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.

Radiative transfer in molecular lines

NASA Astrophysics Data System (ADS)

Asensio Ramos, A.; Trujillo Bueno, J.; Cernicharo, J.

2001-07-01

The highly convergent iterative methods developed by Trujillo Bueno and Fabiani Bendicho (1995) for radiative transfer (RT) applications are generalized to spherical symmetry with velocity fields. These RT methods are based on Jacobi, Gauss-Seidel (GS), and SOR iteration and they form the basis of a new NLTE multilevel transfer code for atomic and molecular lines. The benchmark tests carried out so far are presented and discussed. The main aim is to develop a number of powerful RT tools for the theoretical interpretation of molecular spectra.

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).

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.

MODTRAN6: a major upgrade of the MODTRAN radiative transfer code

NASA Astrophysics Data System (ADS)

Berk, Alexander; Conforti, Patrick; Kennett, Rosemary; Perkins, Timothy; Hawes, Frederick; van den Bosch, Jeannette

2014-06-01

The MODTRAN6 radiative transfer (RT) code is a major advancement over earlier versions of the MODTRAN atmospheric transmittance and radiance model. This version of the code incorporates modern software ar- chitecture including an application programming interface, enhanced physics features including a line-by-line algorithm, a supplementary physics toolkit, and new documentation. The application programming interface has been developed for ease of integration into user applications. The MODTRAN code has been restructured towards a modular, object-oriented architecture to simplify upgrades as well as facilitate integration with other developers' codes. MODTRAN now includes a line-by-line algorithm for high resolution RT calculations as well as coupling to optical scattering codes for easy implementation of custom aerosols and clouds.

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.

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.

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.

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

Transfer of Real-time Dynamic Radiation Environment Assimilation Model; Research to Operation

NASA Astrophysics Data System (ADS)

Cho, K. S. F.; Hwang, J.; Shin, D. K.; Kim, G. J.; Morley, S.; Henderson, M. G.; Friedel, R. H.; Reeves, G. D.

2015-12-01

Real-time Dynamic Radiation Environment Assimilation Model (rtDREAM) was developed by LANL for nowcast of energetic electrons' flux at the radiation belt to quantify potential risks from radiation damage at the satellites. Assimilated data are from multiple sources including LANL assets (GEO, GPS). For transfer from research to operation of the rtDREAM code, LANL/KSWC/NOAA makes a Memorandum Of Understanding (MOU) on the collaboration between three parts. By this MOU, KWSC/RRA provides all the support for transitioning the research version of DREAM to operations. KASI is primarily responsible for providing all the interfaces between the current scientific output formats of the code and useful space weather products that can be used and accessed through the web. In the second phase, KASI will be responsible in performing the work needed to transform the Van Allen Probes beacon data into "DREAM ready" inputs. KASI will also provide the "operational" code framework and additional data preparation, model output, display and web page codes back to LANL and SWPC. KASI is already a NASA partnering ground station for the Van Allen Probes' space weather beacon data and can here show use and utility of these data for comparison between rtDREAM and observations by web. NOAA has offered to take on some of the data processing tasks specific to the GOES data.

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...

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

Overview of NASA Glenn Research Center Programs in Aero-Heat Transfer and Future Needs

NASA Technical Reports Server (NTRS)

Gaugler, Raymond E.

2002-01-01

This presentation concentrates on an overview of the NASA Glenn Research Center and the projects that are supporting Turbine Aero-Heat Transfer Research. The principal areas include the Ultra Efficient Engine Technology (UEET) Project, the Advanced Space Transportation Program (ASTP) Revolutionary Turbine Accelerator (RTA) Turbine Based Combined Cycle (TBCC) project, and the Propulsion & Power Base R&T - Smart Efficient Components (SEC), and Revolutionary Aeropropulsion Concepts (RAC) Projects. In addition, highlights are presented of the turbine aero-heat transfer work currently underway at NASA Glenn, focusing on the use of the Glenn-HT Navier- Stokes code as the vehicle for research in turbulence & transition modeling, grid topology generation, unsteady effects, and conjugate heat transfer.

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.

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

Detailed Validation of the Bidirectional Effect in Various Case 1 and Case 2 Waters

DTIC Science & Technology

2012-03-26

of the viewing direction, i.e., they assumed a completely diffuse BRDF . Previous efforts to model / understand the actual BRDF [4-10] have produced...places. Second, the MAG2002 BRDF tables were developed from a radiative transfer (RT) model that used scattering particle phase functions that...situ measurements from just 3 locations to validate their model ; here we used a much larger data set across a wide variety of inherent optical

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).

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.

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.

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.

Calculation of upper esophageal sphincter restitution time from high resolution manometry data using machine learning.

PubMed

Jungheim, Michael; Busche, Andre; Miller, Simone; Schilling, Nicolas; Schmidt-Thieme, Lars; Ptok, Martin

2016-10-15

After swallowing, the upper esophageal sphincter (UES) needs a certain amount of time to return from maximum pressure to the resting condition. Disturbances of sphincter function not only during the swallowing process but also in this phase of pressure restitution may lead to globus sensation or dysphagia. Since UES pressures do not decrease in a linear or asymptotic manner, it is difficult to determine the exact time when the resting pressure is reached, even when using high resolution manometry (HRM). To overcome this problem a Machine Learning model was established to objectively determine the UES restitution time (RT) and moreover to collect physiological data on sphincter function after swallowing. HRM-data of 15 healthy participants performing 10 swallows each were included. After manual annotation of the RT interval by two swallowing experts, data were transferred to the Machine Learning model, which applied a sequence labeling modeling approach based on logistic regression to learn and objectivize the characteristics of all swallows. Individually computed RT values were then compared with the annotated values. Estimates of the RT were generated by the Machine Learning model for all 150 swallows. When annotated by swallowing experts mean RT of 11.16s±5.7 (SD) and 10.04s±5.74 were determined respectively, compared to model-generated values from 8.91s±3.71 to 10.87s±4.68 depending on model selection. The correlation score for the annotated RT of both examiners was 0.76 and 0.63 to 0.68 for comparison of model predicted values. Restitution time represents an important physiologic swallowing parameter not previously considered in HRM-studies of the UES, especially since disturbances of UES restitution may increase the risk of aspiration. The data presented here show that it takes approximately 9 to 11s for the UES to come to rest after swallowing. Based on maximal RT values, we demonstrate that an interval of 25-30s in between swallows is necessary until the next swallow is initiated. This should be considered in any further HRM-studies designed to evaluate the characteristics of individual swallows. The calculation model enables a quick and reproducible determination of the time it takes for the UES to come to rest after swallowing (RT). The results of the calculation are partially independent of the input of the investigator. Adding more swallows and integrating additional parameters will improve the Machine Leaning model in the future. By applying similar models to other swallowing parameters of the pharynx and UES, such as the relaxation time of the UES or the activity time during swallowing, a complete automatic evaluation of HRM-data of a swallow should be possible. Copyright © 2016 Elsevier Inc. All rights reserved.

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.

The Continuous Intercomparison of Radiation Codes (CIRC): Phase I Cases

NASA Technical Reports Server (NTRS)

Oreopoulos, Lazaros; Mlawer, Eli; Delamere, Jennifer; Shippert, Timothy; Turner, David D.; Miller, Mark A.; Minnis, Patrick; Clough, Shepard; Barker, Howard; Ellingson, Robert

2007-01-01

CIRC aspires to be the successor to ICRCCM (Intercomparison of Radiation Codes in Climate Models). It is envisioned as an evolving and regularly updated reference source for GCM-type radiative transfer (RT) code evaluation with the principle goal to contribute in the improvement of RT parameterizations. CIRC is jointly endorsed by DOE's Atmospheric Radiation Measurement (ARM) program and the GEWEX Radiation Panel (GRP). CIRC's goal is to provide test cases for which GCM RT algorithms should be performing at their best, i.e, well characterized clear-sky and homogeneous, overcast cloudy cases. What distinguishes CIRC from previous intercomparisons is that its pool of cases is based on observed datasets. The bulk of atmospheric and surface input as well as radiative fluxes come from ARM observations as documented in the Broadband Heating Rate Profile (BBHRP) product. BBHRP also provides reference calculations from AER's RRTM RT algorithms that can be used to select the most optimal set of cases and to provide a first-order estimate of our ability to achieve radiative flux closure given the limitations in our knowledge of the atmospheric state.

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

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).

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.

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.

Towards Efficient and Accurate Description of Many-Electron Problems: Developments of Static and Time-Dependent Electronic Structure Methods

NASA Astrophysics Data System (ADS)

Ding, Feizhi

Understanding electronic behavior in molecular and nano-scale systems is fundamental to the development and design of novel technologies and materials for application in a variety of scientific contexts from fundamental research to energy conversion. This dissertation aims to provide insights into this goal by developing novel methods and applications of first-principle electronic structure theory. Specifically, we will present new methods and applications of excited state multi-electron dynamics based on the real-time (RT) time-dependent Hartree-Fock (TDHF) and time-dependent density functional theory (TDDFT) formalism, and new development of the multi-configuration self-consist field theory (MCSCF) for modeling ground-state electronic structure. The RT-TDHF/TDDFT based developments and applications can be categorized into three broad and coherently integrated research areas: (1) modeling of the interaction between moleculars and external electromagnetic perturbations. In this part we will first prove both analytically and numerically the gauge invariance of the TDHF/TDDFT formalisms, then we will present a novel, efficient method for calculating molecular nonlinear optical properties, and last we will study quantum coherent plasmon in metal namowires using RT-TDDFT; (2) modeling of excited-state charge transfer in molecules. In this part, we will investigate the mechanisms of bridge-mediated electron transfer, and then we will introduce a newly developed non-equilibrium quantum/continuum embedding method for studying charge transfer dynamics in solution; (3) developments of first-principles spin-dependent many-electron dynamics. In this part, we will present an ab initio non-relativistic spin dynamics method based on the two-component generalized Hartree-Fock approach, and then we will generalized it to the two-component TDDFT framework and combine it with the Ehrenfest molecular dynamics approach for modeling the interaction between electron spins and nuclear motion. All these developments and applications will open up new computational and theoretical tools to be applied to the development and understanding of chemical reactions, nonlinear optics, electromagnetism, and spintronics. Lastly, we present a new algorithm for large-scale MCSCF calculations that can utilize massively parallel machines while still maintaining optimal performance for each single processor. This will great improve the efficiency in the MCSCF calculations for studying chemical dissociation and high-accuracy quantum-mechanical simulations.

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.

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

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).

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

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

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 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

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.

Performance of the dot product function in radiative transfer code SORD

NASA Astrophysics Data System (ADS)

Korkin, Sergey; Lyapustin, Alexei; Sinyuk, Aliaksandr; Holben, Brent

2016-10-01

The successive orders of scattering radiative transfer (RT) codes frequently call the scalar (dot) product function. In this paper, we study performance of some implementations of the dot product in the RT code SORD using 50 scenarios for light scattering in the atmosphere-surface system. In the dot product function, we use the unrolled loops technique with different unrolling factor. We also considered the intrinsic Fortran functions. We show results for two machines: ifort compiler under Windows, and pgf90 under Linux. Intrinsic DOT_PRODUCT function showed best performance for the ifort. For the pgf90, the dot product implemented with unrolling factor 4 was the fastest. The RT code SORD together with the interface that runs all the mentioned tests are publicly available from ftp://maiac.gsfc.nasa.gov/pub/skorkin/SORD_IP_16B (current release) or by email request from the corresponding (first) author.

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.

Application of Polarization to the MODIS Aerosol Retrieval Over Land

NASA Technical Reports Server (NTRS)

Levy, Robert C.; Remer, Lorraine R.; Kaufman, Yoram J.

2004-01-01

Reflectance measurements in the visible and infrared wavelengths, from the Moderate Resolution Imaging Spectroradiometer (MODIS), are used to derive aerosol optical thicknesses (AOT) and aerosol properties over land surfaces. The measured spectral reflectance is compared with lookup tables, containing theoretical reflectance calculated by radiative transfer (RT) code. Specifically, this RT code calculates top of the atmosphere (TOA) intensities based on a scalar treatment of radiation, neglecting the effects of polarization. In the red and near infrared (NIR) wavelengths the use of the scalar RT code is of sufficient accuracy to model TOA reflectance. However, in the blue, molecular and aerosol scattering dominate the TOA signal. Here, polarization effects can be large, and should be included in the lookup table derivation. Using a RT code that allows for both vector and scalar calculations, we examine the reflectance differences at the TOA, with and without polarization. We find that the differences in blue channel TOA reflectance (vector - scalar) may reach values of 0.01 or greater, depending on the sun/surface/sensor scattering geometry. Reflectance errors of this magnitude translate to AOT differences of 0.1, which is a very large error, especially when the actual AOT is low. As a result of this study, the next version of aerosol retrieval from MODIS over land will include polarization.

Analyze and predict VLTI observations: the Role of 2D/3D dust continuum radiative transfer codes

NASA Astrophysics Data System (ADS)

Pascucci, I.; Henning, Th; Steinacker, J.; Wolf, S.

2003-10-01

Radiative Transfer (RT) codes with image capability are a fundamental tool for preparing interferometric observations and for interpreting visibility data. In view of the upcoming VLTI facilities, we present the first comparison of images/visibilities coming from two 3D codes that use completely different techniques to solve the problem of self-consistent continuum RT. In addition, we focus on the astrophysical case of a disk distorted by tidal interaction with by-passing stars or internal planets and investigate for which parameters the distortion can be best detected in the mid-infrared using the mid-infrared interferometric device MIDI.

2D/3D Dust Continuum Radiative Transfer Codes to Analyze and Predict VLTI Observations

NASA Astrophysics Data System (ADS)

Pascucci, I.; Henning, Th.; Steinacker, J.; Wolf, S.

Radiative Transfer (RT) codes with image capability are a fundamental tool for preparing interferometric observations and for interpreting visibility data. In view of the upcoming VLTI facilities, we present the first comparison of images/visibilities coming from two 3D codes that use completely different techniques to solve the problem of self-consistent continuum RT. In addition, we focus on the astrophysical case of a disk distorted by tidal interaction with by-passing stars or internal planets and investigate for which parameters the distortion can be best detected in the mid-infrared using the mid-infrared interferometric device MIDI.

Intercomparison of Eight Forward 1D Vector Radiative Transfer Models, with the Performance of Satellite Aerosol Remote Sensing Algorithms in Mind

NASA Astrophysics Data System (ADS)

Davis, Anthony B.; Kalashnikova, Olga V.; Diner, David J.; Garay, Michael J.; Lyapustin, Alexei I.; Korkin, Sergey V.; Martonchik, John V.; Natraj, Vijay; Sanghavi, Suniti V.; Xu, Feng; Zhai, Pengwang; Rozanov, Vladimir V.; Kokhanovsky, Alexander A.

2014-05-01

Quantification and characterization of the omnipresent atmospheric aerosol by remote sensing methods is key to answering many challenging questions in atmospheric science, in climate modeling and in air quality monitoring foremost. In recent years, accurate measurement of the state of polarization of photon fluxes at optical sensors in the visible and near-IR spectrum has been hailed as a very promising approach to aerosol remote sensing. Consequently, there has been a flurry of activity in polarized or 'vector' radiative transfer (vRT) model development. This covers the multiple scattering and ground reflection aspects of sensor signal prediction that complement single-particle scattering computation, and lies at the core of all physics-based retrieval algorithms. One can legitimately ask: What level of model fidelity (representativeness of natural scenes) and what computational accuracy should be achieved for this task in view of the practical constraints that apply? These constraints are, at a minimum: (i) the desired accuracy of the retrieved aerosol properties, (ii) observational uncertainties, and (iii) operational efficiency requirements as determined by throughput. We offer a rational and balanced approach to address these questions and illustrate it with a systematic inter-comparison of the performance of a diverse set of 1D vRT models using a small but representative set of test cases. This 'JPL' benchmarking suite of cases is naturally divided into two parts. First the emphasis is on stratified atmospheres with a continuous mixture of molecular and aerosol scattering and absorption over a black surface, with the corresponding pure cases treated for diagnostic purposes. Then the emphasis shifts to the variety of surfaces, both polarizing and not, that can be encountered in real observations and may confuse the aerosol retrieval algorithm if not properly treated.

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.

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.

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.

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.

3D radiative transfer effects in multi-angle/multispectral radio-polarimetric signals from a mixture of clouds and aerosols viewed by a non-imaging sensor

NASA Astrophysics Data System (ADS)

Davis, Anthony B.; Garay, Michael J.; Xu, Feng; Qu, Zheng; Emde, Claudia

2013-09-01

When observing a spatially complex mix of aerosols and clouds in a single relatively large field-of-view, nature entangles their signals non-linearly through polarized radiation transport processes that unfold in the 3D position and direction spaces. In contrast, any practical forward model in a retrieval algorithm will use only 1D vector radiative transfer (vRT) in a linear mixing technique. We assess the difference between the observed and predicted signals using synthetic data from a high-fidelity 3D vRT model with clouds generated using a Large Eddy Simulation model and an aerosol climatology. We find that this difference is signal—not noise—for the Aerosol Polarimetry Sensor (APS), an instrument developed by NASA. Moreover, the worst case scenario is also the most interesting case, namely, when the aerosol burden is large, hence hase the most impact on the cloud microphysics and dynamics. Based on our findings, we formulate a mitigation strategy for these unresolved cloud adjacency effects assuming that some spatial information is available about the structure of the clouds at higher resolution from "context" cameras, as was planned for NASA's ill-fated Glory mission that was to carry the APS but failed to reach orbit. Application to POLDER (POLarization and Directionality of Earth Reflectances) data from the period when PARASOL (Polarization and Anisotropy of Reflectances for Atmospheric Sciences coupled with Observations from a Lidar) was in the A-train is briefly discussed.

3D Radiative Transfer Effects in Multi-Angle/Multi-Spectral Radio-Polarimetric Signals from a Mixture of Clouds and Aerosols Viewed by a Non-Imaging Sensor

NASA Technical Reports Server (NTRS)

Davis, Anthony B.; Garay, Michael J.; Xu, Feng; Qu, Zheng; Emde, Claudia

2013-01-01

When observing a spatially complex mix of aerosols and clouds in a single relatively large field-of-view, nature entangles their signals non-linearly through polarized radiation transport processes that unfold in the 3D position and direction spaces. In contrast, any practical forward model in a retrieval algorithm will use only 1D vector radiative transfer (vRT) in a linear mixing technique. We assess the difference between the observed and predicted signals using synthetic data from a high-fidelity 3D vRT model with clouds generated using a Large Eddy Simulation model and an aerosol climatology. We find that this difference is signal--not noise--for the Aerosol Polarimetry Sensor (APS), an instrument developed by NASA. Moreover, the worst case scenario is also the most interesting case, namely, when the aerosol burden is large, hence hase the most impact on the cloud microphysics and dynamics. Based on our findings, we formulate a mitigation strategy for these unresolved cloud adjacency effects assuming that some spatial information is available about the structure of the clouds at higher resolution from "context" cameras, as was planned for NASA's ill-fated Glory mission that was to carry the APS but failed to reach orbit. Application to POLDER (POLarization and Directionality of Earth Reflectances) data from the period when PARASOL (Polarization and Anisotropy of Reflectances for Atmospheric Sciences coupled with Observations from a Lidar) was in the A-train is briefly discussed.

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.

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.

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.

Modelling Ground Based X- and Ku-Band Observations of Tundra Snow

NASA Astrophysics Data System (ADS)

Kasurak, A.; King, J. M.; Kelly, R. E.

2012-12-01

As part of a radar-based remote sensing field experiment in Churchill, Manitoba ground based Ku- and X-band scatterometers were deployed to observe changing tundra snowpack conditions from November 2010 to March 2011. The research is part of the validation effort for the Cold Regions Hydrology High-resolution Observatory (CoReH2O) mission, a candidate in the European Space Agency's Earth Explorer program. This paper focuses on the local validation of the semi-empirical radiative transfer (sRT) model proposed for use in snow property retrievals as part of the CoReH2O mission. In this validation experiment, sRT was executed in the forward mode, simulating backscatter to assess the ability of the model. This is a necessary precursor to any inversion attempt. Two experiments are considered, both conducted in a hummocky tundra environment with shallow snow cover. In both cases, scatterometer observations were acquired over a field of view of approximately 10 by 20 meters. In the first experiment, radar observations were made of a snow field and then repeated after the snow had been removed. A ground-based scanning LiDAR system was used to characterize the spatial variability of snow depth through measurements of the snow and ground surface. Snow properties were determined in the field of view from two snow pits, 12 density core measurements, and Magnaprobe snow depth measurements. In the second experiment, a site was non-destructively observed from November through March, with snow properties measured out-of-scene, to characterize the snow evolution response. The model results from sRT fit the form of the observations from the two scatterometer field experiments but do not capture the backscatter magnitude. A constant offset for the season of 5 dB for X-band co- and cross-polarization response was required to match observations, in addition to a 3 dB X- and Ku-band co-polarization offset after the 6th of December. To explain these offsets, it is recognized that the two main physical processes represented by the model are snow volume scattering and ground surface reflectance. With a larger correction needed for X-band, where the ground portion of backscatter is expected to be larger, the contribution from the underlying soil is explored first. The ground contribution in sRT is computed using the semi-empirical Oh et al. (1992) model using permittivity from a temperate mineral soil based model. The ground response is tested against two observations of snow-removed tundra, and one observation of snow free tundra. A secondary analysis is completed using a modified sRT ground model, incorporating recent work on frozen organic permittivity by Mironov et al. (2010). Multi-scale surface roughness resulting from superimposed microtopography on regularly distributed hummocks is also addressed. These results demonstrate the applicability of microwave scattering models to tundra snowpacks underlain with peat, and demonstrate the applicability of the CoReH2O sRT model.

Mass-loss From Evolved Stellar Populations In The Large Magellanic Cloud

NASA Astrophysics Data System (ADS)

Riebel, David

2012-01-01

I have conducted a study of a sample of 30,000 evolved stars in the Large Magellanic Cloud (LMC) and 6,000 in the Small Magellanic Cloud (SMC), covering their variability, mass-loss properties, and chemistry. The initial stages of of my thesis work focused on the infrared variability of Asymptotic Giant Branch (AGB) stars in the LMC. I determined the period-luminosity (P-L) relations for 6 separate sequences of 30,000 evolved star candidates at 8 wavelengths, as a function of photometrically assigned chemistry, and showed that the P-L relations are different for different chemical populations (O-rich or C-rich). I also present results from the Grid of Red supergiant and Asymptotic giant branch star ModelS (GRAMS) radiative transfer (RT) model grid applied to the evolved stellar population of the LMC. GRAMS is a pre-computed grid of RT models of RSG and AGB stars and surrounding circumstellar dust. Best-fit models are determined based on 12 bands of photometry from the optical to the mid-infrared. Using a pre-computed grid, I can present the first reasonably detailed radiative transfer modeling for tens of thousands of stars, allowing me to make statistically accurate estimations of the carbon-star luminosity function and the global dust mass return to the interstellar medium from AGB stars, both key parameters for stellar population synthesis models to reproduce. In the SAGE-Var program, I used the warm Spitzer mission to take 4 additional epochs of observations of 7500 AGB stars in the LMC and SMC. These epochs, combined with existing data, enable me to derive mean fluxes at 3.6 and 4.5 microns, that will be used for tighter constraints for GRAMS, which is currently limited by the variability induced error on the photometry. This work is support by NASA NAG5-12595 and Spitzer contract 1415784.

Theoretical quasar emission-line ratios. VII - Energy-balance models for finite hydrogen slabs

NASA Technical Reports Server (NTRS)

Hubbard, E. N.; Puetter, R. C.

1985-01-01

The present energy balance calculations for finite, isobaric, hydrogen-slab quasar emission line clouds incorporate probabilistic radiative transfer (RT) in all lines and bound-free continua of a five-level continuum model hydrogen atom. Attention is given to the line ratios, line formation regions, level populations and model applicability results obtained. H lines and a variety of other considerations suggest the possibility of emission line cloud densities in excess of 10 to the 10th/cu cm. Lyman-beta/Lyman-alpha line ratios that are in agreement with observed values are obtained by the models. The observed Lyman/Balmer ratios can be achieved with clouds whose column depths are about 10 to the 22nd/sq cm.

Can Drugs Enhance Hypofractionated Radiotherapy? A Novel Method of Modeling Radiosensitization Using In Vitro Data

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

Ohri, Nitin; Dicker, Adam P.; Lawrence, Yaacov Richard, E-mail: yaacovla@gmail.com

2012-05-01

Purpose: Hypofractionated radiotherapy (hRT) is being explored for a number of malignancies. The potential benefit of giving concurrent chemotherapy with hRT is not known. We sought to predict the effects of combined modality treatments by using mathematical models derived from laboratory data. Methods and Materials: Data from 26 published clonogenic survival assays for cancer cell lines with and without the use of radiosensitizing chemotherapy were collected. The first three data points of the RT arm of each assay were used to derive parameters for the linear quadratic (LQ) model, the multitarget (MT) model, and the generalized linear quadratic (gLQ) model.more » For each assay and model, the difference between the predicted and observed surviving fractions at the highest tested RT dose was calculated. The gLQ model was fitted to all the data from each RT cell survival assay, and the biologically equivalent doses in 2-Gy fractions (EQD2s) of clinically relevant hRT regimens were calculated. The increase in cell kill conferred by the addition of chemotherapy was used to estimate the EQD2 of hRT along with a radiosensitizing agent. For comparison, this was repeated using conventionally fractionated RT regimens. Results: At a mean RT dose of 8.0 Gy, the average errors for the LQ, MT, and gLQ models were 1.63, 0.83, and 0.56 log units, respectively, favoring the gLQ model (p < 0.05). Radiosensitizing chemotherapy increased the EQD2 of hRT schedules by an average of 28% to 82%, depending on disease site. This increase was similar to the gains predicted for the addition of chemotherapy to conventionally fractionated RT. Conclusions: Based on published in vitro assays, the gLQ equation is superior to the LQ and MT models in predicting cell kill at high doses of RT. Modeling exercises demonstrate that significant increases in biologically equivalent dose may be achieved with the addition of radiosensitizing agents to hRT. Clinical study of this approach is warranted.« less

Modeling Real-Time Applications with Reusable Design Patterns

NASA Astrophysics Data System (ADS)

Rekhis, Saoussen; Bouassida, Nadia; Bouaziz, Rafik

Real-Time (RT) applications, which manipulate important volumes of data, need to be managed with RT databases that deal with time-constrained data and time-constrained transactions. In spite of their numerous advantages, RT databases development remains a complex task, since developers must study many design issues related to the RT domain. In this paper, we tackle this problem by proposing RT design patterns that allow the modeling of structural and behavioral aspects of RT databases. We show how RT design patterns can provide design assistance through architecture reuse of reoccurring design problems. In addition, we present an UML profile that represents patterns and facilitates further their reuse. This profile proposes, on one hand, UML extensions allowing to model the variability of patterns in the RT context and, on another hand, extensions inspired from the MARTE (Modeling and Analysis of Real-Time Embedded systems) profile.

