of the AT1 receptor, NF-κB, could be recruited to the transferred DNAs in the nucleus, and increase the transcription of AT1 receptor in the recipient cells. Moreover, the transferred EV gDNAs have pathophysiological significance. BCR/ABL hybrid gene, involved in the pathogenesis of chronic myeloid leukemia, could be transferred from K562 EVs to HEK293 cells or neutrophils. Our present study shows that the gDNAs transferred from EVs to cells have physiological significance, not only to increase the gDNA-coding mRNA and protein levels, but also to influence function in recipient cells. PMID:23580760

The transfer and transformation of collective network information in gene-matched networks.

PubMed

Kitsukawa, Takashi; Yagi, Takeshi

2015-10-09

Networks, such as the human society network, social and professional networks, and biological system networks, contain vast amounts of information. Information signals in networks are distributed over nodes and transmitted through intricately wired links, making the transfer and transformation of such information difficult to follow. Here we introduce a novel method for describing network information and its transfer using a model network, the Gene-matched network (GMN), in which nodes (neurons) possess attributes (genes). In the GMN, nodes are connected according to their expression of common genes. Because neurons have multiple genes, the GMN is cluster-rich. We show that, in the GMN, information transfer and transformation were controlled systematically, according to the activity level of the network. Furthermore, information transfer and transformation could be traced numerically with a vector using genes expressed in the activated neurons, the active-gene array, which was used to assess the relative activity among overlapping neuronal groups. Interestingly, this coding style closely resembles the cell-assembly neural coding theory. The method introduced here could be applied to many real-world networks, since many systems, including human society and various biological systems, can be represented as a network of this type.