Synergistic estimation of surface parameters from jointly using optical and microwave observations in EOLDAS

NASA Astrophysics Data System (ADS)

Timmermans, Joris; Gomez-Dans, Jose; Lewis, Philip; Loew, Alexander; Schlenz, Florian

2017-04-01

The large amount of remote sensing data nowadays available provides a huge potential for monitoring crop development, drought conditions and water efficiency. This potential however not been realized yet because algorithms for land surface parameter retrieval mostly use data from only a single sensor. Consequently products that combine different low-level observations from different sensors are hard to find. The lack of synergistic retrieval is caused because it is easier to focus on single sensor types/footprints and temporal observation times, than to find a way to compensate for differences. Different sensor types (microwave/optical) require different radiative transfer (RT) models and also require consistency between the models to have any impact on the retrieval of soil moisture by a microwave instrument. Varying spatial footprints require first proper collocation of the data before one can scale between different resolutions. Considering these problems, merging optical and microwave observations have not been performed yet. The goal of this research was to investigate the potential of integrating optical and microwave RT models within the Earth Observation Land Data Assimilation System (EOLDAS) synergistically to derive biophysical parameters. This system uses a Bayesian data assimilation approach together with observation operators such as the PROSAIL model to estimate land surface parameters. For the purpose of enabling the system to integrate passive microwave radiation (from an ELBARRA II passive microwave radiometer), the Community Microwave Emission Model (CMEM) RT-model, was integrated within the EOLDAS system. In order to quantify the potential, a variety of land surface parameters was chosen to be retrieved from the system, in particular variables that a) impact only optical RT (such as leaf water content and leaf dry matter), b) only impact the microwave RT (such as soil moisture and soil temperature), and c) Leaf Area Index (LAI) that impacts both optical and microwave RT. The results show a high potential when both optical and microwave are used independently. Using only RapidEye only with SAIL RT model, LAI was estimated with R=0.68 with p=0.09, although estimating leaf water content and dry matter showed lower correlations |R|<0.4. The results for retrieving soil temperature and leaf area index retrievals using only (passive microwave) Elbarra-II observations were good with respectively R=[0.85, 0.79], P=[0.0, 0.0], when focusing on dry-spells (of at least 9 days) only the results respectively [R=0.73, and P=0.0], and R=0.89 and R=0.77 for respectively the trend and anomalies. Synergistically using optical and microwave shows also a good potential. This scenario shows that absolute errors improved (with RMSE=1.22 and S=0.89), but with degrading correlations (R=0.59 and P=0.04); the sparse optical observations only improved part of the temporal domain. However in general the synergistic retrieval showed good potential; microwave data provides better information concerning the overall trend of the retrieved LAI due to the regular acquisitions, while optical data provides better information concerning the absolute values of the LAI.

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 DICOM-based radiation therapy information system

NASA Astrophysics Data System (ADS)

Law, Maria Y. Y.; Chan, Lawrence W. C.; Zhang, Xiaoyan; Zhang, Jianguo

2004-04-01

Similar to DICOM for PACS (Picture Archiving and Communication System), standards for radiotherapy (RT) information have been ratified with seven DICOM-RT objects and their IODs (Information Object Definitions), which are more than just images. This presentation describes how a DICOM-based RT Information System Server can be built based on the PACS technology and its data model for a web-based distribution. Methods: The RT information System consists of a Modality Simulator, a data format translator, a RT Gateway, the DICOM RT Server, and the Web-based Application Server. The DICOM RT Server was designed based on a PACS data model and was connected to a Web application Server for distribution of the RT information including therapeutic plans, structures, dose distribution, images and records. Various DICOM RT objects of the patient transmitted to the RT Server were routed to the Web Application Server where the contents of the DICOM RT objects were decoded and mapped to the corresponding location of the RT data model for display in the specially-designed Graphic User Interface. The non-DICOM objects were first rendered to DICOM RT Objects in the translator before they were sent to the RT Server. Results: Ten clinical cases have been collected from different hopsitals for evaluation of the DICOM-based RT Information System. They were successfully routed through the data flow and displayed in the client workstation of the RT information System. Conclusion: Using the DICOM-RT standards, integration of RT data from different vendors is possible.

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.

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

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.

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

Hicks, E. P.; Rosner, R., E-mail: eph2001@columbia.edu

In this paper, we provide support for the Rayleigh-Taylor-(RT)-based subgrid model used in full-star simulations of deflagrations in Type Ia supernovae explosions. We use the results of a parameter study of two-dimensional direct numerical simulations of an RT unstable model flame to distinguish between the two main types of subgrid models (RT or turbulence dominated) in the flamelet regime. First, we give scalings for the turbulent flame speed, the Reynolds number, the viscous scale, and the size of the burning region as the non-dimensional gravity (G) is varied. The flame speed is well predicted by an RT-based flame speed model.more » Next, the above scalings are used to calculate the Karlovitz number (Ka) and to discuss appropriate combustion regimes. No transition to thin reaction zones is seen at Ka = 1, although such a transition is expected by turbulence-dominated subgrid models. Finally, we confirm a basic physical premise of the RT subgrid model, namely, that the flame is fractal, and thus self-similar. By modeling the turbulent flame speed, we demonstrate that it is affected more by large-scale RT stretching than by small-scale turbulent wrinkling. In this way, the RT instability controls the flame directly from the large scales. Overall, these results support the RT subgrid model.« less

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

Tyldesley, Scott, E-mail: styldesl@bccancer.bc.c; Delaney, Geoff; Foroudi, Farshad

Purpose: Estimates of the need for radiotherapy (RT) using different methods (criterion based benchmarking [CBB]and the Canadian [C-EBEST]and Australian [A-EBEST]epidemiologically based estimates) exist for various cancer sites. We compared these model estimates to actual RT rates for lung, breast, and prostate cancers in British Columbia (BC). Methods and Materials: All cases of lung, breast, and prostate cancers in BC from 1997 to 2004 and all patients receiving RT within 1 year (RT{sub 1Y}) and within 5 years (RT{sub 5Y}) of diagnosis were identified. The RT{sub 1Y} and RT{sub 5Y} proportions in health regions with a cancer center for the mostmore » recent year were then calculated. RT rates were compared with CBB and EBEST estimates of RT needs. Variation was assessed by time and region. Results: The RT{sub 1Y} in regions with a cancer center for lung, breast, and prostate cancers were 51%, 58%, and 33% compared with 45%, 57%, and 32% for C-EBEST and 41%, 61%, and 37% for CBB models. The RT{sub 5Y} rates in regions with a cancer center for lung, breast, and prostate cancers were 59%, 61%, and 40% compared with 61%, 66%, and 61% for C-EBEST and 75%, 83%, and 60% for A-EBEST models. The RT{sub 1Y} rates increased for breast and prostate cancers. Conclusions: C-EBEST and CBB model estimates are closer to the actual RT rates than the A-EBEST estimates. Application of these model estimates by health care decision makers should be undertaken with an understanding of the methods used and the assumptions on which they were based.« less

Cardiovascular Adaptations Induced by Resistance Training in Animal Models.

PubMed

Melo, S F S; da Silva Júnior, N D; Barauna, V G; Oliveira, E M

2018-01-01

In the last 10 years the number of studies showing the benefits of resistance training (RT) to the cardiovascular system, have grown. In comparison to aerobic training, RT-induced favorable adaptations to the cardiovascular system have been ignored for many years, thus the mechanisms of the RT-induced cardiovascular adaptations are still uncovered. The lack of animal models with comparable protocols to the RT performed by humans hampers the knowledge. We have used squat-exercise model, which is widely used by many others laboratories. However, to a lesser extent, other models are also employed to investigate the cardiovascular adaptations. In the subsequent sections we will review the information regarding cardiac morphological adaptations, signaling pathway of the cardiac cell, cardiac function and the vascular adaptation induced by RT using this animal model developed by Tamaki et al. in 1992. Furthermore, we also describe cardiovascular findings observed using other animal models of RT.

RAYLEIGH–TAYLOR UNSTABLE FLAMES—FAST OR FASTER?

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

Hicks, E. P., E-mail: eph2001@columbia.edu

2015-04-20

Rayleigh–Taylor (RT) unstable flames play a key role in the explosions of supernovae Ia. However, the dynamics of these flames are still not well understood. RT unstable flames are affected by both the RT instability of the flame front and by RT-generated turbulence. The coexistence of these factors complicates the choice of flame speed subgrid models for full-star Type Ia simulations. Both processes can stretch and wrinkle the flame surface, increasing its area and, therefore, the burning rate. In past research, subgrid models have been based on either the RT instability or turbulence setting the flame speed. We evaluate bothmore » models, checking their assumptions and their ability to correctly predict the turbulent flame speed. Specifically, we analyze a large parameter study of 3D direct numerical simulations of RT unstable model flames. This study varies both the simulation domain width and the gravity in order to probe a wide range of flame behaviors. We show that RT unstable flames are different from traditional turbulent flames: they are thinner rather than thicker when turbulence is stronger. We also show that none of the several different types of turbulent flame speed models accurately predicts measured flame speeds. In addition, we find that the RT flame speed model only correctly predicts the measured flame speed in a certain parameter regime. Finally, we propose that the formation of cusps may be the factor causing the flame to propagate more quickly than predicted by the RT model.« less

Rayleigh-Taylor Unstable Flames -- Fast or Faster?

NASA Astrophysics Data System (ADS)

Hicks, E. P.

2015-04-01

Rayleigh-Taylor (RT) unstable flames play a key role in the explosions of supernovae Ia. However, the dynamics of these flames are still not well understood. RT unstable flames are affected by both the RT instability of the flame front and by RT-generated turbulence. The coexistence of these factors complicates the choice of flame speed subgrid models for full-star Type Ia simulations. Both processes can stretch and wrinkle the flame surface, increasing its area and, therefore, the burning rate. In past research, subgrid models have been based on either the RT instability or turbulence setting the flame speed. We evaluate both models, checking their assumptions and their ability to correctly predict the turbulent flame speed. Specifically, we analyze a large parameter study of 3D direct numerical simulations of RT unstable model flames. This study varies both the simulation domain width and the gravity in order to probe a wide range of flame behaviors. We show that RT unstable flames are different from traditional turbulent flames: they are thinner rather than thicker when turbulence is stronger. We also show that none of the several different types of turbulent flame speed models accurately predicts measured flame speeds. In addition, we find that the RT flame speed model only correctly predicts the measured flame speed in a certain parameter regime. Finally, we propose that the formation of cusps may be the factor causing the flame to propagate more quickly than predicted by the RT model.

MO-FG-CAMPUS-TeP1-03: Pre-Treatment Surface Imaging Based Collision Detection

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

Wiant, D; Maurer, J; Liu, H

2016-06-15

Purpose: Modern radiotherapy increasingly employs large immobilization devices, gantry attachments, and couch rotations for treatments. All of which raise the risk of collisions between the patient and the gantry / couch. Collision detection is often achieved by manually checking each couch position in the treatment room and sometimes results in extraneous imaging if collisions are detected after image based setup has begun. In the interest of improving efficiency and avoiding extra imaging, we explore the use of a surface imaging based collision detection model. Methods: Surfaces acquired from AlignRT (VisionRT, London, UK) were transferred in wavefront format to a custommore » Matlab (Mathworks, Natick, MA) software package (CCHECK). Computed tomography (CT) scans acquired at the same time were sent to CCHECK in DICOM format. In CCHECK, binary maps of the surfaces were created and overlaid on the CT images based on the fixed relationship of the AlignRT and CT coordinate systems. Isocenters were added through a graphical user interface (GUI). CCHECK then compares the inputted surfaces to a model of the linear accelerator (linac) to check for collisions at defined gantry and couch positions. Note, CCHECK may be used with or without a CT. Results: The nominal surface image field of view is 650 mm × 900 mm, with variance based on patient position and size. The accuracy of collision detections is primarily based on the linac model and the surface mapping process. The current linac model and mapping process yield detection accuracies on the order of 5 mm, assuming no change in patient posture between surface acquisition and treatment. Conclusions: CCHECK provides a non-ionizing method to check for collisions without the patient in the treatment room. Collision detection accuracy may be improved with more robust linac modeling. Additional gantry attachments (e.g. conical collimators) can be easily added to the model.« less

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.

Predictive Models for Regional Hepatic Function Based on 99mTc-IDA SPECT and Local Radiation Dose for Physiologic Adaptive Radiation Therapy

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

Wang, Hesheng, E-mail: hesheng@umich.edu; Feng, Mary; Frey, Kirk A.

2013-08-01

Purpose: High-dose radiation therapy (RT) for intrahepatic cancer is limited by the development of liver injury. This study investigated whether regional hepatic function assessed before and during the course of RT using 99mTc-labeled iminodiacetic acid (IDA) single photon emission computed tomography (SPECT) could predict regional liver function reserve after RT. Methods and Materials: Fourteen patients treated with RT for intrahepatic cancers underwent dynamic 99mTc-IDA SPECT scans before RT, during, and 1 month after completion of RT. Indocyanine green (ICG) tests, a measure of overall liver function, were performed within 1 day of each scan. Three-dimensional volumetric hepatic extraction fraction (HEF)more » images of the liver were estimated by deconvolution analysis. After coregistration of the CT/SPECT and the treatment planning CT, HEF dose–response functions during and after RT were generated. The volumetric mean of the HEFs in the whole liver was correlated with ICG clearance time. Three models, dose, priori, and adaptive models, were developed using multivariate linear regression to assess whether the regional HEFs measured before and during RT helped predict regional hepatic function after RT. Results: The mean of the volumetric liver HEFs was significantly correlated with ICG clearance half-life time (r=−0.80, P<.0001), for all time points. Linear correlations between local doses and regional HEFs 1 month after RT were significant in 12 patients. In the priori model, regional HEF after RT was predicted by the planned dose and regional HEF assessed before RT (R=0.71, P<.0001). In the adaptive model, regional HEF after RT was predicted by regional HEF reassessed during RT and the remaining planned local dose (R=0.83, P<.0001). Conclusions: 99mTc-IDA SPECT obtained during RT could be used to assess regional hepatic function and helped predict post-RT regional liver function reserve. This could support individualized adaptive radiation treatment strategies to maximize tumor control and minimize the risk of liver damage.« less

Predictive models for regional hepatic function based on 99mTc-IDA SPECT and local radiation dose for physiologic adaptive radiation therapy.

PubMed

Wang, Hesheng; Feng, Mary; Frey, Kirk A; Ten Haken, Randall K; Lawrence, Theodore S; Cao, Yue

2013-08-01

High-dose radiation therapy (RT) for intrahepatic cancer is limited by the development of liver injury. This study investigated whether regional hepatic function assessed before and during the course of RT using 99mTc-labeled iminodiacetic acid (IDA) single photon emission computed tomography (SPECT) could predict regional liver function reserve after RT. Fourteen patients treated with RT for intrahepatic cancers underwent dynamic 99mTc-IDA SPECT scans before RT, during, and 1 month after completion of RT. Indocyanine green (ICG) tests, a measure of overall liver function, were performed within 1 day of each scan. Three-dimensional volumetric hepatic extraction fraction (HEF) images of the liver were estimated by deconvolution analysis. After coregistration of the CT/SPECT and the treatment planning CT, HEF dose-response functions during and after RT were generated. The volumetric mean of the HEFs in the whole liver was correlated with ICG clearance time. Three models, dose, priori, and adaptive models, were developed using multivariate linear regression to assess whether the regional HEFs measured before and during RT helped predict regional hepatic function after RT. The mean of the volumetric liver HEFs was significantly correlated with ICG clearance half-life time (r=-0.80, P<.0001), for all time points. Linear correlations between local doses and regional HEFs 1 month after RT were significant in 12 patients. In the priori model, regional HEF after RT was predicted by the planned dose and regional HEF assessed before RT (R=0.71, P<.0001). In the adaptive model, regional HEF after RT was predicted by regional HEF reassessed during RT and the remaining planned local dose (R=0.83, P<.0001). 99mTc-IDA SPECT obtained during RT could be used to assess regional hepatic function and helped predict post-RT regional liver function reserve. This could support individualized adaptive radiation treatment strategies to maximize tumor control and minimize the risk of liver damage. Published by Elsevier Inc.

Retrieval of ice cloud properties using an optimal estimation algorithm and MODIS infrared observations: 1. Forward model, error analysis, and information content

NASA Astrophysics Data System (ADS)

Wang, Chenxi; Platnick, Steven; Zhang, Zhibo; Meyer, Kerry; Yang, Ping

2016-05-01

An optimal estimation (OE) retrieval method is developed to infer three ice cloud properties simultaneously: optical thickness (τ), effective radius (reff), and cloud top height (h). This method is based on a fast radiative transfer (RT) model and infrared (IR) observations from the MODerate resolution Imaging Spectroradiometer (MODIS). This study conducts thorough error and information content analyses to understand the error propagation and performance of retrievals from various MODIS band combinations under different cloud/atmosphere states. Specifically, the algorithm takes into account four error sources: measurement uncertainty, fast RT model uncertainty, uncertainties in ancillary data sets (e.g., atmospheric state), and assumed ice crystal habit uncertainties. It is found that the ancillary and ice crystal habit error sources dominate the MODIS IR retrieval uncertainty and cannot be ignored. The information content analysis shows that for a given ice cloud, the use of four MODIS IR observations is sufficient to retrieve the three cloud properties. However, the selection of MODIS IR bands that provide the most information and their order of importance varies with both the ice cloud properties and the ambient atmospheric and the surface states. As a result, this study suggests the inclusion of all MODIS IR bands in practice since little a priori information is available.

Retrieval of ice cloud properties using an optimal estimation algorithm and MODIS infrared observations. Part I: Forward model, error analysis, and information content.

PubMed

Wang, Chenxi; Platnick, Steven; Zhang, Zhibo; Meyer, Kerry; Yang, Ping

2016-05-27

An optimal estimation (OE) retrieval method is developed to infer three ice cloud properties simultaneously: optical thickness ( τ ), effective radius ( r eff ), and cloud-top height ( h ). This method is based on a fast radiative transfer (RT) model and infrared (IR) observations from the MODerate resolution Imaging Spectroradiometer (MODIS). This study conducts thorough error and information content analyses to understand the error propagation and performance of retrievals from various MODIS band combinations under different cloud/atmosphere states. Specifically, the algorithm takes into account four error sources: measurement uncertainty, fast RT model uncertainty, uncertainties in ancillary datasets (e.g., atmospheric state), and assumed ice crystal habit uncertainties. It is found that the ancillary and ice crystal habit error sources dominate the MODIS IR retrieval uncertainty and cannot be ignored. The information content analysis shows that, for a given ice cloud, the use of four MODIS IR observations is sufficient to retrieve the three cloud properties. However, the selection of MODIS IR bands that provide the most information and their order of importance varies with both the ice cloud properties and the ambient atmospheric and the surface states. As a result, this study suggests the inclusion of all MODIS IR bands in practice since little a priori information is available.

Reconstruction of 3D Shapes of Opaque Cumulus Clouds from Airborne Multiangle Imaging: A Proof-of-Concept

NASA Astrophysics Data System (ADS)

Davis, A. B.; Bal, G.; Chen, J.

2015-12-01

Operational remote sensing of microphysical and optical cloud properties is invariably predicated on the assumption of plane-parallel slab geometry for the targeted cloud. The sole benefit of this often-questionable assumption about the cloud is that it leads to one-dimensional (1D) radiative transfer (RT)---a textbook, computationally tractable model. We present new results as evidence that, thanks to converging advances in 3D RT, inverse problem theory, algorithm implementation, and computer hardware, we are at the dawn of a new era in cloud remote sensing where we can finally go beyond the plane-parallel paradigm. Granted, the plane-parallel/1D RT assumption is reasonable for spatially extended stratiform cloud layers, as well as the smoothly distributed background aerosol layers. However, these 1D RT-friendly scenarios exclude cases that are critically important for climate physics. 1D RT---whence operational cloud remote sensing---fails catastrophically for cumuliform clouds that have fully 3D outer shapes and internal structures driven by shallow or deep convection. For these situations, the first order of business in a robust characterization by remote sensing is to abandon the slab geometry framework and determine the 3D geometry of the cloud, as a first step toward bone fide 3D cloud tomography. With this specific goal in mind, we deliver a proof-of-concept for an entirely new kind of remote sensing applicable to 3D clouds. It is based on highly simplified 3D RT and exploits multi-angular suites of cloud images at high spatial resolution. Airborne sensors like AirMSPI readily acquire such data. The key element of the reconstruction algorithm is a sophisticated solution of the nonlinear inverse problem via linearization of the forward model and an iteration scheme supported, where necessary, by adaptive regularization. Currently, the demo uses a 2D setting to show how either vertical profiles or horizontal slices of the cloud can be accurately reconstructed. Extension to 3D volumes is straightforward but the next challenge is to accommodate images at lower spatial resolution, e.g., from MISR/Terra. G. Bal, J. Chen, and A.B. Davis (2015). Reconstruction of cloud geometry from multi-angle images, Inverse Problems in Imaging (submitted).

A Quantitative Analysis of the Relationship Between Radiation Therapy Use and Travel Time.

PubMed

Liu, Emma; Santibáñez, Pablo; Puterman, Martin L; Weber, Leah; Ma, Xiang; Sauré, Antoine; Olivotto, Ivo A; Halperin, Ross; French, John; Tyldesley, Scott

2015-11-01

To model and quantify the relationship between radiation therapy (RT) use and travel time to RT services. Population-based registries and databases were used to identify both incident cancer patient and patients receiving RT within 1 year of diagnosis (RT1y) in British Columbia, Canada, between 1992 and 2011. The effects of age, gender, diagnosis year, income, prevailing wait time, and travel duration for RT on RT1y were assessed. Significant factors from univariate analyses were included in a multivariable logistic regression model. The shape of the travel time-RT1y curve was represented by generalized additive and segmented regression models. Analyses were conducted for breast, lung, and genitourinary cancer separately and for all cancer sites combined. After adjustment for age, gender, diagnosis year, income, and prevailing wait times, increasing travel time to the closest RT facility had a negative impact RT1y. The shape of the travel time-RT1y curve varied with cancer type. For breast cancer, the odds of RT1y were constant for the first 2 driving hours and decreased at 17% per hour thereafter. For lung cancer, the odds of RT1y decreased by 16% after 20 minutes and then decreased at 6% per hour. Genitourinary cancer RT1y was relatively independent of travel time. For all cancer sites combined, the odds of RT1y were constant within the first 2 driving hours and decreased at 7% per hour thereafter. Travel time to receive RT has a different impact on RT1y for different tumor sites. The results provide evidence-based insights for the configuration of catchment areas for new and existing cancer centers providing RT. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

A Quantitative Analysis of the Relationship Between Radiation Therapy Use and Travel Time

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

Liu, Emma; Santibáñez, Pablo; Puterman, Martin L.

Purpose: To model and quantify the relationship between radiation therapy (RT) use and travel time to RT services. Methods and Materials: Population-based registries and databases were used to identify both incident cancer patient and patients receiving RT within 1 year of diagnosis (RT1y) in British Columbia, Canada, between 1992 and 2011. The effects of age, gender, diagnosis year, income, prevailing wait time, and travel duration for RT on RT1y were assessed. Significant factors from univariate analyses were included in a multivariable logistic regression model. The shape of the travel time–RT1y curve was represented by generalized additive and segmented regression models. Analysesmore » were conducted for breast, lung, and genitourinary cancer separately and for all cancer sites combined. Results: After adjustment for age, gender, diagnosis year, income, and prevailing wait times, increasing travel time to the closest RT facility had a negative impact RT1y. The shape of the travel time–RT1y curve varied with cancer type. For breast cancer, the odds of RT1y were constant for the first 2 driving hours and decreased at 17% per hour thereafter. For lung cancer, the odds of RT1y decreased by 16% after 20 minutes and then decreased at 6% per hour. Genitourinary cancer RT1y was relatively independent of travel time. For all cancer sites combined, the odds of RT1y were constant within the first 2 driving hours and decreased at 7% per hour thereafter. Conclusions: Travel time to receive RT has a different impact on RT1y for different tumor sites. The results provide evidence-based insights for the configuration of catchment areas for new and existing cancer centers providing RT.« less

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.

Estimating Soil and Vegetation Parameters using Synergies between Optical and Microwave Observations

NASA Astrophysics Data System (ADS)

Timmermans, J.; Gomez-Dans, J. L.; Lewis, P.; Loew, A.; Schlenz, F.; Mathieu, P. P.; Pounder, N. L.; Styles, J.

2017-12-01

The large amount of remote sensing data available provides a huge potential for various applications, such as crop monitoring. This potential has not been realized yet because inversion-algorithms mostly use a single sensor approach. Consequently, products that combine different low-level observations from different sensors are hard to find. The difficulty in a multi-sensor approach is that 1) different sensor types (microwave/ optical) require different radiative transfer (RT) models and 2) it require consistency between the models. The goal of this research was to investigate the synergistic potential of integrating optical (Opt) and passive microwave (PM) RT models within the Earth Observation Land Data Assimilation System (EOLDAS). EOLDAS uses a Bayesian data assimilation approach together with observation operators such as PROSAIL to estimate state variables. In order to use PM observations, the Community Microwave Emission Model was integrated into the system. Results show a high potential when both Opt and PM observations are used independently. Using only RapidEye only with SAIL RT model, LAI was estimated with R=0.68, with leaf water content and dry matter having lower correlations |R|<0.4. Results for retrieving soil temperature and leaf area index retrievals using only Elbarra observations were good with respectively R=[0.85, 0.79], and for soil moisture also very good with R=0.73 (focusing on dry-spells of at least 9 days only), and with R=0.89 and R=0.77 for respectively the trend and anomalies. Synergistically using Opt and MW observations also shows good potential. Results show that absolute errors decreased (with RMSE=1.22 and S=0.89), but with lower R=0.59; sparse optical observations only improved part of the temporal domain. This shows that PM observations provide good information for the overall trend of the retrieved LAI due to the regular acquisitions, while Opt observations provides better information of the absolute values of the LAI.

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

Response to Intervention (RtI) in Secondary Schools: A Comparison of the RtI Service Delivery Model

ERIC Educational Resources Information Center

Epler-Brooks, Pam L.

2011-01-01

This qualitative, collective case study researched how the Response to Intervention (RtI) service delivery model was used within the secondary educational environment in two Ohio schools. Areas researched included the type of professional development used to introduce and sustain RtI, the amount of administrative support, the use of universal…

Estimation of Multiple Parameters over Vegetated Surfaces by Integrating Optical-Thermal Remote Sensing Observations

NASA Astrophysics Data System (ADS)

Ma, H.

2016-12-01

Land surface parameters from remote sensing observations are critical in monitoring and modeling of global climate change and biogeochemical cycles. Current methods for estimating land surface parameters are generally parameter-specific algorithms and are based on instantaneous physical models, which result in spatial, temporal and physical inconsistencies in current global products. Besides, optical and Thermal Infrared (TIR) remote sensing observations are usually separated to use based on different models , and the Middle InfraRed (MIR) observations have received little attention due to the complexity of the radiometric signal that mixes both reflected and emitted fluxes. In this paper, we proposed a unified algorithm for simultaneously retrieving a total of seven land surface parameters, including Leaf Area Index (LAI), Fraction of Absorbed Photosynthetically Active Radiation (FAPAR), land surface albedo, Land Surface Temperature (LST), surface emissivity, downward and upward longwave radiation, by exploiting remote sensing observations from visible to TIR domain based on a common physical Radiative Transfer (RT) model and a data assimilation framework. The coupled PROSPECT-VISIR and 4SAIL RT model were used for canopy reflectance modeling. At first, LAI was estimated using a data assimilation method that combines MODIS daily reflectance observation and a phenology model. The estimated LAI values were then input into the RT model to simulate surface spectral emissivity and surface albedo. Besides, the background albedo and the transmittance of solar radiation, and the canopy albedo were also calculated to produce FAPAR. Once the spectral emissivity of seven MODIS MIR to TIR bands were retrieved, LST can be estimated from the atmospheric corrected surface radiance by exploiting an optimization method. At last, the upward longwave radiation were estimated using the retrieved LST, broadband emissivity (converted from spectral emissivity) and the downward longwave radiation (modeled by MODTRAN). These seven parameters were validated over several representative sites with different biome type, and compared with MODIS and GLASS product. Results showed that this unified inversion algorithm can retrieve temporally complete and physical consistent land surface parameters with high accuracy.

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.

Using the ARTMO toolbox for automated retrieval of biophysical parameters through radiative transfer model inversion: Optimizing LUT-based inversion

NASA Astrophysics Data System (ADS)

Verrelst, J.; Rivera, J. P.; Leonenko, G.; Alonso, L.; Moreno, J.

2012-04-01

Radiative transfer (RT) modeling plays a key role for earth observation (EO) because it is needed to design EO instruments and to develop and test inversion algorithms. The inversion of a RT model is considered as a successful approach for the retrieval of biophysical parameters because of being physically-based and generally applicable. However, to the broader community this approach is considered as laborious because of its many processing steps and expert knowledge is required to realize precise model parameterization. We have recently developed a radiative transfer toolbox ARTMO (Automated Radiative Transfer Models Operator) with the purpose of providing in a graphical user interface (GUI) essential models and tools required for terrestrial EO applications such as model inversion. In short, the toolbox allows the user: i) to choose between various plant leaf and canopy RT models (e.g. models from the PROSPECT and SAIL family, FLIGHT), ii) to choose between spectral band settings of various air- and space-borne sensors or defining own sensor settings, iii) to simulate a massive amount of spectra based on a look up table (LUT) approach and storing it in a relational database, iv) to plot spectra of multiple models and compare them with measured spectra, and finally, v) to run model inversion against optical imagery given several cost options and accuracy estimates. In this work ARTMO was used to tackle some well-known problems related to model inversion. According to Hadamard conditions, mathematical models of physical phenomena are mathematically invertible if the solution of the inverse problem to be solved exists, is unique and depends continuously on data. This assumption is not always met because of the large number of unknowns and different strategies have been proposed to overcome this problem. Several of these strategies have been implemented in ARTMO and were here analyzed to optimize the inversion performance. Data came from the SPARC-2003 dataset, which was acquired on the agricultural test site Barrax, Spain. LUTs were created using the 4SAIL and FLIGHT models and were inverted against CHRIS data in order to retrieve maps of chlorophyll content (chl) and leaf area index (LAI). The following inversion steps have been optimized: 1. Cost function. The performances of about 50 different cost functions (i.e. minimum distance functions) were compared. Remarkably, in none of the studied cases the widely used root mean square error (RMSE) led to most accurate results. Depending on the retrieved parameter, more successful functions were: 'Sharma and Mittal', 'Shannońs entropy', 'Hellinger distance', 'Pearsońs chi-square'. 2. Gaussian noise. Earth observation data typically encompass a certain degree of noise due to errors related to radiometric and geometric processing. In all cases, adding 5% Gaussian noise to the simulated spectra led to more accurate retrievals as compared to without noise. 3. Average of multiple best solutions. Because multiple parameter combinations may lead to the same spectra, a way to overcome this problem is not searching for the top best match but for a percentage of best matches. Optimized retrievals were encountered when including an average of 7% (Chl) to 10% (LAI) top best matches. 4. Integration of estimates. The option is provided to integrate estimates of biochemical contents at the canopy level (e.g., total chlorophyll: Chl × LAI, or water: Cw × LAI), which can lead to increased robustness and accuracy. 5. Class-based inversion. This option is probably ARTMÓs most powerful feature as it allows model parameterization depending on the imagés land cover classes (e.g. different soil or vegetation types). Class-based inversion can lead to considerably improved accuracies compared to one generic class. Results suggest that 4SAIL and FLIGHT performed alike for Chl but not for LAI. While both models rely on the leaf model PROSPECT for Chl retrieval, their different nature (e.g. numerical vs. ray tracing) may cause that retrieval of structural parameters such as LAI differ. Finally, it should be noted that the whole analysis can be intuitively performed by the toolbox. ARTMO is freely available to the EO community for further development. Expressions of interest are welcome and should be directed to the corresponding author.

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

Optimization of Catheter Based rtPA Thrombolysis in a Novel In Vitro Clot Model for Intracerebral Hemorrhage

PubMed Central

Masomi-Bornwasser, Julia; Müller-Werkmeister, Hendrik; Kantelhardt, Sven Rainer; König, Jochem; Kempski, Oliver; Giese, Alf

2017-01-01

Hematoma lysis with recombinant tissue plasminogen activator (rtPA) has emerged as an alternative therapy for spontaneous intracerebral hemorrhage (ICH). Optimal dose and schedule are still unclear. The aim of this study was to create a reliable in vitro blood clot model for investigation of optimal drug dose and timing. An in vitro clot model was established, using 25 mL and 50 mL of human blood. Catheters were placed into the clots and three groups, using intraclot application of rtPA, placebo, and catheter alone, were analyzed. Dose-response relationship, repetition, and duration of rtPA treatment and its effectiveness in aged clots were investigated. A significant relative end weight difference was found in rtPA treated clots compared to catheter alone (p = 0.002) and placebo treated clots (p < 0.001). Dose-response analysis revealed 95% effective dose around 1 mg rtPA in 25 and 50 mL clots. Approximately 80% of relative clot lysis could be achieved after 15 min incubation. Lysis of aged clots was less effective. A new clot model for in vitro investigation was established. Our data suggest that current protocols for rtPA based ICH therapy may be optimized by using less rtPA at shorter incubation times. PMID:28459065

Optimization of Catheter Based rtPA Thrombolysis in a Novel In Vitro Clot Model for Intracerebral Hemorrhage.

PubMed

Keric, Naureen; Masomi-Bornwasser, Julia; Müller-Werkmeister, Hendrik; Kantelhardt, Sven Rainer; König, Jochem; Kempski, Oliver; Giese, Alf

2017-01-01

Hematoma lysis with recombinant tissue plasminogen activator (rtPA) has emerged as an alternative therapy for spontaneous intracerebral hemorrhage (ICH). Optimal dose and schedule are still unclear. The aim of this study was to create a reliable in vitro blood clot model for investigation of optimal drug dose and timing. An in vitro clot model was established, using 25 mL and 50 mL of human blood. Catheters were placed into the clots and three groups, using intraclot application of rtPA, placebo, and catheter alone, were analyzed. Dose-response relationship, repetition, and duration of rtPA treatment and its effectiveness in aged clots were investigated. A significant relative end weight difference was found in rtPA treated clots compared to catheter alone ( p = 0.002) and placebo treated clots ( p < 0.001). Dose-response analysis revealed 95% effective dose around 1 mg rtPA in 25 and 50 mL clots. Approximately 80% of relative clot lysis could be achieved after 15 min incubation. Lysis of aged clots was less effective. A new clot model for in vitro investigation was established. Our data suggest that current protocols for rtPA based ICH therapy may be optimized by using less rtPA at shorter incubation times.

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.

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.

Expansion of the Real-Time SPoRT-Land Information System for NOAA/National Weather Service Situational Awareness and Local Modeling Applications

NASA Technical Reports Server (NTRS)

Case, Jonathan L; White, Kristopher D.

2014-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center in Huntsville, AL is running a real-time configuration of the Noah land surface model (LSM) within the NASA Land Information System (LIS) framework (hereafter referred to as the "SPoRT-LIS"). Output from the real-time SPoRT-LIS is used for (1) initializing land surface variables for local modeling applications, and (2) displaying in decision support systems for situational awareness and drought monitoring at select NOAA/National Weather Service (NWS) partner offices. The experimental CONUS run incorporates hourly quantitative precipitation estimation (QPE) from the National Severe Storms Laboratory Multi- Radar Multi-Sensor (MRMS) which will be transitioned into operations at the National Centers for Environmental Prediction (NCEP) in Fall 2014.This paper describes the current and experimental SPoRT-LIS configurations, and documents some of the limitations still remaining through the advent of MRMS precipitation analyses in the SPoRT-LIS land surface model (LSM) simulations.

The CKM Matrix and The Unitarity Triangle: Another Look

NASA Astrophysics Data System (ADS)

Buras, Andrzej J.; Parodi, Fabrizio; Stocchi, Achille

2003-01-01

The unitarity triangle can be determined by means of two measurements of its sides or angles. Assuming the same relative errors on the angles (alpha,beta,gamma) and the sides (Rb,Rt), we find that the pairs (gamma,beta) and (gamma,Rb) are most efficient in determining (bar varrho,bar eta) that describe the apex of the unitarity triangle. They are followed by (alpha,beta), (alpha,Rb), (Rt,beta), (Rt,Rb) and (Rb,beta). As the set |Vus|, |Vcb|, Rt and beta appears to be the best candidate for the fundamental set of flavour violating parameters in the coming years, we show various constraints on the CKM matrix in the (Rt,beta) plane. Using the best available input we determine the universal unitarity triangle for models with minimal flavour violation (MFV) and compare it with the one in the Standard Model. We present allowed ranges for sin 2beta, sin 2alpha, gamma, Rb, Rt and DeltaMs within the Standard Model and MFV models. We also update the allowed range for the function Ftt that parametrizes various MFV-models.

Real-Time Quantum Dynamics of Long-Range Electronic Excitation Transfer in Plasmonic Nanoantennas.

PubMed

Ilawe, Niranjan V; Oviedo, M Belén; Wong, Bryan M

2017-08-08

Using large-scale, real-time, quantum dynamics calculations, we present a detailed analysis of electronic excitation transfer (EET) mechanisms in a multiparticle plasmonic nanoantenna system. Specifically, we utilize real-time, time-dependent, density functional tight binding (RT-TDDFTB) to provide a quantum-mechanical description (at an electronic/atomistic level of detail) for characterizing and analyzing these systems, without recourse to classical approximations. We also demonstrate highly long-range electronic couplings in these complex systems and find that the range of these couplings is more than twice the conventional cutoff limit considered by Förster resonance energy transfer (FRET)-based approaches. Furthermore, we attribute these unusually long-ranged electronic couplings to the coherent oscillations of conduction electrons in plasmonic nanoparticles. This long-range nature of plasmonic interactions has important ramifications for EET; in particular, we show that the commonly used "nearest-neighbor" FRET model is inadequate for accurately characterizing EET even in simple plasmonic antenna systems. These findings provide a real-time, quantum-mechanical perspective for understanding EET mechanisms and provide guidance in enhancing plasmonic properties in artificial light-harvesting systems.

The quantum interference effects in the SC II 4247 Å line of the second solar spectrum

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

Smitha, H. N.; Nagendra, K. N.; Stenflo, J. O.

2014-10-10

The Sc II 4247 Å line formed in the chromosphere is one of the lines well known, like the Na I D{sub 2} and Ba II D{sub 2}, for its prominent triple-peak structure in Q/I and the underlying quantum interference effects governing it. In this paper, we try to study the nature of this triple-peak structure using the theory of F-state interference including the effects of partial frequency redistribution (PRD) and radiative transfer (RT). We compare our results with the observations taken in a quiet region near the solar limb. In spite of accounting for PRD and RT effects, itmore » has not been possible to reproduce the observed triple-peak structure in Q/I. While the two wing PRD peaks (on either side of central peak) and the near wing continuum can be reproduced, the central peak is completely suppressed by the enhanced depolarization resulting from the hyperfine structure splitting. This suppression remains for all the tested widely different one-dimensional model atmospheres or for any multi-component combinations of them. While multidimensional RT effects may improve the fit to the intensity profiles, they do not appear capable of explaining the enigmatic central Q/I peak. This leads us to suspect that some aspect of quantum physics is missing.« less

Evaluating the Impact of Atmospheric Infrared Sounder (AIRS) Data On Convective Forecasts

NASA Technical Reports Server (NTRS)

Kozlowski, Danielle; Zavodsky, Bradley

2011-01-01

The Short-term Prediction Research and Transition Center (SPoRT) is a collaborative partnership between NASA and operational forecasting partners, including a number of National Weather Service (NWS) offices. SPoRT provides real-time NASA products and capabilities to its partners to address specific operational forecast challenges. The mission of SPoRT is to transition observations and research capabilities into operations to help improve short-term weather forecasts on a regional scale. Two areas of focus are data assimilation and modeling, which can to help accomplish SPoRT's programmatic goals of transitioning NASA data to operational users. Forecasting convective weather is one challenge that faces operational forecasters. Current numerical weather prediction (NWP) models that operational forecasters use struggle to properly forecast location, timing, intensity and/or mode of convection. Given the proper atmospheric conditions, convection can lead to severe weather. SPoRT's partners in the National Oceanic and Atmospheric Administration (NOAA) have a mission to protect the life and property of American citizens. This mission has been tested as recently as this 2011 severe weather season, which has seen more than 300 fatalities and injuries and total damages exceeding $10 billion. In fact, during the three day period from 25-27 April, 1,265 storms reports (362 tornado reports) were collected making this three day period one of most active in American history. To address the forecast challenge of convective weather, SPoRT produces a real-time NWP model called the SPoRT Weather Research and Forecasting (SPoRT-WRF), which incorporates unique NASA data sets. One of the NASA assets used in this unique model configuration is retrieved profiles from the Atmospheric Infrared Sounder (AIRS).The goal of this project is to determine the impact that these AIRS profiles have on the SPoRT-WRF forecasts by comparing to a current operational model and a control SPoRT-WRF model that does not contain AIRS profiles.

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

Assessing medication effects in the MTA study using neuropsychological outcomes.

PubMed

Epstein, Jeffery N; Conners, C Keith; Hervey, Aaron S; Tonev, Simon T; Arnold, L Eugene; Abikoff, Howard B; Elliott, Glen; Greenhill, Laurence L; Hechtman, Lily; Hoagwood, Kimberly; Hinshaw, Stephen P; Hoza, Betsy; Jensen, Peter S; March, John S; Newcorn, Jeffrey H; Pelham, William E; Severe, Joanne B; Swanson, James M; Wells, Karen; Vitiello, Benedetto; Wigal, Timothy

2006-05-01

While studies have increasingly investigated deficits in reaction time (RT) and RT variability in children with attention deficit/hyperactivity disorder (ADHD), few studies have examined the effects of stimulant medication on these important neuropsychological outcome measures. 316 children who participated in the Multimodal Treatment Study of Children with ADHD (MTA) completed the Conners' Continuous Performance Test (CPT) at the 24-month assessment point. Outcome measures included standard CPT outcomes (e.g., errors of commission, mean hit reaction time (RT)) and RT indicators derived from an Ex-Gaussian distributional model (i.e., mu, sigma, and tau). Analyses revealed significant effects of medication across all neuropsychological outcome measures. Results on the Ex-Gaussian outcome measures revealed that stimulant medication slows RT and reduces RT variability. This demonstrates the importance of including analytic strategies that can accurately model the actual distributional pattern, including the positive skew. Further, the results of the study relate to several theoretical models of ADHD.

The SPoRT-WRF: Evaluating the Impact of NASA Datasets on Convective Forecasts

NASA Technical Reports Server (NTRS)

Zavodsky, Bradley; Case, Jonathan; Kozlowski, Danielle; Molthan, Andrew

2012-01-01

The Short-term Prediction Research and Transition Center (SPoRT) is a collaborative partnership between NASA and operational forecasting entities, including a number of National Weather Service offices. SPoRT transitions real-time NASA products and capabilities to its partners to address specific operational forecast challenges. One challenge that forecasters face is applying convection-allowing numerical models to predict mesoscale convective weather. In order to address this specific forecast challenge, SPoRT produces real-time mesoscale model forecasts using the Weather Research and Forecasting (WRF) model that includes unique NASA products and capabilities. Currently, the SPoRT configuration of the WRF model (SPoRT-WRF) incorporates the 4-km Land Information System (LIS) land surface data, 1-km SPoRT sea surface temperature analysis and 1-km Moderate resolution Imaging Spectroradiometer (MODIS) greenness vegetation fraction (GVF) analysis, and retrieved thermodynamic profiles from the Atmospheric Infrared Sounder (AIRS). The LIS, SST, and GVF data are all integrated into the SPoRT-WRF through adjustments to the initial and boundary conditions, and the AIRS data are assimilated into a 9-hour SPoRT WRF forecast each day at 0900 UTC. This study dissects the overall impact of the NASA datasets and the individual surface and atmospheric component datasets on daily mesoscale forecasts. A case study covering the super tornado outbreak across the Ce ntral and Southeastern United States during 25-27 April 2011 is examined. Three different forecasts are analyzed including the SPoRT-WRF (NASA surface and atmospheric data), the SPoRT WRF without AIRS (NASA surface data only), and the operational National Severe Storms Laboratory (NSSL) WRF (control with no NASA data). The forecasts are compared qualitatively by examining simulated versus observed radar reflectivity. Differences between the simulated reflectivity are further investigated using convective parameters along with model soundings to determine the impacts of the various NASA datasets. Additionally, quantitative evaluation of select meteorological parameters is performed using the Meteorological Evaluation Tools model verification package to compare forecasts to in situ surface and upper air observations.

Retrieval of ice cloud properties using an optimal estimation algorithm and MODIS infrared observations. Part I: Forward model, error analysis, and information content

PubMed Central

Wang, Chenxi; Platnick, Steven; Zhang, Zhibo; Meyer, Kerry; Yang, Ping

2018-01-01

An optimal estimation (OE) retrieval method is developed to infer three ice cloud properties simultaneously: optical thickness (τ), effective radius (reff), and cloud-top height (h). This method is based on a fast radiative transfer (RT) model and infrared (IR) observations from the MODerate resolution Imaging Spectroradiometer (MODIS). This study conducts thorough error and information content analyses to understand the error propagation and performance of retrievals from various MODIS band combinations under different cloud/atmosphere states. Specifically, the algorithm takes into account four error sources: measurement uncertainty, fast RT model uncertainty, uncertainties in ancillary datasets (e.g., atmospheric state), and assumed ice crystal habit uncertainties. It is found that the ancillary and ice crystal habit error sources dominate the MODIS IR retrieval uncertainty and cannot be ignored. The information content analysis shows that, for a given ice cloud, the use of four MODIS IR observations is sufficient to retrieve the three cloud properties. However, the selection of MODIS IR bands that provide the most information and their order of importance varies with both the ice cloud properties and the ambient atmospheric and the surface states. As a result, this study suggests the inclusion of all MODIS IR bands in practice since little a priori information is available. PMID:29707470

Retrieval of Ice Cloud Properties Using an Optimal Estimation Algorithm and MODIS Infrared Observations. Part I: Forward Model, Error Analysis, and Information Content

NASA Technical Reports Server (NTRS)

Wang, Chenxi; Platnick, Steven; Zhang, Zhibo; Meyer, Kerry; Yang, Ping

2016-01-01

An optimal estimation (OE) retrieval method is developed to infer three ice cloud properties simultaneously: optical thickness (tau), effective radius (r(sub eff)), and cloud-top height (h). This method is based on a fast radiative transfer (RT) model and infrared (IR) observations from the MODerate resolution Imaging Spectroradiometer (MODIS). This study conducts thorough error and information content analyses to understand the error propagation and performance of retrievals from various MODIS band combinations under different cloud/atmosphere states. Specifically, the algorithm takes into account four error sources: measurement uncertainty, fast RT model uncertainty, uncertainties in ancillary datasets (e.g., atmospheric state), and assumed ice crystal habit uncertainties. It is found that the ancillary and ice crystal habit error sources dominate the MODIS IR retrieval uncertainty and cannot be ignored. The information content analysis shows that, for a given ice cloud, the use of four MODIS IR observations is sufficient to retrieve the three cloud properties. However, the selection of MODIS IR bands that provide the most information and their order of importance varies with both the ice cloud properties and the ambient atmospheric and the surface states. As a result, this study suggests the inclusion of all MODIS IR bands in practice since little a priori information is available.

Retrieval of Ice Cloud Properties Using an Optimal Estimation Algorithm and MODIS Infrared Observations. Part I: Forward Model, Error Analysis, and Information Content

NASA Technical Reports Server (NTRS)

Wang, Chenxi; Platnick, Steven; Zhang, Zhibo; Meyer, Kerry; Yang, Ping

2016-01-01

An optimal estimation (OE) retrieval method is developed to infer three ice cloud properties simultaneously: optical thickness (tau), effective radius (r(sub eff)), and cloud top height (h). This method is based on a fast radiative transfer (RT) model and infrared (IR) observations from the MODerate resolution Imaging Spectroradiometer (MODIS). This study conducts thorough error and information content analyses to understand the error propagation and performance of retrievals from various MODIS band combinations under different cloud/atmosphere states. Specifically, the algorithm takes into account four error sources: measurement uncertainty, fast RT model uncertainty, uncertainties in ancillary data sets (e.g., atmospheric state), and assumed ice crystal habit uncertainties. It is found that the ancillary and ice crystal habit error sources dominate the MODIS IR retrieval uncertainty and cannot be ignored. The information content analysis shows that for a given ice cloud, the use of four MODIS IR observations is sufficient to retrieve the three cloud properties. However, the selection of MODIS IR bands that provide the most information and their order of importance varies with both the ice cloud properties and the ambient atmospheric and the surface states. As a result, this study suggests the inclusion of all MODIS IR bands in practice since little a priori information is available.

First Principles Modeling and Interpretation of Ionization-Triggered Charge Migration in Molecules

NASA Astrophysics Data System (ADS)

Bruner, Adam; Hernandez, Sam; Mauger, Francois; Abanador, Paul; Gaarde, Mette; Schafer, Ken; Lopata, Ken

Modeling attosecond coherent charge migration in molecules is important for understanding initial steps of photochemistry and light harvesting processes. Ionization triggered hole migration can be difficult to characterize and interpret as the dynamics can be convoluted with excited states. Here, we introduce a real-time time-dependent density functional theory (RT-TDDFT) approach for modeling such dynamics from first principles. To isolate the specific hole dynamics from excited states, Fourier transform analysis and orbital occupations are used to provide a spatial hole representation in the frequency domain. These techniques are applied to hole transfer across a thiophene dimer as well as core-hole triggered valence motion in nitrosobenzene. This work was supported by U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Award No. DE-SC0012462.

Evaluating the Impacts of NASA/SPoRT Daily Greenness Vegetation Fraction on Land Surface Model and Numerical Weather Forecasts

NASA Technical Reports Server (NTRS)

Bell, Jordan R.; Case, Jonathan L.; Molthan, Andrew L.

2011-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center develops new products and techniques that can be used in operational meteorology. The majority of these products are derived from NASA polar-orbiting satellite imagery from the Earth Observing System (EOS) platforms. One such product is a Greenness Vegetation Fraction (GVF) dataset, which is produced from Moderate Resolution Imaging Spectroradiometer (MODIS) data aboard the NASA EOS Aqua and Terra satellites. NASA SPoRT began generating daily real-time GVF composites at 1-km resolution over the Continental United States (CONUS) on 1 June 2010. The purpose of this study is to compare the National Centers for Environmental Prediction (NCEP) climatology GVF product (currently used in operational weather models) to the SPoRT-MODIS GVF during June to October 2010. The NASA Land Information System (LIS) was employed to study the impacts of the new SPoRT-MODIS GVF dataset on land surface models apart from a full numerical weather prediction (NWP) model. For the 2010 warm season, the SPoRT GVF in the western portion of the CONUS was generally higher than the NCEP climatology. The eastern CONUS GVF had variations both above and below the climatology during the period of study. These variations in GVF led to direct impacts on the rates of heating and evaporation from the land surface. The second phase of the project is to examine the impacts of the SPoRT GVF dataset on NWP using the Weather Research and Forecasting (WRF) model. Two separate WRF model simulations were made for individual severe weather case days using the NCEP GVF (control) and SPoRT GVF (experimental), with all other model parameters remaining the same. Based on the sensitivity results in these case studies, regions with higher GVF in the SPoRT model runs had higher evapotranspiration and lower direct surface heating, which typically resulted in lower (higher) predicted 2-m temperatures (2-m dewpoint temperatures). The opposite was true for areas with lower GVF in the SPoRT model runs. These differences in the heating and evaporation rates produced subtle yet quantifiable differences in the simulated convective precipitation systems for the selected severe weather case examined.

Combining of different data pools for calculating a reliable POD for real defects

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

Kanzler, Daniel, E-mail: daniel.kanzler@bam.de, E-mail: christina.mueller@bam.de; Müller, Christina, E-mail: daniel.kanzler@bam.de, E-mail: christina.mueller@bam.de; Pitkänen, Jorma, E-mail: jorma.pitkanen@posiva.fi

2015-03-31

Real defects are essential for the evaluation of the reliability of non destructive testing (NDT) methods, especially in relation to the integrity of components. But in most of the cases the amount of available real defects is not sufficient to evaluate the system. Model-assisted and transfer functions are one way to handle that challenge. This study is focused on a combination of different data pools to create a sufficient amount of data for the reliability estimation. A widespread approach for calculating the Probability of Detection (POD) was used on a radiographic testing (RT) method. The highest contrast to noise ratiomore » (CNR) of each indication is usually selected as the signal in the 'â vs. a' (signal-response) approach for RT. By combining real and artificial defects (flat bottom holes, side drill holes, flat bottom squares, notches, etc) in RT the highest signals are close to each other, but the process of creating and evaluating real defects is much more complex. The solution is seen in the combination of real and artificial data using a weighted least square approach. The weights for real or artificial data were based on the importance, the value and the different detection behavior of the different data. For comparison, the alternative combination through the Bayesian Updating was also applied. As verification, a data pool with a large amount of real data was available. In an advanced approach for evaluating the digital RT data, the size of the indication (perpendicular to the X-ray beam) was introduced as additional information. The signal now consists of the CNR and the area of the indication. The detectability is changing depending on the area of the indication, a fact that was ignored in the previous POD calculations for RT. This points out that a weighted least square approach to pool the data might no longer be adequate. The Bayesian Updating of the estimated parameters of the relationship between the signal field (the area of the indication) and the geometry of the defects is seen as the appropriate model to combine the different defect types in a useful and meaningful way. This work was carried out together with the Finnish company for spent nuclear fuel and waste management - Posiva Oy. The digital RT is one of the NDT methods that might be used for the inspection of the weld of the copper canister to be used for the spent nuclear fuel in the Scandinavian concept of final disposal.« less

NASA SPoRT Modeling and Data Assimilation Research and Transition Activities Using WRF, LIS and GSI

NASA Technical Reports Server (NTRS)

Case, Jonathan L.; Blankenship, Clay B.; Zavodsky, Bradley T.; Srikishen, Jayanthi; Berndt, Emily B.

2014-01-01

weather research and forecasting ===== The NASA Short-term Prediction Research and Transition (SPoRT) program has numerous modeling and data assimilation (DA) activities in which the WRF model is a key component. SPoRT generates realtime, research satellite products from the MODIS and VIIRS instruments, making the data available to NOAA/NWS partners running the WRF/EMS, including: (1) 2-km northwestern-hemispheric SST composite, (2) daily, MODIS green vegetation fraction (GVF) over CONUS, and (3) NASA Land Information System (LIS) runs of the Noah LSM over the southeastern CONUS. Each of these datasets have been utilized by specific SPoRT partners in local EMS model runs, with select offices evaluating the impacts using a set of automated scripts developed by SPoRT that manage data acquisition and run the NCAR Model Evaluation Tools verification package. SPoRT is engaged in DA research with the Gridpoint Statistical Interpolation (GSI) and Ensemble Kalman Filter in LIS for soil moisture DA. Ongoing DA projects using GSI include comparing the impacts of assimilating Atmospheric Infrared Sounder (AIRS) radiances versus retrieved profiles, and an analysis of extra-tropical cyclones with intense non-convective winds. As part of its Early Adopter activities for the NASA Soil Moisture Active Passive (SMAP) mission, SPoRT is conducting bias correction and soil moisture DA within LIS to improve simulations using the NASA Unified-WRF (NU-WRF) for both the European Space Agency's Soil Moisture Ocean Salinity and upcoming SMAP mission data. SPoRT has also incorporated real-time global GVF data into LIS and WRF from the VIIRS product being developed by NOAA/NESDIS. This poster will highlight the research and transition activities SPoRT conducts using WRF, NU-WRF, EMS, LIS, and GSI.

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.

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.

Spectral Bio-indicator Simulations for Tracking Photosynthetic Activities in a Corn Field

NASA Technical Reports Server (NTRS)

Cheng, Yen-Ben; Middleton, Elizabeth M.; Huemmrich, K. Fred; Zhang, Qingyuan; Corp, Lawrence; Campbell, Petya; Kustas, William

2011-01-01

Accurate assessment of vegetation canopy optical properties plays a critical role in monitoring natural and managed ecosystems under environmental changes. In this context, radiative transfer (RT) models simulating vegetation canopy reflectance have been demonstrated to be a powerful tool for understanding and estimating spectral bio-indicators. In this study, two narrow band spectroradiometers were utilized to acquire observations over corn canopies for two summers. These in situ spectral data were then used to validate a two-layer Markov chain-based canopy reflectance model for simulating the Photochemical Reflectance Index (PRI), which has been widely used in recent vegetation photosynthetic light use efficiency (LUE) studies. The in situ PRI derived from narrow band hyperspectral reflectance exhibited clear responses to: 1) viewing geometry which affects the asset of light environment; and 2) seasonal variation corresponding to the growth stage. The RT model (ACRM) successfully simulated the responses to the variable viewing geometry. The best simulations were obtained when the model was set to run in the two layer mode using the sunlit leaves as the upper layer and shaded leaves as the lower layer. Simulated PRI values yielded much better correlations to in situ observations when the cornfield was dominated by green foliage during the early growth, vegetative and reproductive stages (r = 0.78 to 0.86) than in the later senescent stage (r = 0.65). Further sensitivity analyses were conducted to show the important influences of leaf area index (LAI) and the sunlit/shaded ratio on PRI observations.

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.

Evaluating model parameterizations of submicron aerosol scattering and absorption with in situ data from ARCTAS 2008

NASA Astrophysics Data System (ADS)

Alvarado, Matthew J.; Lonsdale, Chantelle R.; Macintyre, Helen L.; Bian, Huisheng; Chin, Mian; Ridley, David A.; Heald, Colette L.; Thornhill, Kenneth L.; Anderson, Bruce E.; Cubison, Michael J.; Jimenez, Jose L.; Kondo, Yutaka; Sahu, Lokesh K.; Dibb, Jack E.; Wang, Chien

2016-07-01

Accurate modeling of the scattering and absorption of ultraviolet and visible radiation by aerosols is essential for accurate simulations of atmospheric chemistry and climate. Closure studies using in situ measurements of aerosol scattering and absorption can be used to evaluate and improve models of aerosol optical properties without interference from model errors in aerosol emissions, transport, chemistry, or deposition rates. Here we evaluate the ability of four externally mixed, fixed size distribution parameterizations used in global models to simulate submicron aerosol scattering and absorption at three wavelengths using in situ data gathered during the 2008 Arctic Research of the Composition of the Troposphere from Aircraft and Satellites (ARCTAS) campaign. The four models are the NASA Global Modeling Initiative (GMI) Combo model, GEOS-Chem v9-02, the baseline configuration of a version of GEOS-Chem with online radiative transfer calculations (called GC-RT), and the Optical Properties of Aerosol and Clouds (OPAC v3.1) package. We also use the ARCTAS data to perform the first evaluation of the ability of the Aerosol Simulation Program (ASP v2.1) to simulate submicron aerosol scattering and absorption when in situ data on the aerosol size distribution are used, and examine the impact of different mixing rules for black carbon (BC) on the results. We find that the GMI model tends to overestimate submicron scattering and absorption at shorter wavelengths by 10-23 %, and that GMI has smaller absolute mean biases for submicron absorption than OPAC v3.1, GEOS-Chem v9-02, or GC-RT. However, the changes to the density and refractive index of BC in GC-RT improve the simulation of submicron aerosol absorption at all wavelengths relative to GEOS-Chem v9-02. Adding a variable size distribution, as in ASP v2.1, improves model performance for scattering but not for absorption, likely due to the assumption in ASP v2.1 that BC is present at a constant mass fraction throughout the aerosol size distribution. Using a core-shell mixing rule in ASP overestimates aerosol absorption, especially for the fresh biomass burning aerosol measured in ARCTAS-B, suggesting the need for modeling the time-varying mixing states of aerosols in future versions of ASP.

Modeling qRT-PCR dynamics with application to cancer biomarker quantification.

PubMed

Chervoneva, Inna; Freydin, Boris; Hyslop, Terry; Waldman, Scott A

2017-01-01

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is widely used for molecular diagnostics and evaluating prognosis in cancer. The utility of mRNA expression biomarkers relies heavily on the accuracy and precision of quantification, which is still challenging for low abundance transcripts. The critical step for quantification is accurate estimation of efficiency needed for computing a relative qRT-PCR expression. We propose a new approach to estimating qRT-PCR efficiency based on modeling dynamics of polymerase chain reaction amplification. In contrast, only models for fluorescence intensity as a function of polymerase chain reaction cycle have been used so far for quantification. The dynamics of qRT-PCR efficiency is modeled using an ordinary differential equation model, and the fitted ordinary differential equation model is used to obtain effective polymerase chain reaction efficiency estimates needed for efficiency-adjusted quantification. The proposed new qRT-PCR efficiency estimates were used to quantify GUCY2C (Guanylate Cyclase 2C) mRNA expression in the blood of colorectal cancer patients. Time to recurrence and GUCY2C expression ratios were analyzed in a joint model for survival and longitudinal outcomes. The joint model with GUCY2C quantified using the proposed polymerase chain reaction efficiency estimates provided clinically meaningful results for association between time to recurrence and longitudinal trends in GUCY2C expression.

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

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.

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

Working memory and intraindividual variability as neurocognitive indicators in ADHD: examining competing model predictions.

PubMed

Kofler, Michael J; Alderson, R Matt; Raiker, Joseph S; Bolden, Jennifer; Sarver, Dustin E; Rapport, Mark D

2014-05-01

The current study examined competing predictions of the default mode, cognitive neuroenergetic, and functional working memory models of attention-deficit/hyperactivity disorder (ADHD) regarding the relation between neurocognitive impairments in working memory and intraindividual variability. Twenty-two children with ADHD and 15 typically developing children were assessed on multiple tasks measuring intraindividual reaction time (RT) variability (ex-Gaussian: tau, sigma) and central executive (CE) working memory. Latent factor scores based on multiple, counterbalanced tasks were created for each construct of interest (CE, tau, sigma) to reflect reliable variance associated with each construct and remove task-specific, test-retest, and random error. Bias-corrected, bootstrapped mediation analyses revealed that CE working memory accounted for 88% to 100% of ADHD-related RT variability across models, and between-group differences in RT variability were no longer detectable after accounting for the mediating role of CE working memory. In contrast, RT variability accounted for 10% to 29% of between-group differences in CE working memory, and large magnitude CE working memory deficits remained after accounting for this partial mediation. Statistical comparison of effect size estimates across models suggests directionality of effects, such that the mediation effects of CE working memory on RT variability were significantly greater than the mediation effects of RT variability on CE working memory. The current findings question the role of RT variability as a primary neurocognitive indicator in ADHD and suggest that ADHD-related RT variability may be secondary to underlying deficits in CE working memory.

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

The timing of surgery after neoadjuvant radiotherapy influences tumor dissemination in a preclinical model

PubMed Central

Leroi, Natacha; Sounni, Nor Eddine; Van Overmeire, Eva; Blacher, Silvia; Marée, Raphael; Van Ginderachter, Jo; Lallemand, François; Lenaerts, Eric; Coucke, Philippe; Noel, Agnès; Martinive, Philippe

2015-01-01

Neoadjuvant radiotherapy (neoRT) used in cancer treatments aims at improving local tumor control and patient overall survival. The neoRT schedule and the timing of the surgical treatment (ST) are empirically based and influenced by the clinician's experience. The current study examines how the sequencing of neoRT and ST affects metastatic dissemination. In a breast carcinoma model, tumors were exposed to different neoRT schedules (2x5Gy or 5x2Gy) followed by surgery at day 4 or 11 post-RT. The impact on the tumor microenvironment and lung metastases was evaluated through immunohistochemical and flow cytometry analyses. After 2x5Gy, early ST (at day 4 post-RT) led to increased size and number of lung metastases as compared to ST performed at day 11. Inversely, after 5x2Gy neoRT, early ST protected the mice against lung metastases. This intriguing relationship between tumor aggressiveness and ST timing could not be explained by differences in classical parameters studied such as hypoxia, vessel density and matrix remodeling. The study of tumor-related inflammation and immunity reveals an increased circulating NK cell percentage following neoRT as compared to non irradiated mice. Then, radiation treatment and surgery were applied to tumor-bearing NOD/SCID mice. In the absence of NK cells, neoRT appears to increase lung metastatic dissemination as compared to non irradiated tumor-bearing mice. Altogether our data demonstrate that the neoRT schedule and the ST timing affect metastasis formation in a pre-clinical model and points out the potential role of NK cells. These findings highlight the importance to cautiously tailor the optimal window for ST following RT. PMID:26440148

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.

Joint retrieval of aerosol and water-leaving radiance from multispectral, multiangular and polarimetric measurements over ocean

NASA Astrophysics Data System (ADS)

Xu, Feng; Dubovik, Oleg; Zhai, Peng-Wang; Diner, David J.; Kalashnikova, Olga V.; Seidel, Felix C.; Litvinov, Pavel; Bovchaliuk, Andrii; Garay, Michael J.; van Harten, Gerard; Davis, Anthony B.

2016-07-01

An optimization approach has been developed for simultaneous retrieval of aerosol properties and normalized water-leaving radiance (nLw) from multispectral, multiangular, and polarimetric observations over ocean. The main features of the method are (1) use of a simplified bio-optical model to estimate nLw, followed by an empirical refinement within a specified range to improve its accuracy; (2) improved algorithm convergence and stability by applying constraints on the spatial smoothness of aerosol loading and Chlorophyll a (Chl a) concentration across neighboring image patches and spectral constraints on aerosol optical properties and nLw across relevant bands; and (3) enhanced Jacobian calculation by modeling and storing the radiative transfer (RT) in aerosol/Rayleigh mixed layer, pure Rayleigh-scattering layers, and ocean medium separately, then coupling them to calculate the field at the sensor. This approach avoids unnecessary and time-consuming recalculations of RT in unperturbed layers in Jacobian evaluations. The Markov chain method is used to model RT in the aerosol/Rayleigh mixed layer and the doubling method is used for the uniform layers of the atmosphere-ocean system. Our optimization approach has been tested using radiance and polarization measurements acquired by the Airborne Multiangle SpectroPolarimetric Imager (AirMSPI) over the AERONET USC_SeaPRISM ocean site (6 February 2013) and near the AERONET La Jolla site (14 January 2013), which, respectively, reported relatively high and low aerosol loadings. Validation of the results is achieved through comparisons to AERONET aerosol and ocean color products. For comparison, the USC_SeaPRISM retrieval is also performed by use of the Generalized Retrieval of Aerosol and Surface Properties algorithm (Dubovik et al., 2011). Uncertainties of aerosol and nLw retrievals due to random and systematic instrument errors are analyzed by truth-in/truth-out tests with three Chl a concentrations, five aerosol loadings, three different types of aerosols, and nine combinations of solar incidence and viewing geometries.

Effective Tree Scattering and Opacity at L-Band

NASA Technical Reports Server (NTRS)

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

2011-01-01

This paper investigates vegetation effects at L-band by using a first-order radiative transfer (RT) model and truck-based microwave measurements over natural conifer stands to assess the applicability of the tau-omega) model over trees. The tau-omega model is a zero-order RT solution that accounts for vegetation effects with effective vegetation parameters (vegetation opacity and single-scattering albedo), which represent the canopy as a whole. This approach inherently ignores multiple-scattering effects and, therefore, has a limited validity depending on the level of scattering within the canopy. The fact that the scattering from large forest components such as branches and trunks is significant at L-band requires that zero-order vegetation parameters be evaluated (compared) along with their theoretical definitions to provide a better understanding of these parameters in the retrieval algorithms as applied to trees. This paper compares the effective vegetation opacities, computed from multi-angular pine tree brightness temperature data, against the results of two independent approaches that provide theoretical and measured optical depths. These two techniques are based on forward scattering theory and radar corner reflector measurements, respectively. The results indicate that the effective vegetation opacity values are smaller than but of similar magnitude to both radar and theoretical estimates. The effective opacity of the zero-order model is thus set equal to the theoretical opacity and an explicit expression for the effective albedo is then obtained from the zero- and first- order RT model comparison. The resultant albedo is found to have a similar magnitude as the effective albedo value obtained from brightness temperature measurements. However, it is less than half of that estimated using the theoretical calculations (0.5 - 0.6 for tree canopies at L-band). This lower observed albedo balances the scattering darkening effect of the large theoretical albedo with a first-order multiple-scattering contribution. The retrieved effective albedo is different from theoretical definitions and not the albedo of single forest elements anymore, but it becomes a global parameter, which depends on all the processes taking place within the canopy, including multiple-scattering.

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.

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.

The Population Benefit of Radiotherapy for Malignant Brain Tumors: Local Control and Survival Estimates for Guideline-Based Use.

PubMed

Hanna, Timothy Paul; Delaney, Geoffrey Paul; Barton, Michael Bernard

2016-09-01

To estimate the population benefit of radiotherapy (RT) for primary malignant brain tumors if evidence-based guidelines were routinely followed. This study investigated 5-year local control (LC) and 2- and 5-year overall survival (OS) benefits. RT benefit was the absolute proportional benefit of RT alone over no RT for radical indications, and over surgery alone for adjuvant indications. Chemoradiotherapy (CRT) benefit was the absolute incremental benefit of concurrent chemotherapy and RT over RT alone. Decision tree models were adapted to define the incidence of each indication. Citation databases were systematically queried for the highest level of evidence defining indication benefits. Meta-analysis was performed if there were multiple sources of the same evidence level, and deterministic and probabilistic sensitivity analysis was also performed. Among all patients with malignant brain tumors, 82% had indications for curative- or adjuvant-intent RT. The magnitude of benefit was based on level I or II evidence in 44% of all patients. A total of 25 relevant studies were used to quantify indication benefits. All RT benefit included in the model was irreplaceable. For malignant brain tumors, the estimated population benefit for RT alone was 9% for 5-year LC (95% CI, 7%-10%), 9% for 2-year OS (95% CI, 8%-11%), and 5% for 5-year OS (95% CI, 4%-5%). The incremental benefit of CRT was 1% for 5-year LC (95% CI, 0%-2%), 7% for 2-year OS (95% CI, 4%-11%), and 3% for 5-year OS (95% CI, 1%-5%). The model was robust in sensitivity analysis. When optimally used, RT provides an important benefit for many patients with malignant brain tumors. The model provided a robust means for estimating the magnitude of this benefit. Copyright © 2016 by the National Comprehensive Cancer Network.

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)

Does the patient's inherent rating tendency influence reported satisfaction scores and affect division ranking?

PubMed

Francis, Patricia; Agoritsas, Thomas; Chopard, Pierre; Perneger, Thomas

2016-04-01

To determine the impact of adjusting for rating tendency (RT) on patient satisfaction scores in a large teaching hospital and to assess the impact of adjustment on the ranking of divisions. Cross-sectional survey. Large 2200-bed university teaching hospital. All adult patients hospitalized during a 1-month period in one of 20 medical divisions. None. Patient experience of care measured by the Picker Patient Experience questionnaire and RT scores. Problem scores were weakly but significantly associated with RT. Division ranking was slightly modified in RT adjusted models. Division ranking changed substantially in case-mix adjusted models. Adjusting patient self-reported problem scores for RT did impact ranking of divisions, although marginally. Further studies are needed to determine the impact of RT when comparing different institutions, particularly across inter-cultural settings, where the difference in RT may be more substantial. © The Author 2016. Published by Oxford University Press in association with the International Society for Quality in Health Care; all rights reserved.

The SPoRT-WRF: Evaluating the Impact of NASA Datasets on Convective Forecasts

NASA Technical Reports Server (NTRS)

Zavodsky, Bradley; Kozlowski, Danielle; Case, Jonathan; Molthan, Andrew

2012-01-01

Short-term Prediction Research and Transition (SPoRT) seeks to improve short-term, regional weather forecasts using unique NASA products and capabilities SPoRT has developed a unique, real-time configuration of the NASA Unified Weather Research and Forecasting (WRF)WRF (ARW) that integrates all SPoRT modeling research data: (1) 2-km SPoRT Sea Surface Temperature (SST) Composite, (2) 3-km LIS with 1-km Greenness Vegetation Fraction (GVFs) (3) 45-km AIRS retrieved profiles. Transitioned this real-time forecast to NOAA's Hazardous Weather Testbed (HWT) as deterministic model at Experimental Forecast Program (EFP). Feedback from forecasters/participants and internal evaluation of SPoRT-WRF shows a cool, dry bias that appears to suppress convection likely related to methodology for assimilation of AIRS profiles Version 2 of the SPoRT-WRF will premier at the 2012 EFP and include NASA physics, cycling data assimilation methodology, better coverage of precipitation forcing, and new GVFs

Evaluating the Impacts of NASA/SPoRT Daily Greenness Vegetation Fraction on Land Surface Model and Numerical Weather Forecasts

NASA Technical Reports Server (NTRS)

Bell, Jordan R.; Case, Jonathan L.; LaFontaine, Frank J.; Kumar, Sujay V.

2012-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center has developed a Greenness Vegetation Fraction (GVF) dataset, which is updated daily using swaths of Normalized Difference Vegetation Index data from the Moderate Resolution Imaging Spectroradiometer (MODIS) data aboard the NASA EOS Aqua and Terra satellites. NASA SPoRT began generating daily real-time GVF composites at 1-km resolution over the Continental United States (CONUS) on 1 June 2010. The purpose of this study is to compare the National Centers for Environmental Prediction (NCEP) climatology GVF product (currently used in operational weather models) to the SPoRT-MODIS GVF during June to October 2010. The NASA Land Information System (LIS) was employed to study the impacts of the SPoRT-MODIS GVF dataset on a land surface model (LSM) apart from a full numerical weather prediction (NWP) model. For the 2010 warm season, the SPoRT GVF in the western portion of the CONUS was generally higher than the NCEP climatology. The eastern CONUS GVF had variations both above and below the climatology during the period of study. These variations in GVF led to direct impacts on the rates of heating and evaporation from the land surface. In the West, higher latent heat fluxes prevailed, which enhanced the rates of evapotranspiration and soil moisture depletion in the LSM. By late Summer and Autumn, both the average sensible and latent heat fluxes increased in the West as a result of the more rapid soil drying and higher coverage of GVF. The impacts of the SPoRT GVF dataset on NWP was also examined for a single severe weather case study using the Weather Research and Forecasting (WRF) model. Two separate coupled LIS/WRF model simulations were made for the 17 July 2010 severe weather event in the Upper Midwest using the NCEP and SPoRT GVFs, with all other model parameters remaining the same. Based on the sensitivity results, regions with higher GVF in the SPoRT model runs had higher evapotranspiration and lower direct surface heating, which typically resulted in lower (higher) predicted 2-m temperatures (2-m dewpoint temperatures). Portions of the Northern Plains states experienced substantial increases in convective available potential energy as a result of the higher SPoRT/MODIS GVFs. These differences produced subtle yet quantifiable differences in the simulated convective precipitation systems for this event.

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.

The BCD of response time analysis in experimental economics.

PubMed

Spiliopoulos, Leonidas; Ortmann, Andreas

2018-01-01

For decisions in the wild, time is of the essence. Available decision time is often cut short through natural or artificial constraints, or is impinged upon by the opportunity cost of time. Experimental economists have only recently begun to conduct experiments with time constraints and to analyze response time (RT) data, in contrast to experimental psychologists. RT analysis has proven valuable for the identification of individual and strategic decision processes including identification of social preferences in the latter case, model comparison/selection, and the investigation of heuristics that combine speed and performance by exploiting environmental regularities. Here we focus on the benefits, challenges, and desiderata of RT analysis in strategic decision making. We argue that unlocking the potential of RT analysis requires the adoption of process-based models instead of outcome-based models, and discuss how RT in the wild can be captured by time-constrained experiments in the lab. We conclude that RT analysis holds considerable potential for experimental economics, deserves greater attention as a methodological tool, and promises important insights on strategic decision making in naturally occurring environments.

Projected Applications of a "Weather in a Box" Computing System at the NASA Short-Term Prediction Research and Transition (SPoRT) Center

NASA Technical Reports Server (NTRS)

Jedlovec, Gary J.; Molthan, Andrew; Zavodsky, Bradley T.; Case, Jonathan L.; LaFontaine, Frank J.; Srikishen, Jayanthi

2010-01-01

The NASA Short-term Prediction Research and Transition Center (SPoRT)'s new "Weather in a Box" resources will provide weather research and forecast modeling capabilities for real-time application. Model output will provide additional forecast guidance and research into the impacts of new NASA satellite data sets and software capabilities. By combining several research tools and satellite products, SPoRT can generate model guidance that is strongly influenced by unique NASA contributions.

Administrator Perceptions Regarding Pennsylvania's MTSS/RtII Framework and Gifted Elementary Students

ERIC Educational Resources Information Center

Murin, Tricia M.

2016-01-01

Providing equitable education for all students is the responsibility of administrators, teachers, and parents. Even though the MTSS/RtII Framework has evolved from the RtI and RtII models, the basis is the same: intervening and identifying students' needs and analyzing data and programming instruction to meet all students' needs. Even though in…

Implementing RtI with Gifted Students

ERIC Educational Resources Information Center

Coleman, Mary Ruth, Ed.; Johnsen, Susan K., Ed.

2012-01-01

"Implementing RtI With Gifted Students" shares how RtI can fit within the framework of gifted education programming models. This edited book will serve as a reference guide for those interested in learning more about RtI and how it might be effectively implemented to meet the needs of all gifted students. Chapters contributed by top gifted…

The spatial extent of polycyclic aromatic hydrocarbons emission in the Herbig star HD 179218

NASA Astrophysics Data System (ADS)

Taha, A. S.; Labadie, L.; Pantin, E.; Matter, A.; Alvarez, C.; Esquej, P.; Grellmann, R.; Rebolo, R.; Telesco, C.; Wolf, S.

2018-04-01

Aim. We investigate, in the mid-infrared, the spatial properties of the polycyclic aromatic hydrocarbons (PAHs) emission in the disk of HD 179218, an intermediate-mass Herbig star at 300 pc. Methods: We obtained mid-infrared images in the PAH-1, PAH-2 and Si-6 filters centered at 8.6, 11.3, and 12.5 μm, and N-band low-resolution spectra using CanariCam on the 10-m Gran Telescopio Canarias (GTC). We compared the point spread function (PSF) profiles measured in the PAH filters to the profile derived in the Si-6 filter, where the thermal continuum emission dominates. We performed radiative transfer modeling of the spectral energy distribution (SED) and produced synthetic images in the three filters to investigate different spatial scenarios. Results: Our data show that the disk emission is spatially resolved in the PAH-1 and PAH-2 filters, while unresolved in the Si-6 filter. Thanks to very good observing conditions, an average full width at half maximum (FWHM) of 0.232'', 0.280'' and 0.293'' is measured in the three filters, respectively. Gaussian disk fitting and quadratic subtraction of the science and calibrator PSFs suggests a lower-limit characteristic angular diameter of the emission of 100 mas, or 30 au. The photometric and spectroscopic results are compatible with previous findings. Our radiative transfer (RT) modeling of the continuum suggests that the resolved emission should result from PAH molecules on the disk atmosphere being UV-excited by the central star. Simple geometrical models of the PAH component compared to the underlying continuum point to a PAH emission uniformly extended out to the physical limits of the disk model. Furthermore, our RT best model of the continuum requires a negative exponent of the surface density power-law, in contrast with earlier modeling pointing to a positive exponent. Conclusions: We have spatially resolved - for the first time to our knowledge - the PAHs emission in the disk of HD 179218 and set constraints on its spatial extent. Based on spatial and spectroscopic considerations as well as on qualitative comparison with IRS 48 and HD 97048, we favor a scenario in which PAHs extend out to large radii across the flared disk surface and are at the same time predominantly in an ionized charge state due to the strong UV radiation field of the 180 L⊙ central star.

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.

The reverse transcriptase encoded by LINE-1 retrotransposons in the genesis, progression and therapy of cancer

NASA Astrophysics Data System (ADS)

Sciamanna, Ilaria; De Luca, Chiara; Spadafora, Corrado

2016-02-01

In higher eukaryotic genomes, Long Interspersed Nuclear Element 1 (LINE-1) retrotransposons represent a large family of repeated genomic elements. They transpose using a reverse transcriptase (RT), which they encode as part of the ORF2p product. RT inhibition in cancer cells, either via RNA interference-dependent silencing of active LINE-1 elements, or using RT inhibitory drugs, reduces cancer cell proliferation, promotes their differentiation and antagonizes tumor progression in animal models. Indeed, the nonnucleoside RT inhibitor efavirenz has recently been tested in a phase II clinical trial with metastatic prostate cancer patients. An in-depth analysis of ORF2p in a mouse model of breast cancer showed ORF2p to be precociously expressed in precancerous lesions and highly abundant in advanced cancer stages, while being barely detectable in normal breast tissue, providing a rationale for the finding that RT-expressing tumours are therapeutically sensitive to RT inhibitors. We summarise mechanistic and gene profiling studies indicating that highly abundant LINE-1-derived RT can “sequester” RNA substrates for reverse transcription in tumor cells, entailing the formation of RNA:DNA hybrid molecules and impairing the overall production of regulatory miRNAs, with a global impact on the cell transcriptome. Based on these data, LINE-1-ORF2 encoded RT has a tumor-promoting potential that is exerted at an epigenetic level. We propose a model whereby LINE1-RT drives a previously unrecognized global regulatory process, the deregulation of which drives cell transformation and tumorigenesis and possibly implicated in cancer cell heterogeneity.

Cost-Effectiveness Analysis of Preoperative Versus Postoperative Radiation Therapy in Extremity Soft Tissue Sarcoma

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

Qu, Xuanlu M.; Louie, Alexander V.; Ashman, Jonathan

Purpose: Surgery combined with radiation therapy (RT) is the cornerstone of multidisciplinary management of extremity soft tissue sarcoma (STS). Although RT can be given in either the preoperative or the postoperative setting with similar local recurrence and survival outcomes, the side effect profiles, costs, and long-term functional outcomes are different. The aim of this study was to use decision analysis to determine optimal sequencing of RT with surgery in patients with extremity STS. Methods and Materials: A cost-effectiveness analysis was conducted using a state transition Markov model, with quality-adjusted life years (QALYs) as the primary outcome. A time horizon ofmore » 5 years, a cycle length of 3 months, and a willingness-to-pay threshold of $50,000/QALY was used. One-way deterministic sensitivity analyses were performed to determine the thresholds at which each strategy would be preferred. The robustness of the model was assessed by probabilistic sensitivity analysis. Results: Preoperative RT is a more cost-effective strategy ($26,633/3.00 QALYs) than postoperative RT ($28,028/2.86 QALYs) in our base case scenario. Preoperative RT is the superior strategy with either 3-dimensional conformal RT or intensity-modulated RT. One-way sensitivity analyses identified the relative risk of chronic adverse events as having the greatest influence on the preferred timing of RT. The likelihood of preoperative RT being the preferred strategy was 82% on probabilistic sensitivity analysis. Conclusions: Preoperative RT is more cost effective than postoperative RT in the management of resectable extremity STS, primarily because of the higher incidence of chronic adverse events with RT in the postoperative setting.« 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.

Design, synthesis and biological evaluations of N-Hydroxy thienopyrimidine-2,4-diones as inhibitors of HIV reverse transcriptase-associated RNase H.

PubMed

Kankanala, Jayakanth; Kirby, Karen A; Huber, Andrew D; Casey, Mary C; Wilson, Daniel J; Sarafianos, Stefan G; Wang, Zhengqiang

2017-12-01

Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) is the only HIV enzymatic function not targeted by current antiviral drugs. Although various chemotypes have been reported to inhibit HIV RNase H, few have shown significant antiviral activities. We report herein the design, synthesis and biological evaluation of a novel N-hydroxy thienopyrimidine-2,3-dione chemotype (11) which potently and selectively inhibited RNase H with considerable potency against HIV-1 in cell culture. Current structure-activity-relationship (SAR) identified analogue 11d as a nanomolar inhibitor of RNase H (IC 50  = 0.04 μM) with decent antiviral potency (EC 50  = 7.4 μM) and no cytotoxicity (CC 50  > 100 μM). In extended biochemical assays compound 11d did not inhibit RT polymerase (pol) while inhibiting integrase strand transfer (INST) with 53 fold lower potency (IC 50  = 2.1 μM) than RNase H inhibition. Crystallographic and molecular modeling studies confirmed the RNase H active site binding mode. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

New quality assurance program integrating "modern radiotherapy" within the German Hodgkin Study Group.

PubMed

Kriz, J; Baues, C; Engenhart-Cabillic, R; Haverkamp, U; Herfarth, K; Lukas, P; Schmidberger, H; Marnitz-Schulze, S; Fuchs, M; Engert, A; Eich, H T

2017-02-01

Field design changed substantially from extended-field RT (EF-RT) to involved-field RT (IF-RT) and now to involved-node RT (IN-RT) and involved-site RT (IS-RT) as well as treatment techniques in radiotherapy (RT) of Hodgkin's lymphoma (HL). The purpose of this article is to demonstrate the establishment of a quality assurance program (QAP) including modern RT techniques and field designs within the German Hodgkin Study Group (GHSG). In the era of modern conformal RT, this QAP had to be fundamentally adapted and a new evaluation process has been intensively discussed by the radiotherapeutic expert panel of the GHSG. The expert panel developed guidelines and criteria to analyse "modern" field designs and treatment techniques. This work is based on a dataset of 11 patients treated within the sixth study generation (HD16-17). To develop a QAP of "modern RT", the expert panel defined criteria for analysing current RT procedures. The consensus of a modified QAP in ongoing and future trials is presented. With this schedule, the QAP of the GHSG could serve as a model for other study groups.

Rumination time as a potential predictor of common diseases in high-productive Holstein dairy cows.

PubMed

Moretti, Riccardo; Biffani, Stefano; Tiezzi, Francesco; Maltecca, Christian; Chessa, Stefania; Bozzi, Riccardo

2017-11-01

We examined the hypothesis that rumination time (RT) could serve as a useful predictor of various common diseases of high producing dairy cows and hence improve herd management and animal wellbeing. We measured the changes in rumination time (RT) in the days before the recording of diseases (specifically: mastitis, reproductive system diseases, locomotor system issues, and gastroenteric diseases). We built predictive models to assess the association between RT and these diseases, using the former as the outcome variable, and to study the effects of the latter on the former. The average Pseudo-R 2 of the fitted models was moderate to low, and this could be due to the fact that RT is influenced by other additional factors which have a greater effect than the predictors used here. Although remaining in a moderate-to-low range, the average Pseudo-R 2 of the models regarding locomotion issues and gastroenteric diseases was higher than the others, suggesting the greater effect of these diseases on RT. The results are encouraging, but further work is needed if these models are to become useful predictors.

A meta-analysis of response-time tests of the sequential two-systems model of moral judgment.

PubMed

Baron, Jonathan; Gürçay, Burcu

2017-05-01

The (generalized) sequential two-system ("default interventionist") model of utilitarian moral judgment predicts that utilitarian responses often arise from a system-two correction of system-one deontological intuitions. Response-time (RT) results that seem to support this model are usually explained by the fact that low-probability responses have longer RTs. Following earlier results, we predicted response probability from each subject's tendency to make utilitarian responses (A, "Ability") and each dilemma's tendency to elicit deontological responses (D, "Difficulty"), estimated from a Rasch model. At the point where A = D, the two responses are equally likely, so probability effects cannot account for any RT differences between them. The sequential two-system model still predicts that many of the utilitarian responses made at this point will result from system-two corrections of system-one intuitions, hence should take longer. However, when A = D, RT for the two responses was the same, contradicting the sequential model. Here we report a meta-analysis of 26 data sets, which replicated the earlier results of no RT difference overall at the point where A = D. The data sets used three different kinds of moral judgment items, and the RT equality at the point where A = D held for all three. In addition, we found that RT increased with A-D. This result holds for subjects (characterized by Ability) but not for items (characterized by Difficulty). We explain the main features of this unanticipated effect, and of the main results, with a drift-diffusion model.

Computational models of the Posner simple and choice reaction time tasks

PubMed Central

Feher da Silva, Carolina; Baldo, Marcus V. C.

2015-01-01

The landmark experiments by Posner in the late 1970s have shown that reaction time (RT) is faster when the stimulus appears in an expected location, as indicated by a cue; since then, the so-called Posner task has been considered a “gold standard” test of spatial attention. It is thus fundamental to understand the neural mechanisms involved in performing it. To this end, we have developed a Bayesian detection system and small integrate-and-fire neural networks, which modeled sensory and motor circuits, respectively, and optimized them to perform the Posner task under different cue type proportions and noise levels. In doing so, main findings of experimental research on RT were replicated: the relative frequency effect, suboptimal RTs and significant error rates due to noise and invalid cues, slower RT for choice RT tasks than for simple RT tasks, fastest RTs for valid cues and slowest RTs for invalid cues. Analysis of the optimized systems revealed that the employed mechanisms were consistent with related findings in neurophysiology. Our models predict that (1) the results of a Posner task may be affected by the relative frequency of valid and neutral trials, (2) in simple RT tasks, input from multiple locations are added together to compose a stronger signal, and (3) the cue affects motor circuits more strongly in choice RT tasks than in simple RT tasks. In discussing the computational demands of the Posner task, attention has often been described as a filter that protects the nervous system, whose capacity is limited, from information overload. Our models, however, reveal that the main problems that must be overcome to perform the Posner task effectively are distinguishing signal from external noise and selecting the appropriate response in the presence of internal noise. PMID:26190997

Expansion of the Real-time Sport-land Information System for NOAA / National Weather Service Situational Awareness and Local Modeling Applications

NASA Technical Reports Server (NTRS)

Case, Jonathan L.; White, Kristopher D.

2014-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center in Huntsville, AL (Jedlovec 2013; Ralph et al. 2013; Merceret et al. 2013) is running a real-time configuration of the Noah land surface model (LSM) within the NASA Land Information System (LIS) framework (hereafter referred to as the "SPoRT-LIS"). Output from the real-time SPoRT-LIS is used for (1) initializing land surface variables for local modeling applications, and (2) displaying in decision support systems for situational awareness and drought monitoring at select NOAA/National Weather Service (NWS) partner offices. The SPoRT-LIS is currently run over a domain covering the southeastern half of the Continental United States (CONUS), with an additional experimental real-time run over the entire CONUS and surrounding portions of southern Canada and northern Mexico. The experimental CONUS run incorporates hourly quantitative precipitation estimation (QPE) from the National Severe Storms Laboratory Multi- Radar Multi-Sensor (MRMS) product (Zhang et al. 2011, 2014), which will be transitioned into operations at the National Centers for Environmental Prediction (NCEP) in Fall 2014. This paper describes the current and experimental SPoRT-LIS configurations, and documents some of the limitations still remaining through the advent of MRMS precipitation analyses in the SPoRT-LIS land surface model (LSM) simulations. Section 2 gives background information on the NASA LIS and describes the realtime SPoRT-LIS configurations being compared. Section 3 presents recent work done to develop a training module on situational awareness applications of real-time SPoRT-LIS output. Comparisons between output from the two SPoRT-LIS runs are shown in Section 4, including a documentation of issues encountered in using the MRMS precipitation dataset. A summary and future work in given in Section 5, followed by acknowledgements and references.

A response-time approach to comparing generalized rational and take-the-best models of decision making.

PubMed

Bergert, F Bryan; Nosofsky, Robert M

2007-01-01

The authors develop and test generalized versions of take-the-best (TTB) and rational (RAT) models of multiattribute paired-comparison inference. The generalized models make allowances for subjective attribute weighting, probabilistic orders of attribute inspection, and noisy decision making. A key new test involves a response-time (RT) approach. TTB predicts that RT is determined solely by the expected time required to locate the 1st discriminating attribute, whereas RAT predicts that RT is determined by the difference in summed evidence between the 2 alternatives. Critical test pairs are used that partially decouple these 2 factors. Under conditions in which ideal observer TTB and RAT strategies yield equivalent decisions, both the RT results and the estimated attribute weights suggest that the vast majority of subjects adopted the generalized TTB strategy. The RT approach is also validated in an experimental condition in which use of a RAT strategy is essentially forced upon subjects. (c) 2007 APA, all rights reserved.

Experimental and theoretical study of diesel soot reactivity

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

Marcuccilli, F; Gilot, P.; Stanmore, B.

1994-12-31

In order to provide data for modelling the performance of a regenerative soot filter, a study of the oxidation kinetics of diesel soot in the temperature range from 600 C to 800 C was undertaken. Isothermal burning rates at a number of temperatures were measured in rectangular soot beds within a thermobalance. The technique was easy to use, but the combustion rate was found to depend on bed mass. The oxidation process was thus limited by mass transfer effects. A two-dimensional mathematical model of oxygen transfer was developed to extract the true kinetic rates from experimental data. The two-dimensional approachmore » was required because significant oxygen depletion occurred along both axes. Using assumed kinetic rates, oxygen concentration profiles in the gas phase above the bed and within the bed were calculated. The true kinetics at a number of temperatures were, then established by matching predicted oxygen consumption with measured consumption. Application of the model required values of the effective diffusion coefficient for oxygen within the bed. Accordingly, the structure and properties of the soot aggregates were determined. A supplements study was carried out to identify the appropriate primary reaction products. The measured kinetic rates were then used in a simpler, monodimensional model to evaluate the mean oxygen mass transfer coefficients to the surface of the bed. The results show that burning below about 730 C is in regime 1 and can be described by K = 6.9 {times} 10{sup 12} exp ({minus}207,000/RT) (s{sup {minus}1}) with R = 8.314 J/mol {times} K. Above, 730 C, there is a decrease in apparent activation energy, probably due to thermal ``annealing,`` which changes the microstructure of the carbon. As a result, the inherent reactivity declines and/or the bed becomes less accessible to oxygen.« less

MZC Gel Inhibits SHIV-RT and HSV-2 in Macaque Vaginal Mucosa and SHIV-RT in Rectal Mucosa.

PubMed

Calenda, Giulia; Villegas, Guillermo; Barnable, Patrick; Litterst, Claudia; Levendosky, Keith; Gettie, Agegnehu; Cooney, Michael L; Blanchard, James; Fernández-Romero, José A; Zydowsky, Thomas M; Teleshova, Natalia

2017-03-01

The Population Council's microbicide gel MZC (also known as PC-1005) containing MIV-150 and zinc acetate dihydrate (ZA) in carrageenan (CG) has shown promise as a broad-spectrum microbicide against HIV, herpes simplex virus (HSV), and human papillomavirus. Previous data show antiviral activity against these viruses in cell-based assays, prevention of vaginal and rectal simian-human immunodeficiency virus reverse transcriptase (SHIV-RT) infection, and reduction of vaginal HSV shedding in rhesus macaques and also excellent antiviral activity against HSV and human papillomavirus in murine models. Recently, we demonstrated that MZC is safe and effective against SHIV-RT in macaque vaginal explants. Here we established models of ex vivo SHIV-RT/HSV-2 coinfection of vaginal mucosa and SHIV-RT infection of rectal mucosa in macaques (challenge of rectal mucosa with HSV-2 did not result in reproducible tissue infection), evaluated antiviral activity of MZC, and compared quantitative polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay readouts for monitoring SHIV-RT infection. MZC (at nontoxic dilutions) significantly inhibited SHIV-RT in vaginal and rectal mucosas and HSV-2 in vaginal mucosa when present during viral challenge. Analysis of SHIV-RT infection and MZC activity by 1-step simian immunodeficiency virus gag quantitative RT-PCR and p27 enzyme-linked immunosorbent assay demonstrated similar virus growth dynamics and MZC activity by both methods and higher sensitivity of quantitative RT-PCR. Our data provide more evidence that MZC is a promising dual compartment multipurpose prevention technology candidate.

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.

Radiative transfer codes for atmospheric correction and aerosol retrieval: intercomparison study.

PubMed

Kotchenova, Svetlana Y; Vermote, Eric F; Levy, Robert; Lyapustin, Alexei

2008-05-01

Results are summarized for a scientific project devoted to the comparison of four atmospheric radiative transfer codes incorporated into different satellite data processing algorithms, namely, 6SV1.1 (second simulation of a satellite signal in the solar spectrum, vector, version 1.1), RT3 (radiative transfer), MODTRAN (moderate resolution atmospheric transmittance and radiance code), and SHARM (spherical harmonics). The performance of the codes is tested against well-known benchmarks, such as Coulson's tabulated values and a Monte Carlo code. The influence of revealed differences on aerosol optical thickness and surface reflectance retrieval is estimated theoretically by using a simple mathematical approach. All information about the project can be found at http://rtcodes.ltdri.org.

Radiative transfer codes for atmospheric correction and aerosol retrieval: intercomparison study

NASA Astrophysics Data System (ADS)

Kotchenova, Svetlana Y.; Vermote, Eric F.; Levy, Robert; Lyapustin, Alexei

2008-05-01

Results are summarized for a scientific project devoted to the comparison of four atmospheric radiative transfer codes incorporated into different satellite data processing algorithms, namely, 6SV1.1 (second simulation of a satellite signal in the solar spectrum, vector, version 1.1), RT3 (radiative transfer), MODTRAN (moderate resolution atmospheric transmittance and radiance code), and SHARM (spherical harmonics). The performance of the codes is tested against well-known benchmarks, such as Coulson's tabulated values and a Monte Carlo code. The influence of revealed differences on aerosol optical thickness and surface reflectance retrieval is estimated theoretically by using a simple mathematical approach. All information about the project can be found at http://rtcodes.ltdri.org.

Flow Residence Time and Regions of Intraluminal Thrombus Deposition in Intracranial Aneurysms

PubMed Central

Boussel, L.; Ge, L.; Leach, J. R.; Martin, A. J.; Lawton, M. T.; McCulloch, C.; Saloner, D.

2010-01-01

Thrombus formation in intracranial aneurysms, while sometimes stabilizing lesion growth, can present additional risk of thrombo-embolism. The role of hemodynamics in the progression of aneurysmal disease can be elucidated by patient-specific computational modeling. In our previous work, patient-specific computational fluid dynamics (CFD) models were constructed from MRI data for three patients who had fusiform basilar aneurysms that were thrombus-free and then proceeded to develop intraluminal thrombus. In this study, we investigated the effect of increased flow residence time (RT) by modeling passive scalar advection in the same aneurysmal geometries. Non-Newtonian pulsatile flow simulations were carried out in base-line geometries and a new postprocessing technique, referred to as “virtual ink” and based on the passive scalar distribution maps, was used to visualize the flow and estimate the flow RT. The virtual ink technique clearly depicted regions of flow separation. The flow RT at different locations adjacent to aneurysmal walls was calculated as the time the virtual ink scalar remained above a threshold value. The RT values obtained in different areas were then correlated with the location of intra-aneurysmal thrombus observed at a follow-up MR study. For each patient, the wall shear stress (WSS) distribution was also obtained from CFD simulations and correlated with thrombus location. The correlation analysis determined a significant relationship between regions where CFD predicted either an increased RT or low WSS and the regions where thrombus deposition was observed to occur in vivo. A model including both low WSS and increased RT predicted thrombus-prone regions significantly better than the models with RT or WSS alone. PMID:20499185

Effect of atmospheric refraction on radiative transfer in visible and near-infrared band: Model development, validation, and applications

NASA Astrophysics Data System (ADS)

Hu, Shuai; Gao, Tai-chang; Li, Hao; Liu, Lei; Liu, Xi-chuan; Zhang, Ting; Cheng, Tian-ji; Li, Wan-tong; Dai, Zhong-hua; Su, Xiaojian

2016-03-01

Refraction is an important factor influencing radiative transfer since it can modify the propagation trajectory and polarization states of lights; therefore, it is necessary to quantitively evaluate the effect of atmospheric refraction on radiative transfer process. To this end, a new atmospheric radiative transfer model including refraction process is proposed. The model accuracy is validated against benchmark results, literature results, and well-tested radiative transfer models such as discrete coordinate method and RT3/PolRadtran. The impact of atmospheric refraction on both polarized radiance and fluxes is discussed for pure Rayleigh scattering atmosphere, atmosphere with aerosol, and cloud. The results show that atmospheric refraction has a significant influence on both the radiance and polarization states of diffuse light, where the relative change of the radiance of reflected light and transmitted light due to refraction can achieve 6.3% and 7.4% for Rayleigh scattering atmosphere, 7.2% and 7.8% for atmosphere with aerosol, and 6.2% and 6.8% for cloudy atmosphere, respectively. The relative change of the degree of polarization ranges from near zero in the horizon to 9.5% near neutral points. The angular distribution pattern of the relative change of the radiance for atmosphere with aerosol and cloud is very similar to that for pure Rayleigh scattering case, where its magnitude decreases gradually with the increasing of zenith angle for reflected light; but for transmitted light, the variation characteristics is opposite. The impact of refraction is gradually enhanced with the increasing of solar zenith angles and the optical depth of aerosol and cloud. As the wavelength of incident light increases, the impact declines rapidly for Rayleigh scattering medium. The relative change of the fluxes due to refraction is most notable for Middle Latitude Winter profile (about 8.2043% and 7.3225% for the transmitted and reflected light, respectively, at 0.35 µm). With increasing the optical depth of aerosol, the influence of refraction on the fluxes is gradually enhanced. For cloudy atmosphere, the relative changes of the fluxes due to refraction are not very sensitive to the variation of cloud optical depth and effective radius of cloud drops.

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

A New Code SORD for Simulation of Polarized Light Scattering in the Earth Atmosphere

NASA Technical Reports Server (NTRS)

Korkin, Sergey; Lyapustin, Alexei; Sinyuk, Aliaksandr; Holben, Brent

2016-01-01

We report a new publicly available radiative transfer (RT) code for numerical simulation of polarized light scattering in plane-parallel atmosphere of the Earth. Using 44 benchmark tests, we prove high accuracy of the new RT code, SORD (Successive ORDers of scattering). We describe capabilities of SORD and show run time for each test on two different machines. At present, SORD is supposed to work as part of the Aerosol Robotic NETwork (AERONET) inversion algorithm. For natural integration with the AERONET software, SORD is coded in Fortran 90/95. The code is available by email request from the corresponding (first) author or from ftp://climate1.gsfc.nasa.gov/skorkin/SORD/.

The role of RT carry-over for congruence sequence effects in masked priming.

PubMed

Huber-Huber, Christoph; Ansorge, Ulrich

2017-05-01

The present study disentangles 2 sources of the congruence sequence effect with masked primes: congruence and response time of the previous trial (reaction time [RT] carry-over). Using arrows as primes and targets and a metacontrast masking procedure we found congruence as well as congruence sequence effects. In addition, congruence sequence effects decreased when RT carry-over was accounted for in a mixed model analysis, suggesting that RT carry-over contributes to congruence sequence effects in masked priming. Crucially, effects of previous trial congruence were not cancelled out completely indicating that RT carry-over and previous trial congruence are 2 sources feeding into the congruence sequence effect. A secondary task requiring response speed judgments demonstrated general awareness of response speed (Experiments 1), but removing this secondary task (Experiment 2) showed that RT carry-over effects were also present in single-task conditions. During (dual-task) prime-awareness test parts of both experiments, however, RT carry-over failed to modulate congruence effects, suggesting that some task sets of the participants can prevent the effect. The basic RT carry-over effects are consistent with the conflict adaptation account, with the adaptation to the statistics of the environment (ASE) model, and possibly with the temporal learning explanation. Additionally considering the task-dependence of RT carry-over, the results are most compatible with the conflict adaptation account. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Hypofractionated Radiotherapy Is Superior to Conventional Fractionation in an Orthotopic Model of Anaplastic Thyroid Cancer.

PubMed

Oweida, Ayman; Phan, Andy; Vancourt, Benjamin; Robin, Tyler; Hararah, Mohammad K; Bhatia, Shilpa; Milner, Dallin; Lennon, Shelby; Pike, Laura; Raben, David; Haugen, Bryan; Pozdeyev, Nikita; Schweppe, Rebecca; Karam, Sana D

2018-06-01

Anaplastic thyroid cancer (ATC) is an aggressive and highly lethal disease with poor outcomes and resistance to therapy. Despite multimodality treatment, including radiation therapy and chemotherapy, response rates remain <15%, with a median time to progression of less than three months. Recent advances in radiotherapy (RT) delivery and gene-expression profiling may help guide patient selection for personalized therapy. The purpose of this study was to characterize the response to radiation in a panel of ATC cell lines and to test alternative RT fractionation schedules for overcoming radioresistance. The cellular response to radiation was characterized based on clonogenic assays. Radiation response was correlated with microarray gene-expression data. Hypofractionated and conventional RT was tested in an orthotopic ATC tumor model, and tumor growth was assayed locally and distantly with in vivo and ex vivo bioluminescence imaging. A spectrum of radiosensitivities was observed in ATC cell lines. Radioresistant cell lines had higher levels of CXCR4 compared to radiosensitive cell lines. Compared to conventionally fractionated RT, hypofractionated RT resulted in significantly improved tumor growth delay, decreased regional and distant metastases, and improved overall survival. The findings demonstrate the heterogeneity of response to radiation in ATC tumors and the superiority of hypofractionated RT in improving local control, metastatic spread, and survival in preclinical models. These data support the design of clinical trials targeting radioresistant pathways in combination with hypofractionated RT.

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.

Murine Leukemia Virus Reverse Transcriptase: Structural Comparison with HIV-1 Reverse Transcriptase

PubMed Central

Coté, Marie L.; Roth, Monica J.

2008-01-01

Recent X-ray crystal structure determinations of Moloney murine leukemia virus reverse transcriptase (MoMLV RT) have allowed for more accurate structure/function comparisons to HIV-1 RT than were formerly possible. Previous biochemical studies of MoMLV RT in conjunction with knowledge of sequence homologies to HIV-1 RT and overall fold similarities to RTs in general, provided a foundation upon which to build. In addition, numerous crystal structures of the MoMLV RT fingers/palm subdomain had also shed light on one of the critical functions of the enzyme, specifically polymerization. Now in the advent of new structural information, more intricate examination of MoMLV RT in its entirety can be realized, and thus the comparisons with HIV-1 RT may be more critically elucidated. Here, we will review the similarities and differences between MoMLV RT and HIV-1 RT via structural analysis, and propose working models for the MoMLV RT based upon that information. PMID:18294720

Risk management of a fund for natural disasters

NASA Astrophysics Data System (ADS)

Flores, C.

2003-04-01

Mexico is a country which has to deal with several natural disaster risks: earthquakes, droughts, volcanic eruptions, floods, slides, wild fires, extreme temperatures, etc. In order to reduce the country's vulnerability to the impact of these natural disasters and to support rapid recovery when they occur, the government established in 1996 Mexico's Fund for Natural Disasters (FONDEN). Since its creation, its resources have been insufficient to meet all government obligations. The aim of this project is the development of a dynamic strategy to optimise the management of a fund for natural disasters starting from the example of FONDEN. The problem of budgetary planning is being considered for the modelling. We control the level of the fund's cash (R_t)0<= t0 at t=0 and then we try to pull at every moment the process to this objective. Multifractal models in geophysics are physically based stochastic models. A multiplicative cascade model fitted to a data set can be used for generation of synthetic sequences that resemble the original data in terms of its scaling properties. Since recent years, uncertainty concepts based on multifractal fields are being applied to the development of techniques to calculate marginal and conditional probabilities of an extreme rainfall event in a determined zone. As initial point to the development of the model, a multifractal model for extreme rainfall events will be used as part of the input for the stochastic control model. A theme for further research is linking more warning systems to the model. Keywords: risk management, stochastic control, multifractal measures, multiplicative cascades, heavy rainfall events.

Assessment of Oco-2 Target Mode Vulnerability Against Horizontal Variability of Surface Reflectivity Neglected in the Operational Forward Model

NASA Astrophysics Data System (ADS)

Davis, A. B.; Qu, Z.

2014-12-01

The main goal of NASA's OCO-2 mission is to perform XCO2 column measurements from space with an unprecedented (~1 ppm) precision and accuracy that will enable modelers to globally map CO2 sources and sinks. To achieve this goal, the mission is critically dependent on XCO2product validation that, in turn, is highly dependent on successful use of OCO-2's "target mode" data acquisition. In target mode, OCO-2 rotates in such a way that, as long as it is above the horizon, it looks at a Total Carbon Column Observing Network (TCCON) station equipped with a powerful Fourier Transform spectrometer. TCCON stations measure, among other things, XCO2by looking straight at the Sun. This translates to a far simpler forward model for TCCON than for OCO-2. In the ideal world, OCO-2's spectroscopic signals result from the cumulative gaseous absorption for one direct transmission of sunlight to the ground (like for TCCON), followed by one diffuse reflection, and one direct transmission to the instrument—at a variety of viewing angles in traget mode. In the real world, all manner of multiple surface reflections and/or scatterings contribute to the signal. See figure. In the idealized world of the OCO-2 operational forward model (used in nadir, glint and target modes), the horizontal variability of the scattering atmosphere and reflecting surface are ignored, leading to the adoption of a 1D vector radiative transfer (vRT) model. This is the source of forward model error that we are investigating, with a focus on target mode. In principle, atmospheric variability in the horizontal plane—largely due to clouds—can be avoided by careful screening. Also, it is straightforward to account for angular variability of the surface reflection model in the 1D vRT framework. But it is not clear how unavoidable horizontal variations of the surface reflectivity affects the OCO-2 signal, even if the reflection was isotropic (Lambertian). To characterize this OCO-2 "adjacency" effect, we use a simple surface variability model with a single spatial frequency in each direction, and a single albedo contrast at a time for realistic aerosol and gaseous profiles. This specific 3D RT error is compared with other documented forward model errors and translated into XCO2 error in ppm, for programatic consideration and eventual mitigation.

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

Discrete-Slots Models of Visual Working-Memory Response Times

PubMed Central

Donkin, Christopher; Nosofsky, Robert M.; Gold, Jason M.; Shiffrin, Richard M.

2014-01-01

Much recent research has aimed to establish whether visual working memory (WM) is better characterized by a limited number of discrete all-or-none slots or by a continuous sharing of memory resources. To date, however, researchers have not considered the response-time (RT) predictions of discrete-slots versus shared-resources models. To complement the past research in this field, we formalize a family of mixed-state, discrete-slots models for explaining choice and RTs in tasks of visual WM change detection. In the tasks under investigation, a small set of visual items is presented, followed by a test item in 1 of the studied positions for which a change judgment must be made. According to the models, if the studied item in that position is retained in 1 of the discrete slots, then a memory-based evidence-accumulation process determines the choice and the RT; if the studied item in that position is missing, then a guessing-based accumulation process operates. Observed RT distributions are therefore theorized to arise as probabilistic mixtures of the memory-based and guessing distributions. We formalize an analogous set of continuous shared-resources models. The model classes are tested on individual subjects with both qualitative contrasts and quantitative fits to RT-distribution data. The discrete-slots models provide much better qualitative and quantitative accounts of the RT and choice data than do the shared-resources models, although there is some evidence for “slots plus resources” when memory set size is very small. PMID:24015956

Hyperthermia enhances radiosensitivity of colorectal cancer cells through ROS inducing autophagic cell death.

PubMed

Ba, Ming-Chen; Long, Hui; Wang, Shuai; Wu, Yin-Bing; Zhang, Bo-Huo; Yan, Zhao-Fei; Yu, Fei-Hong; Cui, Shu-Zhong

2018-04-01

Hyperthermia (HT) enhances the anti-cancer effects of radiotherapy (RT), but the precise biochemical mechanisms involved are unclear. This study was aim to investigate if mild HT sensitizes colorectal cancer cells to RT through reactive oxygen species (ROS)-inducing autophagic cell death in a mice model of HCT116 human colorectal cancer. HCT116 mice model were randomly divided into five groups: mock group, hyperthermia group (HT), radiotherapy group (RT), HT + RT group, and HT + RT +N-acetyl L-cysteine (NAC) group (HT + CT + NAC). After four weeks of treatment, cancer growth inhibition, rate and mitochondrial membrane potential were measured with MTT and JC-1 assays, respectively, while ROS were estimated fluorimetrically. The relationship of these parameters to expressions of autophagy-related genes Beclin1, LC3B, and mTOR was analyzed. Gene expression was measured by Real-Time polymerase chain reaction (RT-PCR). There were significant increases in ROS levels and mitochondrial membrane potential in the HT + RT group. ROS levels in the HT + RT group increased more significantly than in any other group. In contrast, ROS levels in the HT + RT + NAC group were significantly decreased relative to the HT + RT group. The number of autophagic bodies in HT + RT group was higher than that of mock group. There were significant increases in the expression of Beclin1 and LC3B genes, while mTOR expression was significantly decreased in the HT + CT group. Treatment with NAC reversed the pattern of these changes. These results indicate that HT enhances the radiosensitivity of colorectal cancer cells to RT through ROS inducing autophagic cell death. © 2017 Wiley Periodicals, Inc.

Efficacy of Sunitinib and Radiotherapy in Genetically Engineered Mouse Model of Soft-Tissue Sarcoma

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

Yoon, Sam S.; Stangenberg, Lars; Lee, Yoon-Jin

Purpose: Sunitinib (SU) is a multitargeted receptor tyrosine kinase inhibitor of the vascular endothelial growth factor and platelet-derived growth factor receptors. The present study examined SU and radiotherapy (RT) in a genetically engineered mouse model of soft tissue sarcoma (STS). Methods and Materials: Primary extremity STSs were generated in genetically engineered mice. The mice were randomized to treatment with SU, RT (10 Gy x 2), or both (SU+RT). Changes in the tumor vasculature before and after treatment were assessed in vivo using fluorescence-mediated tomography. The control and treated tumors were harvested and extensively analyzed. Results: The mean fluorescence in themore » tumors was not decreased by RT but decreased 38-44% in tumors treated with SU or SU+RT. The control tumors grew to a mean of 1378 mm{sup 3} after 12 days. SU alone or RT alone delayed tumor growth by 56% and 41%, respectively, but maximal growth inhibition (71%) was observed with the combination therapy. SU target effects were confirmed by loss of target receptor phosphorylation and alterations in SU-related gene expression. Cancer cell proliferation was decreased and apoptosis increased in the SU and RT groups, with a synergistic effect on apoptosis observed in the SU+RT group. RT had a minimal effect on the tumor microvessel density and endothelial cell-specific apoptosis, but SU alone or SU+RT decreased the microvessel density by >66% and induced significant endothelial cell apoptosis. Conclusion: SU inhibited STS growth by effects on both cancer cells and tumor vasculature. SU also augmented the efficacy of RT, suggesting that this combination strategy could improve local control of STS.« less

A common stochastic accumulator with effector-dependent noise can explain eye-hand coordination

PubMed Central

Gopal, Atul; Viswanathan, Pooja

2015-01-01

The computational architecture that enables the flexible coupling between otherwise independent eye and hand effector systems is not understood. By using a drift diffusion framework, in which variability of the reaction time (RT) distribution scales with mean RT, we tested the ability of a common stochastic accumulator to explain eye-hand coordination. Using a combination of behavior, computational modeling and electromyography, we show how a single stochastic accumulator to threshold, followed by noisy effector-dependent delays, explains eye-hand RT distributions and their correlation, while an alternate independent, interactive eye and hand accumulator model does not. Interestingly, the common accumulator model did not explain the RT distributions of the same subjects when they made eye and hand movements in isolation. Taken together, these data suggest that a dedicated circuit underlies coordinated eye-hand planning. PMID:25568161

Telomerase inhibition improves tumor response to radiotherapy in a murine orthotopic model of human glioblastoma.

PubMed

Ferrandon, Sylvain; Malleval, Céline; El Hamdani, Badia; Battiston-Montagne, Priscillia; Bolbos, Radu; Langlois, Jean-Baptiste; Manas, Patrick; Gryaznov, Sergei M; Alphonse, Gersende; Honnorat, Jérôme; Rodriguez-Lafrasse, Claire; Poncet, Delphine

2015-07-17

Glioblastoma (GBM) is the most frequent and aggressive type of adult brain tumor. Most GBMs express telomerase; a high level of intra-tumoral telomerase activity (TA) is predictive of poor prognosis. Thus, telomerase inhibitors are promising options to treat GBM. These inhibitors increase the response to radiotherapy (RT), in vitro as well as in vivo. Since typical treatments for GBM include RT, our objective was to evaluate the efficiency of Imetelstat (TA inhibitor) combined with RT. We used a murine orthotopic model of human GBM (N = 8 to11 mice per group) and μMRI imaging to evaluate the efficacy of Imetelstat (delivered by intra-peritoneal injection) alone and combined with RT. Using a clinically established protocol, we demonstrated that Imetelstat significantly: (i) inhibited the TA in the very center of the tumor, (ii) reduced tumor volume as a proportion of TA inhibition, and (iii) increased the response to RT, in terms of tumor volume regression and survival increase. Imetelstat is currently evaluated in refractory brain tumors in young patients (without RT). Our results support its clinical evaluation combined with RT to treat GBM.

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

Modern Radiotherapy Concepts and the Impact of Radiation on Immune Activation

PubMed Central

Deloch, Lisa; Derer, Anja; Hartmann, Josefin; Frey, Benjamin; Fietkau, Rainer; Gaipl, Udo S.

2016-01-01

Even though there is extensive research carried out in radiation oncology, most of the clinical studies focus on the effects of radiation on the local tumor tissue and deal with normal tissue side effects. The influence of dose fractionation and timing particularly with regard to immune activation is not satisfactorily investigated so far. This review, therefore, summarizes current knowledge on concepts of modern radiotherapy (RT) and evaluates the potential of RT for immune activation. Focus is set on radiation-induced forms of tumor cell death and consecutively the immunogenicity of the tumor cells. The so-called non-targeted, abscopal effects can contribute to anti-tumor responses in a specific and systemic manner and possess the ability to target relapsing tumor cells as well as metastases. The impact of distinct RT concepts on immune activation is outlined and pre-clinical evidence and clinical observations on RT-induced immunity will be discussed. Knowledge on the radiosensitivity of immune cells as well as clinical evidence for enhanced immunity after RT will be considered. While stereotactic ablative body radiotherapy seem to have a beneficial outcome over classical RT fractionation in pre-clinical animal models, in vitro model systems suggest an advantage for classical fractionated RT for immune activation. Furthermore, the optimal approach may differ based on the tumor site and/or genetic signature. These facts highlight that clinical trials are urgently needed to identify whether high-dose RT is superior to induce anti-tumor immune responses compared to classical fractionated RT and in particular how the outcome is when RT is combined with immunotherapy in selected tumor entities. PMID:27379203

Compilation of a near-infrared library for the construction of quantitative models of amoxicillin and potassium clavulanate oral dosage forms

NASA Astrophysics Data System (ADS)

Zou, Wen-bo; Chong, Xiao-meng; Wang, Yan; Hu, Chang-qin

2018-05-01

The accuracy of NIR quantitative models depends on calibration samples with concentration variability. Conventional sample collecting methods have some shortcomings especially the time-consuming which remains a bottleneck in the application of NIR models for Process Analytical Technology (PAT) control. A study was performed to solve the problem of sample selection collection for construction of NIR quantitative models. Amoxicillin and potassium clavulanate oral dosage forms were used as examples. The aim was to find a normal approach to rapidly construct NIR quantitative models using an NIR spectral library based on the idea of a universal model [2021]. The NIR spectral library of amoxicillin and potassium clavulanate oral dosage forms was defined and consisted of spectra of 377 batches of samples produced by 26 domestic pharmaceutical companies, including tablets, dispersible tablets, chewable tablets, oral suspensions, and granules. The correlation coefficient (rT) was used to indicate the similarities of the spectra. The samples’ calibration sets were selected from a spectral library according to the median rT of the samples to be analyzed. The rT of the samples selected was close to the median rT. The difference in rT of those samples was 1.0% to 1.5%. We concluded that sample selection is not a problem when constructing NIR quantitative models using a spectral library versus conventional methods of determining universal models. The sample spectra with a suitable concentration range in the NIR models were collected quickly. In addition, the models constructed through this method were more easily targeted.

Constructive and Unconstructive Repetitive Thought

PubMed Central

Watkins, Edward R.

2008-01-01

The author reviews research showing that repetitive thought (RT) can have constructive or unconstructive consequences. The main unconstructive consequences of RT are (a) depression, (b) anxiety, and (c) difficulties in physical health. The main constructive consequences of RT are (a) recovery from upsetting and traumatic events, (b) adaptive preparation and anticipatory planning, (c) recovery from depression, and (d) uptake of health-promoting behaviors. Several potential principles accounting for these distinct consequences of RT are identified within this review: (a) the valence of thought content, (b) the intrapersonal and situational context in which RT occurs, and (c) the level of construal (abstract vs. concrete processing) adopted during RT. Of the existing models of RT, it is proposed that an elaborated version of the control theory account provides the best theoretical framework to account for its distinct consequences. PMID:18298268

Trends in erythemal doses at the Polish Polar Station, Hornsund, Svalbard based on the homogenized measurements (1996-2016) and reconstructed data (1983-1995)

NASA Astrophysics Data System (ADS)

Krzyścin, Janusz W.; Sobolewski, Piotr S.

2018-01-01

Erythemal daily doses measured at the Polish Polar Station, Hornsund (77°00' N, 15°33' E), for the periods 1996-2001 and 2005-2016 are homogenized using yearly calibration constants derived from the comparison of observed doses for cloudless conditions with the corresponding doses calculated by radiative transfer (RT) simulations. Modeled all-sky doses are calculated by the multiplication of cloudless RT doses by the empirical cloud modification factor dependent on the daily sunshine duration. An all-sky model is built using daily erythemal doses measured in the period 2005-2006-2007. The model is verified by comparisons with the 1996-1997-1998 and 2009-2010-2011 measured data. The daily doses since 1983 (beginning of the proxy data) are reconstructed using the all-sky model with the historical data of the column ozone from satellite measurements (SBUV merged ozone data set), the snow depth (for ground albedo estimation), and the observed daily sunshine duration at the site. Trend analyses of the monthly and yearly time series comprised of the reconstructed and observed doses do not reveal a statistically significant trend in the period 1983-2016. The trends based on the observed data only (1996-2001 and 2005-2016) show declining tendency (about -1 % per year) in the monthly mean of daily erythemal doses in May and June, and in the yearly sum of daily erythemal doses. An analysis of sources of the yearly dose variability since 1983 shows that cloud cover changes are a basic driver of the long-term UV changes at the site.

Effects of Real-Time NASA Vegetation Data on Model Forecasts of Severe Weather

NASA Technical Reports Server (NTRS)

Case, Jonathan L.; Bell, Jordan R.; LaFontaine, Frank J.; Peters-Lidard, Christa D.

2012-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center has developed a Greenness Vegetation Fraction (GVF) dataset, which is updated daily using swaths of Normalized Difference Vegetation Index data from the Moderate Resolution Imaging Spectroradiometer (MODIS) data aboard the NASA-EOS Aqua and Terra satellites. NASA SPoRT started generating daily real-time GVF composites at 1-km resolution over the Continental United States beginning 1 June 2010. A companion poster presentation (Bell et al.) primarily focuses on impact results in an offline configuration of the Noah land surface model (LSM) for the 2010 warm season, comparing the SPoRT/MODIS GVF dataset to the current operational monthly climatology GVF available within the National Centers for Environmental Prediction (NCEP) and Weather Research and Forecasting (WRF) models. This paper/presentation primarily focuses on individual case studies of severe weather events to determine the impacts and possible improvements by using the real-time, high-resolution SPoRT-MODIS GVFs in place of the coarser-resolution NCEP climatological GVFs in model simulations. The NASA-Unified WRF (NU-WRF) modeling system is employed to conduct the sensitivity simulations of individual events. The NU-WRF is an integrated modeling system based on the Advanced Research WRF dynamical core that is designed to represents aerosol, cloud, precipitation, and land processes at satellite-resolved scales in a coupled simulation environment. For this experiment, the coupling between the NASA Land Information System (LIS) and the WRF model is utilized to measure the impacts of the daily SPoRT/MODIS versus the monthly NCEP climatology GVFs. First, a spin-up run of the LIS is integrated for two years using the Noah LSM to ensure that the land surface fields reach an equilibrium state on the 4-km grid mesh used. Next, the spin-up LIS is run in two separate modes beginning on 1 June 2010, one continuing with the climatology GVFs while the other uses the daily SPoRT/MODIS GVFs. Finally, snapshots of the LIS land surface fields are used to initialize two different simulations of the NU-WRF, one running with climatology LIS and GVFs, and the other running with experimental LIS and NASA/SPoRT GVFs. In this paper/presentation, case study results will be highlighted in regions with significant differences in GVF between the NCEP climatology and SPoRT product during severe weather episodes.

On the linear relation between the mean and the standard deviation of a response time distribution.

PubMed

Wagenmakers, Eric-Jan; Brown, Scott

2007-07-01

Although it is generally accepted that the spread of a response time (RT) distribution increases with the mean, the precise nature of this relation remains relatively unexplored. The authors show that in several descriptive RT distributions, the standard deviation increases linearly with the mean. Results from a wide range of tasks from different experimental paradigms support a linear relation between RT mean and RT standard deviation. Both R. Ratcliff's (1978) diffusion model and G. D. Logan's (1988) instance theory of automatization provide explanations for this linear relation. The authors identify and discuss 3 specific boundary conditions for the linear law to hold. The law constrains RT models and supports the use of the coefficient of variation to (a) compare variability while controlling for differences in baseline speed of processing and (b) assess whether changes in performance with practice are due to quantitative speedup or qualitative reorganization. Copyright 2007 APA.

The cost of radiotherapy in a decade of technology evolution.

PubMed

Van de Werf, Evelyn; Verstraete, Jan; Lievens, Yolande

2012-01-01

To quantify changes in radiotherapy costs occurring in a decade of medical-technological evolution. The activity-based costing (ABC) model of the University Hospitals Leuven (UHL) radiotherapy (RT) department was adapted to current RT standards. It allocated actual resource costs to the treatments based on the departmental work-flow and patient mix in 2009. A benchmark with the former model analyzed the cost increases related to changes in RT infrastructure and practice over 10 years. A considerable increase in total RT costs was observed, resulting from higher capital investments (96%) and personnel cost (103%), the latter dominating the total picture. Treatment delivery remains the most costly activity, boosted by the cost of improved quality assurance (QA), 23% of total product costs, coming along with more advanced RT techniques. Hence, cost increases at the product level are most obvious for complex treatments, such as intensity-modulated radiotherapy (IMRT), representing cost increases ranging between 38% and 88% compared to conformal approaches. The ABC model provides insight into the financial consequences of evolving technology and practice. Such data are a mandatory first step in our strive to prove RT cost-effectiveness and thus support optimal reimbursement and provision of radiotherapy departments. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Establishment of mammary gland model in vitro: culture and evaluation of a yak mammary epithelial cell line.

PubMed

Fu, Mei; Chen, Yabing; Xiong, Xianrong; Lan, Daoliang; Li, Jian

2014-01-01

This study aimed to establish yak mammary epithelial cells (YMECs) for an in vitro model of yak mammary gland biology. The primary culture of YMECs was obtained from mammary gland tissues of lactating yak and then characterized using immunocytochemistry, RT-PCR, and western blot analysis. Whether foreign genes could be transfected into the YMECs were examined by transfecting the EGFP gene into the cells. Finally, the effect of Staphylococcus aureus infection on YMECs was determined. The established YMECs retained the mammary epithelial cell characteristics. A spontaneously immortalized yak mammary epithelial cell line was established and could be continuously subcultured for more than 60 passages without senescence. The EGFP gene was successfully transferred into the YMECs, and the transfected cells could be maintained for a long duration in the culture by continuous subculturing. The cells expressed more antimicrobial peptides upon S.aureus invasion. Therefore, the established cell line could be considered a model system to understand yak mammary gland biology.

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.

RT-PCR detection of Candida albicans ALS gene expression in the reconstituted human epithelium (RHE) model of oral candidiasis and in model biofilms.

PubMed

Green, Clayton B; Cheng, Georgina; Chandra, Jyotsna; Mukherjee, Pranab; Ghannoum, Mahmoud A; Hoyer, Lois L

2004-02-01

An RT-PCR assay was developed to analyse expression patterns of genes in the Candida albicans ALS (agglutinin-like sequence) family. Inoculation of a reconstituted human buccal epithelium (RHE) model of mucocutaneous candidiasis with strain SC5314 showed destruction of the epithelial layer by C. albicans and also formation of an upper fungal layer that had characteristics similar to a biofilm. RT-PCR analysis of total RNA samples extracted from C. albicans-inoculated buccal RHE showed that ALS1, ALS2, ALS3, ALS4, ALS5 and ALS9 were consistently detected over time as destruction of the RHE progressed. Detection of transcripts from ALS7, and particularly from ALS6, was more sporadic, but not associated with a strictly temporal pattern. The expression pattern of ALS genes in C. albicans cultures used to inoculate the RHE was similar to that observed in the RHE model, suggesting that contact of C. albicans with buccal RHE does little to alter ALS gene expression. RT-PCR analysis of RNA samples extracted from model denture and catheter biofilms showed similar gene expression patterns to the buccal RHE specimens. Results from the RT-PCR analysis of biofilm RNA specimens were consistent between various C. albicans strains during biofilm development and were comparable to gene expression patterns in planktonic cells. The RT-PCR assay described here will be useful for analysis of human clinical specimens and samples from other disease models. The method will provide further insight into the role of ALS genes and their encoded proteins in the diverse interactions between C. albicans and its host.

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

Clot retraction affects the extent of ultrasound-enhanced thrombolysis in an ex vivo porcine thrombosis model

PubMed Central

Sutton, Jonathan T.; Ivancevich, Nikolas M.; Perrin, Stephen R.; Vela, Deborah C.; Holland, Christy K.

2013-01-01

Using an FDA-approved contrast agent (Definity®) and thrombolytic drug (rt-PA), we investigated ultrasound-enhanced thrombolysis in two whole-blood clot models. Porcine venous blood was collected from donor hogs and coagulated in two different materials. This method produced clots with differing compositional properties, as determined by routine scanning electron microscopy and histology. Clots were deployed in an ex vivo porcine thrombolysis model, while an intermittent ultrasound scheme previously developed to maximize stable cavitation was applied and acoustic emissions were detected. Exposure of clots to 3.15 μg/mL rt-PA promoted lysis in both clot models, compared to exposure to plasma alone. However, in the presence of rt-PA, Definity®, and ultrasound, only unretracted clots experienced significant enhancement of thrombolysis compared to treatment with rt-PA. In these clots, microscopy studies revealed loose erythrocyte aggregates, a significantly less extensive fibrin network, and a higher porosity, which may facilitate increase penetration of thrombolytics by cavitation. PMID:23453629

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.

Propidium monoazide reverse transcription PCR and RT-qPCR for detecting infectious enterovirus and norovirus

EPA Science Inventory

Presently there is no established cell line or small animal model that allows for the detection of infectious human norovirus. Current methods based on RT-PCR and RT-qPCR detect both infectious and non-infectious virus and thus the conclusions that may be drawn regarding the publ...

Academic Interventions and Academic Achievement in the Middle School Grades

ERIC Educational Resources Information Center

Kite, Toby G.

2015-01-01

After the passing of the Individuals with Disabilities Act of 2004, many schools began to use a Response to Intervention (RtI) model instead of the discrepancy model when identifying students with specific learning disabilities (National Center on Response to Intervention, 2011). When elementary schools adopted the RtI model, it was shown to be…

Evaluating the Contribution of NASA Remotely-Sensed Data Sets on a Convection-Allowing Forecast Model

NASA Technical Reports Server (NTRS)

Zavodsky, Bradley T.; Case, Jonathan L.; Molthan, Andrew L.

2012-01-01

The Short-term Prediction Research and Transition (SPoRT) Center is a collaborative partnership between NASA and operational forecasting partners, including a number of National Weather Service forecast offices. SPoRT provides real-time NASA products and capabilities to help its partners address specific operational forecast challenges. One challenge that forecasters face is using guidance from local and regional deterministic numerical models configured at convection-allowing resolution to help assess a variety of mesoscale/convective-scale phenomena such as sea-breezes, local wind circulations, and mesoscale convective weather potential on a given day. While guidance from convection-allowing models has proven valuable in many circumstances, the potential exists for model improvements by incorporating more representative land-water surface datasets, and by assimilating retrieved temperature and moisture profiles from hyper-spectral sounders. In order to help increase the accuracy of deterministic convection-allowing models, SPoRT produces real-time, 4-km CONUS forecasts using a configuration of the Weather Research and Forecasting (WRF) model (hereafter SPoRT-WRF) that includes unique NASA products and capabilities including 4-km resolution soil initialization data from the Land Information System (LIS), 2-km resolution SPoRT SST composites over oceans and large water bodies, high-resolution real-time Green Vegetation Fraction (GVF) composites derived from the Moderate-resolution Imaging Spectroradiometer (MODIS) instrument, and retrieved temperature and moisture profiles from the Atmospheric Infrared Sounder (AIRS) and Infrared Atmospheric Sounding Interferometer (IASI). NCAR's Model Evaluation Tools (MET) verification package is used to generate statistics of model performance compared to in situ observations and rainfall analyses for three months during the summer of 2012 (June-August). Detailed analyses of specific severe weather outbreaks during the summer will be presented to assess the potential added-value of the SPoRT datasets and data assimilation methodology compared to a WRF configuration without the unique datasets and data assimilation.

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

Modeling of polarimetric BRDF characteristics of painted surfaces

NASA Astrophysics Data System (ADS)

Zhang, Ying; Wang, Zeying; Zhao, Huijie

2014-11-01

In this paper a pBRDF (polarimetric Bidirectional Reflectance Distribution Function) model of painted surfaces coupled with atmospheric polarization characteristics is built and the method of simulating polarimetric radiation reaching the imaging system is advanced. Firstly, the composition of the radiation reaching the sensor is analyzed. Then, the pBRDF model of painted surfaces is developed according to the microfacet theory presented by G. Priest and the downwelled skylight polarization is modeled based on the vector radiative transfer model RT3. Furthermore, the modeled polarization state of reflected light from the surfaces was achieved through integrating the directional polarimetric information of the whole hemisphere, adding the modeled polarimetric factors of incident diffused skylight. Finally, the polarimetric radiance reaching the sensor is summed up with the assumption that the target-sensor path is assumed to be negligible since it is relatively short in the current imaging geometry. The modeled results are related to the solar-sensor geometry, atmospheric conditions and the features of the painted surfaces. This result can be used to simulate the imaging under different weather conditions and further work for the validation experiments of the model need to be done.

A new code SORD for simulation of polarized light scattering in the Earth atmosphere

NASA Astrophysics Data System (ADS)

Korkin, Sergey; Lyapustin, Alexei; Sinyuk, Aliaksandr; Holben, Brent

2016-05-01

We report a new publicly available radiative transfer (RT) code for numerical simulation of polarized light scattering in plane-parallel Earth atmosphere. Using 44 benchmark tests, we prove high accuracy of the new RT code, SORD (Successive ORDers of scattering1, 2). We describe capabilities of SORD and show run time for each test on two different machines. At present, SORD is supposed to work as part of the Aerosol Robotic NETwork3 (AERONET) inversion algorithm. For natural integration with the AERONET software, SORD is coded in Fortran 90/95. The code is available by email request from the corresponding (first) author or from ftp://climate1.gsfc.nasa.gov/skorkin/SORD/ or ftp://maiac.gsfc.nasa.gov/pub/SORD.zip

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

Effects of Resistance Training in Youth Athletes on Muscular Fitness and Athletic Performance: A Conceptual Model for Long-Term Athlete Development

PubMed Central

Granacher, Urs; Lesinski, Melanie; Büsch, Dirk; Muehlbauer, Thomas; Prieske, Olaf; Puta, Christian; Gollhofer, Albert; Behm, David G.

2016-01-01

During the stages of long-term athlete development (LTAD), resistance training (RT) is an important means for (i) stimulating athletic development, (ii) tolerating the demands of long-term training and competition, and (iii) inducing long-term health promoting effects that are robust over time and track into adulthood. However, there is a gap in the literature with regards to optimal RT methods during LTAD and how RT is linked to biological age. Thus, the aims of this scoping review were (i) to describe and discuss the effects of RT on muscular fitness and athletic performance in youth athletes, (ii) to introduce a conceptual model on how to appropriately implement different types of RT within LTAD stages, and (iii) to identify research gaps from the existing literature by deducing implications for future research. In general, RT produced small-to-moderate effects on muscular fitness and athletic performance in youth athletes with muscular strength showing the largest improvement. Free weight, complex, and plyometric training appear to be well-suited to improve muscular fitness and athletic performance. In addition, balance training appears to be an important preparatory (facilitating) training program during all stages of LTAD but particularly during the early stages. As youth athletes become more mature, specificity, and intensity of RT methods increase. This scoping review identified research gaps that are summarized in the following and that should be addressed in future studies: (i) to elucidate the influence of gender and biological age on the adaptive potential following RT in youth athletes (especially in females), (ii) to describe RT protocols in more detail (i.e., always report stress and strain-based parameters), and (iii) to examine neuromuscular and tendomuscular adaptations following RT in youth athletes. PMID:27242538

Statistical models for incorporating data from routine HIV testing of pregnant women at antenatal clinics into HIV/AIDS epidemic estimates.

PubMed

Sheng, Ben; Marsh, Kimberly; Slavkovic, Aleksandra B; Gregson, Simon; Eaton, Jeffrey W; Bao, Le

2017-04-01

HIV prevalence data collected from routine HIV testing of pregnant women at antenatal clinics (ANC-RT) are potentially available from all facilities that offer testing services to pregnant women and can be used to improve estimates of national and subnational HIV prevalence trends. We develop methods to incorporate these new data source into the Joint United Nations Programme on AIDS Estimation and Projection Package in Spectrum 2017. We develop a new statistical model for incorporating ANC-RT HIV prevalence data, aggregated either to the health facility level (site-level) or regionally (census-level), to estimate HIV prevalence alongside existing sources of HIV prevalence data from ANC unlinked anonymous testing (ANC-UAT) and household-based national population surveys. Synthetic data are generated to understand how the availability of ANC-RT data affects the accuracy of various parameter estimates. We estimate HIV prevalence and additional parameters using both ANC-RT and other existing data. Fitting HIV prevalence using synthetic data generally gives precise estimates of the underlying trend and other parameters. More years of ANC-RT data should improve prevalence estimates. More ANC-RT sites and continuation with existing ANC-UAT sites may improve the estimate of calibration between ANC-UAT and ANC-RT sites. We have proposed methods to incorporate ANC-RT data into Spectrum to obtain more precise estimates of prevalence and other measures of the epidemic. Many assumptions about the accuracy, consistency, and representativeness of ANC-RT prevalence underlie the use of these data for monitoring HIV epidemic trends and should be tested as more data become available from national ANC-RT programs.

Statistical Models for Incorporating Data from Routine HIV Testing of Pregnant Women at Antenatal Clinics into HIV/AIDS Epidemic Estimates

PubMed Central

Sheng, Ben; Marsh, Kimberly; Slavkovic, Aleksandra B.; Gregson, Simon; Eaton, Jeffrey W.; Bao, Le

2017-01-01

Objective HIV prevalence data collected from routine HIV testing of pregnant women at antenatal clinics (ANC-RT) are potentially available from all facilities that offer testing services to pregnant women, and can be used to improve estimates of national and sub-national HIV prevalence trends. We develop methods to incorporate this new data source into the UNAIDS Estimation and Projection Package (EPP) in Spectrum 2017. Methods We develop a new statistical model for incorporating ANC-RT HIV prevalence data, aggregated either to the health facility level (‘site-level’) or regionally (‘census-level’), to estimate HIV prevalence alongside existing sources of HIV prevalence data from ANC unlinked anonymous testing (ANC-UAT) and household-based national population surveys. Synthetic data are generated to understand how the availability of ANC-RT data affects the accuracy of various parameter estimates. Results We estimate HIV prevalence and additional parameters using both ANC-RT and other existing data. Fitting HIV prevalence using synthetic data generally gives precise estimates of the underlying trend and other parameters. More years of ANC-RT data should improve prevalence estimates. More ANC-RT sites and continuation with existing ANC-UAT sites may improve the estimate of calibration between ANC-UAT and ANC-RT sites. Conclusion We have proposed methods to incorporate ANC-RT data into Spectrum to obtain more precise estimates of prevalence and other measures of the epidemic. Many assumptions about the accuracy, consistency, and representativeness of ANC-RT prevalence underlie the use of these data for monitoring HIV epidemic trends, and should be tested as more data become available from national ANC-RT programs. PMID:28296804

The Cost-Effectiveness of Real-Time Continuous Glucose Monitoring (RT-CGM) in Type 2 Diabetes.

PubMed

Fonda, Stephanie J; Graham, Claudia; Munakata, Julie; Powers, Julia M; Price, David; Vigersky, Robert A

2016-07-01

This analysis models the cost-effectiveness of real-time continuous glucose monitoring (RT-CGM) using evidence from a randomized controlled trial (RCT) that demonstrated RT-CGM reduced A1C, for up to 9 months after using the technology, among patients with type 2 diabetes not on prandial insulin. RT-CGM was offered short-term and intermittently as a self-care tool to inform patients' behavior. The analyses projected lifetime clinical and economic outcomes for RT-CGM versus self-monitoring of blood glucose by fingerstick only. The base-case analysis was consistent with the RCT (RT-CGM for 2 weeks on/1 week off over 3 months). A scenario analysis simulated outcomes of an RT-CGM "refresher" after the active intervention of the RCT. Analyses used the IMS CORE Diabetes Model and were conducted from a US third-party payer perspective, including direct costs obtained from published sources and inflated to 2011 US dollars. Costs and health outcomes were discounted at 3% per annum. Life expectancy (LE) and quality-adjusted life expectancy (QALE) from RT-CGM were 0.10 and 0.07, with a cost of $653/patient over a lifetime. Incremental LE and QALE from a "refresher" were 0.14 and 0.10, with a cost of $1312/patient over a lifetime, and incremental cost-effectiveness ratios were $9319 and $13 030 per LY and QALY gained. RT-CGM, as a self-care tool, is a cost-effective disease management option in the US for people with type 2 diabetes not on prandial insulin. Repeated use of RT-CGM may result in additional cost-effectiveness. © 2016 Diabetes Technology Society.

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

Mackillop, William J., E-mail: william.mackillop@krcc.on.ca; Kong, Weidong; Brundage, Michael

Purpose: Estimates of the appropriate rate of use of radiation therapy (RT) are required for planning and monitoring access to RT. Our objective was to compare estimates of the appropriate rate of use of RT derived from mathematical models, with the rate observed in a population of patients with optimal access to RT. Methods and Materials: The rate of use of RT within 1 year of diagnosis (RT{sub 1Y}) was measured in the 134,541 cases diagnosed in Ontario between November 2009 and October 2011. The lifetime rate of use of RT (RT{sub LIFETIME}) was estimated by the multicohort utilization tablemore » method. Poisson regression was used to evaluate potential barriers to access to RT and to identify a benchmark subpopulation with unimpeded access to RT. Rates of use of RT were measured in the benchmark subpopulation and compared with published evidence-based estimates of the appropriate rates. Results: The benchmark rate for RT{sub 1Y}, observed under conditions of optimal access, was 33.6% (95% confidence interval [CI], 33.0%-34.1%), and the benchmark for RT{sub LIFETIME} was 41.5% (95% CI, 41.2%-42.0%). Benchmarks for RT{sub LIFETIME} for 4 of 5 selected sites and for all cancers combined were significantly lower than the corresponding evidence-based estimates. Australian and Canadian evidence-based estimates of RT{sub LIFETIME} for 5 selected sites differed widely. RT{sub LIFETIME} in the overall population of Ontario was just 7.9% short of the benchmark but 20.9% short of the Australian evidence-based estimate of the appropriate rate. Conclusions: Evidence-based estimates of the appropriate lifetime rate of use of RT may overestimate the need for RT in Ontario.« less

What is access to radiation therapy? A conceptual framework and review of influencing factors.

PubMed

Sundaresan, Puma; Stockler, Martin R; Milross, Christopher G

2016-02-01

Optimal radiation therapy (RT) utilisation rates (RURs) have been defined for various cancer indications through extensive work in Australia and overseas. These benchmarks remain unrealised. The gap between optimal RUR and actual RUR has been attributed to inadequacies in 'RT access'. We aimed to develop a conceptual framework for the consideration of 'RT access' by examining the literature for existing constructs and translating it to the context of RT services. We further aimed to use this framework to identify and examine factors influencing 'RT access'. Existing models of health care access were reviewed and used to develop a multi-dimensional conceptual framework for 'RT access'. A review of the literature was then conducted to identify factors reported to affect RT access and utilisation. The electronic databases searched, the host platform and date range of the databases searched were Ovid MEDLINE, 1946 to October 2014 and PsycINFO via OvidSP,1806 to October 2014. The framework developed demonstrates that 'RT access' encompasses opportunity for RT as well as the translation of this opportunity to RT utilisation. Opportunity for RT includes availability, affordability, adequacy (quality) and acceptability of RT services. Several factors at the consumer, referrer and RT service levels affect the translation of this opportunity for RT to actual RT utilisation. 'Access' is a term that is widely used in the context of health service related research, planning and political discussions. It is a multi-faceted concept with many descriptions. We propose a conceptual framework for the consideration of 'RT access' so that factors affecting RT access and utilisation may be identified and examined. Understanding these factors, and quantifying them where possible, will allow objective evaluation of their impact on RT utilisation and guide implementation of strategies to modify their effects.

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.

Towards an integrative computational model for simulating tumor growth and response to radiation therapy

NASA Astrophysics Data System (ADS)

Marrero, Carlos Sosa; Aubert, Vivien; Ciferri, Nicolas; Hernández, Alfredo; de Crevoisier, Renaud; Acosta, Oscar

2017-11-01

Understanding the response to irradiation in cancer radiotherapy (RT) may help devising new strategies with improved tumor local control. Computational models may allow to unravel the underlying radiosensitive mechanisms intervening in the dose-response relationship. By using extensive simulations a wide range of parameters may be evaluated providing insights on tumor response thus generating useful data to plan modified treatments. We propose in this paper a computational model of tumor growth and radiation response which allows to simulate a whole RT protocol. Proliferation of tumor cells, cell life-cycle, oxygen diffusion, radiosensitivity, RT response and resorption of killed cells were implemented in a multiscale framework. The model was developed in C++, using the Multi-formalism Modeling and Simulation Library (M2SL). Radiosensitivity parameters extracted from literature enabled us to simulate in a regular grid (voxel-wise) a prostate cell tissue. Histopathological specimens with different aggressiveness levels extracted from patients after prostatectomy were used to initialize in silico simulations. Results on tumor growth exhibit a good agreement with data from in vitro studies. Moreover, standard fractionation of 2 Gy/fraction, with a total dose of 80 Gy as a real RT treatment was applied with varying radiosensitivity and oxygen diffusion parameters. As expected, the high influence of these parameters was observed by measuring the percentage of survival tumor cell after RT. This work paves the way to further models allowing to simulate increased doses in modified hypofractionated schemes and to develop new patient-specific combined therapies.

US geographic distribution of rt-PA utilization by hospital for acute ischemic stroke.

PubMed

Kleindorfer, Dawn; Xu, Yingying; Moomaw, Charles J; Khatri, Pooja; Adeoye, Opeolu; Hornung, Richard

2009-11-01

Previously, we have estimated US national rates of recombinant tissue plasminogen activator (rt-PA) use to be 1.8% to 3.0% of all ischemic stroke patients. However, we hypothesized that the rate of rt-PA use may vary widely depending on regional variation, and that a large percentage of the US population likely does not have access to hospitals using rt-PA regularly. We describe the US geographic distribution of hospitals using rt-PA for acute ischemic stroke. This analysis used the MEDPAR database, which is a claims-based dataset that contains every fee-for-service Medicare-eligible hospital discharge in the US. Cases potentially eligible for rt-PA treatment based on diagnosis were defined as those with a hospital DRG code of 14, 15, or 559, and that also had an ICD-9 code of 433, 434, or 436. Thrombolysis use was defined as an ICD-9 code of 99.1. Study interval was July 1, 2005 to June 30, 2007. Hospital locations were mapped using ArcView software; population densities and regions of the US are based on US Census 2000. There were 4750 hospitals in the MEDPAR database, which included 495 186 ischemic stroke admissions during the study period. Of these hospitals, 64% had no reported treatments with rt-PA for ischemic stroke, and 0.9% reported >10% treatment rates within the MEDPAR dataset. Bed size, rural or underserved designation, and population density were significantly associated with reported rt-PA treatment rates, and remained significant in the multivariable regression. Approximately 162 million US citizens reside in counties containing a hospital reporting a >or=2.4% treatment rate within the MEDPAR dataset. We report the first description of US hospital rt-PA treatment rates by hospital. Unfortunately, we found that 64% of US hospitals did not report giving rt-PA at all within the MEDPAR database within a 2-year period. These tended to be hospitals that were smaller (average bed size of 95), located in less densely populated areas, or located in the South or Midwest. In addition, 40% of the US population resides in counties without a hospital that administered rt-PA to at least 2.4% of ischemic stroke patients, although distinguishing transferred patients is problematic within administrative datasets. Such national-based resource-utilization data is important for planning at the local and national level, especially for such initiatives as telemedicine, to reach underserved areas.

Combinatorial Motor Training Results in Functional Reorganization of Remaining Motor Cortex after Controlled Cortical Impact in Rats

PubMed Central

Combs, Hannah L.; Jones, Theresa A.; Kozlowski, Dorothy A.

2016-01-01

Abstract Cortical reorganization subsequent to post-stroke motor rehabilitative training (RT) has been extensively examined in animal models and humans. However, similar studies focused on the effects of motor training after traumatic brain injury (TBI) are lacking. We previously reported that after a moderate/severe TBI in adult male rats, functional improvements in forelimb use were accomplished only with a combination of skilled forelimb reach training and aerobic exercise, with or without nonimpaired forelimb constraint. Thus, the current study was designed to examine the relationship between functional motor cortical map reorganization after experimental TBI and the behavioral improvements resulting from this combinatorial rehabilitative regime. Adult male rats were trained to proficiency on a skilled reaching task, received a unilateral controlled cortical impact (CCI) over the forelimb area of the caudal motor cortex (CMC). Three days post-CCI, animals began RT (n = 13) or no rehabilitative training (NoRT) control procedures (n = 13). The RT group participated in daily skilled reach training, voluntary aerobic exercise, and nonimpaired forelimb constraint. This RT regimen significantly improved impaired forelimb reaching success and normalized reaching strategies, consistent with previous findings. RT also enlarged the area of motor cortical wrist representation, derived by intracortical microstimulation, compared to NoRT. These findings indicate that sufficient RT can greatly improve motor function and improve the functional integrity of remaining motor cortex after a moderate/severe CCI. When compared with findings from stroke models, these findings also suggest that more intense RT may be needed to improve motor function and remodel the injured cortex after TBI. PMID:26421759

Combinatorial Motor Training Results in Functional Reorganization of Remaining Motor Cortex after Controlled Cortical Impact in Rats.

PubMed

Combs, Hannah L; Jones, Theresa A; Kozlowski, Dorothy A; Adkins, DeAnna L

2016-04-15

Cortical reorganization subsequent to post-stroke motor rehabilitative training (RT) has been extensively examined in animal models and humans. However, similar studies focused on the effects of motor training after traumatic brain injury (TBI) are lacking. We previously reported that after a moderate/severe TBI in adult male rats, functional improvements in forelimb use were accomplished only with a combination of skilled forelimb reach training and aerobic exercise, with or without nonimpaired forelimb constraint. Thus, the current study was designed to examine the relationship between functional motor cortical map reorganization after experimental TBI and the behavioral improvements resulting from this combinatorial rehabilitative regime. Adult male rats were trained to proficiency on a skilled reaching task, received a unilateral controlled cortical impact (CCI) over the forelimb area of the caudal motor cortex (CMC). Three days post-CCI, animals began RT (n = 13) or no rehabilitative training (NoRT) control procedures (n = 13). The RT group participated in daily skilled reach training, voluntary aerobic exercise, and nonimpaired forelimb constraint. This RT regimen significantly improved impaired forelimb reaching success and normalized reaching strategies, consistent with previous findings. RT also enlarged the area of motor cortical wrist representation, derived by intracortical microstimulation, compared to NoRT. These findings indicate that sufficient RT can greatly improve motor function and improve the functional integrity of remaining motor cortex after a moderate/severe CCI. When compared with findings from stroke models, these findings also suggest that more intense RT may be needed to improve motor function and remodel the injured cortex after TBI.

An analysis of needs for respiratory therapists in northeast Ohio and development of strategies to meet increased recruitment demands.

PubMed

Orens, Douglas K; Chatburn, Robert L; Volsko, Teresa A; Stoller, James K

2007-12-01

The 2005 American Association for Respiratory Care Human Resources Survey suggested that the national demand for respiratory therapists (RTs) exceeds the supply. At the Cleveland Clinic an expected hospital expansion of 350 beds by 2008 has increased the need for RT staff. This report describes a strategy by which we developed a plan, in concert with local RT colleges, to recruit RTs. Local RT managers were surveyed regarding demand for RTs. We developed a recruitment plan, based on discussions with RT program directors. The survey data and models estimated an annual mean of 33.4 new positions in northeast Ohio. Despite the fact that approximately 84 people graduated from northeast Ohio RT programs yearly in 2004 to 2007, the growth in demand for RTs exceeded the estimated supply. The main factor that caused RT schools to limit the supply of RTs was the paucity of clinical sites. Our analysis shows the schools could achieve a 40% increase in student output, and that if the Cleveland Clinic could essentially double its graduate hires, all RT staff needs in our hospital would be met by 2010. To assure a needed supply of RTs, this work shows the value of modeling supply and demand scenarios, coupled with surveying local RT leaders and fostering dialog between local RT leaders in hospitals and colleges. The product of this activity was a strategy for achieving recruitment goals while assuring that other regional demands for RTs are also met. We recommend this approach to colleagues facing similar challenges.

Concurrent versus sequential sorafenib therapy in combination with radiation for hepatocellular carcinoma.

PubMed

Wild, Aaron T; Gandhi, Nishant; Chettiar, Sivarajan T; Aziz, Khaled; Gajula, Rajendra P; Williams, Russell D; Kumar, Rachit; Taparra, Kekoa; Zeng, Jing; Cades, Jessica A; Velarde, Esteban; Menon, Siddharth; Geschwind, Jean F; Cosgrove, David; Pawlik, Timothy M; Maitra, Anirban; Wong, John; Hales, Russell K; Torbenson, Michael S; Herman, Joseph M; Tran, Phuoc T

2013-01-01

Sorafenib (SOR) is the only systemic agent known to improve survival for hepatocellular carcinoma (HCC). However, SOR prolongs survival by less than 3 months and does not alter symptomatic progression. To improve outcomes, several phase I-II trials are currently examining SOR with radiation (RT) for HCC utilizing heterogeneous concurrent and sequential treatment regimens. Our study provides preclinical data characterizing the effects of concurrent versus sequential RT-SOR on HCC cells both in vitro and in vivo. Concurrent and sequential RT-SOR regimens were tested for efficacy among 4 HCC cell lines in vitro by assessment of clonogenic survival, apoptosis, cell cycle distribution, and γ-H2AX foci formation. Results were confirmed in vivo by evaluating tumor growth delay and performing immunofluorescence staining in a hind-flank xenograft model. In vitro, concurrent RT-SOR produced radioprotection in 3 of 4 cell lines, whereas sequential RT-SOR produced decreased colony formation among all 4. Sequential RT-SOR increased apoptosis compared to RT alone, while concurrent RT-SOR did not. Sorafenib induced reassortment into less radiosensitive phases of the cell cycle through G1-S delay and cell cycle slowing. More double-strand breaks (DSBs) persisted 24 h post-irradiation for RT alone versus concurrent RT-SOR. In vivo, sequential RT-SOR produced the greatest tumor growth delay, while concurrent RT-SOR was similar to RT alone. More persistent DSBs were observed in xenografts treated with sequential RT-SOR or RT alone versus concurrent RT-SOR. Sequential RT-SOR additionally produced a greater reduction in xenograft tumor vascularity and mitotic index than either concurrent RT-SOR or RT alone. In conclusion, sequential RT-SOR demonstrates greater efficacy against HCC than concurrent RT-SOR both in vitro and in vivo. These results may have implications for clinical decision-making and prospective trial design.

Concurrent versus Sequential Sorafenib Therapy in Combination with Radiation for Hepatocellular Carcinoma

PubMed Central

Chettiar, Sivarajan T.; Aziz, Khaled; Gajula, Rajendra P.; Williams, Russell D.; Kumar, Rachit; Taparra, Kekoa; Zeng, Jing; Cades, Jessica A.; Velarde, Esteban; Menon, Siddharth; Geschwind, Jean F.; Cosgrove, David; Pawlik, Timothy M.; Maitra, Anirban; Wong, John; Hales, Russell K.; Torbenson, Michael S.; Herman, Joseph M.; Tran, Phuoc T.

2013-01-01

Sorafenib (SOR) is the only systemic agent known to improve survival for hepatocellular carcinoma (HCC). However, SOR prolongs survival by less than 3 months and does not alter symptomatic progression. To improve outcomes, several phase I-II trials are currently examining SOR with radiation (RT) for HCC utilizing heterogeneous concurrent and sequential treatment regimens. Our study provides preclinical data characterizing the effects of concurrent versus sequential RT-SOR on HCC cells both in vitro and in vivo. Concurrent and sequential RT-SOR regimens were tested for efficacy among 4 HCC cell lines in vitro by assessment of clonogenic survival, apoptosis, cell cycle distribution, and γ-H2AX foci formation. Results were confirmed in vivo by evaluating tumor growth delay and performing immunofluorescence staining in a hind-flank xenograft model. In vitro, concurrent RT-SOR produced radioprotection in 3 of 4 cell lines, whereas sequential RT-SOR produced decreased colony formation among all 4. Sequential RT-SOR increased apoptosis compared to RT alone, while concurrent RT-SOR did not. Sorafenib induced reassortment into less radiosensitive phases of the cell cycle through G1-S delay and cell cycle slowing. More double-strand breaks (DSBs) persisted 24 h post-irradiation for RT alone versus concurrent RT-SOR. In vivo, sequential RT-SOR produced the greatest tumor growth delay, while concurrent RT-SOR was similar to RT alone. More persistent DSBs were observed in xenografts treated with sequential RT-SOR or RT alone versus concurrent RT-SOR. Sequential RT-SOR additionally produced a greater reduction in xenograft tumor vascularity and mitotic index than either concurrent RT-SOR or RT alone. In conclusion, sequential RT-SOR demonstrates greater efficacy against HCC than concurrent RT-SOR both in vitro and in vivo. These results may have implications for clinical decision-making and prospective trial design. PMID:23762417

Linking Action Research to Response to Intervention (RtI): The Strategy Implementation Project

ERIC Educational Resources Information Center

Hoppey, David

2013-01-01

This paper showcases how one teacher preparation program embedded action research within the Response to Intervention (RtI) model. This integration helped preservice teachers gain a deeper knowledge of RtI key concepts and pedagogical decision making for meeting diverse students' needs. Examples from a course assignment are provided to demonstrate…

School Psychologists' Willingness to Implement RtI: The Role of Philosophical and Practical Readiness

ERIC Educational Resources Information Center

Fan, Chung-Hau; Denner, Peter R.; Bocanegra, Joel O.; Ding, Yi

2016-01-01

After the change in IDEIA, different models of response to intervention (RtI) have been practiced widely in American school systems. School psychologists are in an important position to facilitate RtI practice and provide professional development in order to help their school systems successfully undergo this transformation. However, there is a…

Assessment of the Accuracy of the Conventional Ray-Tracing Technique: Implications in Remote Sensing and Radiative Transfer Involving Ice Clouds.

NASA Technical Reports Server (NTRS)

Bi, Lei; Yang, Ping; Liu, Chao; Yi, Bingqi; Baum, Bryan A.; Van Diedenhoven, Bastiaan; Iwabuchi, Hironobu

2014-01-01

A fundamental problem in remote sensing and radiative transfer simulations involving ice clouds is the ability to compute accurate optical properties for individual ice particles. While relatively simple and intuitively appealing, the conventional geometric-optics method (CGOM) is used frequently for the solution of light scattering by ice crystals. Due to the approximations in the ray-tracing technique, the CGOM accuracy is not well quantified. The result is that the uncertainties are introduced that can impact many applications. Improvements in the Invariant Imbedding T-matrix method (II-TM) and the Improved Geometric-Optics Method (IGOM) provide a mechanism to assess the aforementioned uncertainties. The results computed by the II-TMþIGOM are considered as a benchmark because the IITM solves Maxwell's equations from first principles and is applicable to particle size parameters ranging into the domain at which the IGOM has reasonable accuracy. To assess the uncertainties with the CGOM in remote sensing and radiative transfer simulations, two independent optical property datasets of hexagonal columns are developed for sensitivity studies by using the CGOM and the II-TMþIGOM, respectively. Ice cloud bulk optical properties obtained from the two datasets are compared and subsequently applied to retrieve the optical thickness and effective diameter from Moderate Resolution Imaging Spectroradiometer (MODIS) measurements. Additionally, the bulk optical properties are tested in broadband radiative transfer (RT) simulations using the general circulation model (GCM) version of the Rapid Radiative Transfer Model (RRTMG) that is adopted in the National Center for Atmospheric Research (NCAR) Community Atmosphere Model (CAM, version 5.1). For MODIS retrievals, the mean bias of uncertainties of applying the CGOM in shortwave bands (0.86 and 2.13 micrometers) can be up to 5% in the optical thickness and as high as 20% in the effective diameter, depending on cloud optical thickness and effective diameter. In the MODIS infrared window bands centered at 8.5, 11, and 12 micrometers biases in the optical thickness and effective diameter are up to 12% and 10%, respectively. The CGOM-based simulation errors in ice cloud radiative forcing calculations are on the order of 10Wm(exp 2).

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).

Declining Use of Radiotherapy in Stage I and II Hodgkin's Disease and Its Effect on Survival and Secondary Malignancies

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

Koshy, Matthew, E-mail: mkoshy@radonc.uchicago.edu; Department of Radiation Oncology, University of Illinois at Chicago, Chicago, IL; Rich, Shayna E.

2012-02-01

Purpose: Concerns regarding long-term toxicities have led some to withhold radiotherapy (RT) for the treatment of Stage I and II Hodgkin's disease (HD). The present study was undertaken to assess the use of RT for HD and its effect on overall survival and the development of secondary malignancies. Methods and Materials: The present study included data from the Surveillance, Epidemiology, and End Results database from patients aged {>=}20 years who had been diagnosed with Stage I or II HD between 1988 and 2006. Overall survival was estimated using the Kaplan-Meier method, and the Cox multivariate regression model was used tomore » analyze trends. Results: A total of 12,247 patients were selected, and 51.5% had received RT. The median follow-up for the present cohort was 4.9 years, with 21% of the cohort having >10 years of follow-up. Between 1988 and 1991, 62.9% had undergone RT, but between 2004 and 2006, only 43.7% had undergone RT (p < .001). The 5-year overall survival rate was 76% for patients who had not received RT and 87% for those who had (p < .001). The hazard ratio adjusted for other variables in the regression model showed that patients who had not undergone RT (hazard ratio, 1.72; 95% confidence interval, 1.72-2.02) was associated with significantly worse survival compared with patients who had received RT. The actuarial rate of developing a second malignancy was 14.6% vs. 15.0% at 15 years for those who had and had not undergone RT, respectively (p = .089). Conclusions: The present study is one of the largest studies to examine the role of RT for Stage I and II HD. Our results revealed a survival benefit with the addition of RT with no increase in the development of secondary malignancies compared with patients who had not received RT. Furthermore, the present nationwide study revealed a >20% absolute decrease in the use of RT from 1988 to 2006.« less

Open-source software for collision detection in external beam radiation therapy

NASA Astrophysics Data System (ADS)

Suriyakumar, Vinith M.; Xu, Renee; Pinter, Csaba; Fichtinger, Gabor

2017-03-01

PURPOSE: Collision detection for external beam radiation therapy (RT) is important for eliminating the need for dryruns that aim to ensure patient safety. Commercial treatment planning systems (TPS) offer this feature but they are expensive and proprietary. Cobalt-60 RT machines are a viable solution to RT practice in low-budget scenarios. However, such clinics are hesitant to invest in these machines due to a lack of affordable treatment planning software. We propose the creation of an open-source room's eye view visualization module with automated collision detection as part of the development of an open-source TPS. METHODS: An openly accessible linac 3D geometry model is sliced into the different components of the treatment machine. The model's movements are based on the International Electrotechnical Commission standard. Automated collision detection is implemented between the treatment machine's components. RESULTS: The room's eye view module was built in C++ as part of SlicerRT, an RT research toolkit built on 3D Slicer. The module was tested using head and neck and prostate RT plans. These tests verified that the module accurately modeled the movements of the treatment machine and radiation beam. Automated collision detection was verified using tests where geometric parameters of the machine's components were changed, demonstrating accurate collision detection. CONCLUSION: Room's eye view visualization and automated collision detection are essential in a Cobalt-60 treatment planning system. Development of these features will advance the creation of an open-source TPS that will potentially help increase the feasibility of adopting Cobalt-60 RT.

Reaction Time Correlations during Eye–Hand Coordination:Behavior and Modeling

PubMed Central

Dean, Heather L.; Martí, Daniel; Tsui, Eva; Rinzel, John; Pesaran, Bijan

2011-01-01

During coordinated eye– hand movements, saccade reaction times (SRTs) and reach reaction times (RRTs) are correlated in humans and monkeys. Reaction times (RTs) measure the degree of movement preparation and can correlate with movement speed and accuracy. However, RTs can also reflect effector nonspecific influences, such as motivation and arousal. We use a combination of behavioral psychophysics and computational modeling to identify plausible mechanisms for correlations in SRTs and RRTs. To disambiguate nonspecific mechanisms from mechanisms specific to movement coordination, we introduce a dual-task paradigm in which a reach and a saccade are cued with a stimulus onset asynchrony (SOA). We then develop several variants of integrate-to-threshold models of RT, which postulate that responses are initiated when the neural activity encoding effector-specific movement preparation reaches a threshold. The integrator models formalize hypotheses about RT correlations and make predictions for how each RT should vary with SOA. To test these hypotheses, we trained three monkeys to perform the eye– hand SOA task and analyzed their SRTs and RRTs. In all three subjects, RT correlations decreased with increasing SOA duration. Additionally, mean SRT decreased with decreasing SOA, revealing facilitation of saccades with simultaneous reaches, as predicted by the model. These results are not consistent with the predictions of the models with common modulation or common input but are compatible with the predictions of a model with mutual excitation between two effector-specific integrators. We propose that RT correlations are not simply attributable to motivation and arousal and are a signature of coordination. PMID:21325507

Associations between adjuvant radiotherapy and different causes of death in a German breast cancer cohort.

PubMed

Obi, Nadia; Eulenburg, Christine; Seibold, Petra; Eilber, Ursula; Thöne, Kathrin; Behrens, Sabine; Chang-Claude, Jenny; Flesch-Janys, Dieter

2018-04-01

Studies of cohorts of breast cancer (BC) patients diagnosed before 1990 showed radiotherapy (RT) to be associated with increased cardiovascular (CVD) and lung cancer mortality many years after diagnosis. In the late 1990s, improvements in RT planning techniques reduced radiation doses to normal tissues. Recent studies did not consistently report higher RT-related mortality for CVD and second cancers. Aim of the study was to analyze specific causes of death after 3D-conformal RT in a recent BC cohort. Stage I-III BC patients diagnosed 2001-2005 and enrolled in the population based MARIEplus study were followed-up for 11.9 years (median). Associations between adjuvant RT and cause-specific mortality were analyzed by using competing risks models, yielding subdistribution hazard ratios (SHR) for RT directly related to cumulative incidences. Models were adjusted for differences in baseline characteristics applying inverse-probability-of-treatment-weighting (IPTW). Of the 2951 patients, 2439 (83.0%) received RT. No significant association of RT with lung cancer mortality (SHR IPTW 0.88, 0.35-2.12), other cancer mortality (SHR IPTW 1.04, 95% CI 0.62-1.73) or cardiac mortality was observed (SHR IPTW 1.57, 0.75-3.29). Mortality from lung and other diseases were significantly lower in irradiated women (SHR IPTW 0.39, 95% CI 0.17-0.90 and SHR IPTW 0.58, 95% CI 0.34-0.97, respectively). In line with recent studies, 3D-conformal RT did not significantly increase mortality from non-BC causes in the German MARIEplus cohort. Since long-term data are still sparse and event rates low in BC-cohorts, who received modern RT, investigation of possible late RT effects on mortality beyond 14 years of follow-up is warranted. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

Allosteric mechanism of quinoline inhibitors for HIV RT-associated RNase with MD simulation and dynamics fluctuation network.

PubMed

Cai, Yi; Liu, Hao; Chen, Haifeng

2018-03-01

The human immunodeficiency virus (HIV) is a retrovirus which infects T lymphocyte of human body and causes immunodeficiency. Reverse transcriptase inhibitors (RTIs) can inhibit some functions of RT, preventing virus synthesis (double-stranded DNA), so that HIV virus replication can be reduced. Experimental results indicate a series of benzimidazole-based inhibitors which target HIV RT-associated RNase to inhibit the reverse transcription of HIV virus. However, the allosteric mechanism is still unclear. Here, molecular dynamics simulations and dynamics fluctuation network analysis were used to reveal the binding mode between the inhibitors and RT-associated RNase. The most active molecule has more hydrophobic and electrostatic interactions than the less active inhibitor. Dynamics correlation network analysis indicates that the most active inhibitor perturbs the network of RT-associated RNase and decreases the correlation of nodes. 3D-QSAR model suggests that two robust and reliable models were constructed and validated by independent test set. 3D-QSAR model also shows that bulky negatively charged or hydrophilic substituent is favorable to bioactivity. These results reveal the allosteric mechanism of quinoline inhibitors and help to improve the bioactivity. © 2017 John Wiley & Sons A/S.

RT-LAMP assay: an alternative approach for profiling of bovine heat shock protein 70 gene in PBMC cultured model.

PubMed

Sengar, Gyanendra Singh; Deb, Rajib; Raja, T V; Singh, Umesh; Kant, Rajiv; Bhanuprakash, V; Alyethodi, R R; Kumar, Sushil; Verma, Preetam; Chakraborty, Soumendu; Alex, Rani; Singh, Rani

2017-07-01

The purpose of this study is to develop a novel Reverse Transcriptase Loop-mediated isothermal amplification (RT-LAMP) based assay for in vitro profiling of heat shock protein 70 (Hsp70) in bovine peripheral blood mononuclear cell (PBMC) culture model utilizing the absorbance level of magnesium pyrophosphate-a by-product of LAMP reaction. A set of bovine Hsp70 specific RT-LAMP primers were designed to detect the differential absorbance level of magnesium pyrophosphate by-product which signifies the degree of Hsp70 amplification from cDNA of thermally induced cultured cells at different recovery periods. The study revealed significant (P < 0.05) correlation between absorbance level and the fold change of Hsp70 transcripts at different kinetic intervals of heat stress recovery in bovine PBMC cell culture models. RT-LAMP based absorbance assay can be used as an indicator to measure the degree of bovine Hsp70 transcripts produced during thermal stress and can be used as an alternative to the traditional Real time PCR assay. Developed RT-LAMP assay can be used as a cost-effective method for profiling of bovine HSP70 gene.

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.

Variations in automatically recorded rumination time as explained by variations in intake of dietary fractions and milk production, and between-cow variation.

PubMed

Byskov, M V; Nadeau, E; Johansson, B E O; Nørgaard, P

2015-06-01

Individual recording of rumination time (RT) is now possible in commercial dairy herds, through development of a microphone-based sensor, which is able to record RT by the sound of rumination activity. The objectives of this study were to examine the relationship between daily RT and intakes of different dietary fractions, the relationship between RT in minutes per kilogram of dry matter intake (DMI) and milk production, and to examine the variation in RT within and between mid-lactating dairy cows. Data from 3 production trials were used in which a total of 27 different diets were fed. The data contained 761, 290, and 203 daily recordings of RT, milk yield, milk components, DMI, and intake of dietary fractions recorded on 29, 26, and 24 Holstein and Swedish Red cows from trials 1, 2, and 3, respectively. The dietary fractions included forage neutral detergent fiber (NDF), concentrate NDF, crude protein, sugar, starch, and the remaining fraction represented by organic matter--(forage NDF+concentrate NDF+crude protein+sugar+starch). The relationship between the dietary fractions and RT was analyzed in 2 steps. In step 1, the dietary fractions, which were significantly related to RT, were selected and simultaneously checked for multicollinearity between the dietary components; in step 2, a multivariate model, including the effect of repeated measurements, the main effect of the selected dietary fractions from step 1, random effects of cow(trial) and trial, and information on breed, days in milk, and parity was used to analyze the relationship between RT and the selected dietary fractions. Relationships between RT in minutes per kilogram of DMI and milk yield and milk components were analyzed, using the same multivariate model as in step 2. Approximately 32% of the variation in daily RT could be explained by variations in intakes of the dietary fractions, whereas 48% of the total variation in RT was accounted for by individual variations between cows. Intakes of forage NDF and starch were positively related to daily RT, whereas intakes of sugar and the remaining fraction were negatively related to daily RT. Rumination time in minutes per kilogram of DMI was negatively related to milk yield and protein percentage, but positively related to milk fat percentage. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Middle School Teacher Satisfaction with Response to Intervention (RtI): An Assessment between Inception and Implementation

ERIC Educational Resources Information Center

Zahedi, Karynn Jensen

2010-01-01

Response to intervention (RtI) is a multi-tiered process of monitoring student responses to remediation that is designed to help struggling learners succeed within the purview of regular education. Under the RtI model, students are referred to special education only after a series of documented interventions have been attempted. This study…

Looking beyond RtI Standard Treatment Approach: It's Not Too Late to Embrace the Problem-Solving Approach

ERIC Educational Resources Information Center

King, Diane; Coughlin, Patricia Kathleen

2016-01-01

There are two approaches for providing Tier 2 interventions within Response to Intervention (RtI): standard treatment protocol (STP) and the problem-solving approach (PSA). This article describes the multi-tiered RtI prevention model being implemented across the United States through an analysis of these two approaches in reading instruction. It…

Room-temperature ballistic transport in III-nitride heterostructures.

PubMed

Matioli, Elison; Palacios, Tomás

2015-02-11

Room-temperature (RT) ballistic transport of electrons is experimentally observed and theoretically investigated in III-nitrides. This has been largely investigated at low temperatures in low band gap III-V materials due to their high electron mobilities. However, their application to RT ballistic devices is limited by their low optical phonon energies, close to KT at 300 K. In addition, the short electron mean-free-path at RT requires nanoscale devices for which surface effects are a limitation in these materials. We explore the unique properties of wide band-gap III-nitride semiconductors to demonstrate RT ballistic devices. A theoretical model is proposed to corroborate experimentally their optical phonon energy of 92 meV, which is ∼4× larger than in other III-V semiconductors. This allows RT ballistic devices operating at larger voltages and currents. An additional model is described to determine experimentally a characteristic dimension for ballistic transport of 188 nm. Another remarkable property is their short carrier depletion at device sidewalls, down to 13 nm, which allows top-down nanofabrication of very narrow ballistic devices. These results open a wealth of new systems and basic transport studies possible at RT.

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.

The stochastic Beer-Lambert-Bouguer law for discontinuous vegetation canopies

NASA Astrophysics Data System (ADS)

Shabanov, N.; Gastellu-Etchegorry, J.-P.

2018-07-01

The 3D distribution of canopy foliage affects the radiation regime and retrievals of canopy biophysical parameters. The gap fraction is one primary indicator of a canopy structure. Historically the Beer-Lambert-Bouguer law and the linear mixture model have served as a basis for multiple technologies for retrievals of the gap (or vegetation) fraction and Leaf Area Index (LAI). The Beer-Lambert-Bouguer law is a form of the Radiative Transfer (RT) equation for homogeneous canopies, which was later adjusted for a correlation between fitoelements using concept of the clumping index. The Stochastic Radiative Transfer (SRT) approach has been developed specifically for heterogeneous canopies, however the approach lacks a proper model of the vegetation fraction. This study is focused on the implementation of the stochastic version of the Beer-Lambert-Bouguer law for heterogeneous canopies, featuring the following principles: 1) two mechanisms perform photon transport- transmission through the turbid medium of foliage crowns and direct streaming through canopy gaps, 2) the radiation field is influenced by a canopy structure (quantified by the statistical moments of a canopy structure) and a foliage density (quantified by the gap fraction as a function of LAI), 3) the notions of canopy transmittance and gap fraction are distinct. The derived stochastic Beer-Lambert-Bouguer law is consistent with the Geometrical Optical and Radiative Transfer (GORT) derivations. Analytical and numerical analysis of the stochastic Beer-Lambert-Bouguer law presented in this study provides the basis to reformulate widely used technologies for retrievals of the gap fraction and LAI from ground and satellite radiation measurements.

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.

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.

The Use of Piecewise Growth Models to Estimate Learning Trajectories and RtI Instructional Effects in a Comparative Interrupted Time-Series Design

ERIC Educational Resources Information Center

Zvoch, Keith

2016-01-01

Piecewise growth models (PGMs) were used to estimate and model changes in the preliteracy skill development of kindergartners in a moderately sized school district in the Pacific Northwest. PGMs were applied to interrupted time-series (ITS) data that arose within the context of a response-to-intervention (RtI) instructional framework. During the…

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.

Expansion of the Real-time Sport-land Information System for NOAA/National Weather Service Situational Awareness and Local Modeling Applications

NASA Technical Reports Server (NTRS)

Case, Jonathan L.

2014-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center has been running a real-time version of the Land Information System (LIS) since summer 2010 (hereafter, SPoRTLIS). The real-time SPoRT-LIS runs the Noah land surface model (LSM) in an offline capacity apart from a numerical weather prediction model, using input atmospheric and precipitation analyses (i.e., "forcings") to drive the Noah LSM integration at 3-km resolution. Its objectives are to (1) produce local-scale information about the soil state for NOAA/National Weather Service (NWS) situational awareness applications such as drought monitoring and assessing flood potential, and (2) provide land surface initialization fields for local modeling initiatives. The current domain extent has been limited by the input atmospheric analyses that drive the Noah LSM integration within SPoRT-LIS, specifically the National Centers for Environmental Prediction (NCEP) Stage IV precipitation analyses. Due to the nature of the geographical edges of the Stage IV precipitation grid and its limitations in the western U.S., the SPoRT-LIS was originally confined to a domain fully nested within the Stage IV grid, over the southeastern half of the Conterminous United States (CONUS). In order to expand the real-time SPoRT-LIS to a full CONUS domain, alternative precipitation forcing datasets were explored in year-long, offline comparison runs of the Noah LSM. Based on results of these comparison simulations, we chose to implement the radar/gauge-based precipitation analyses from the National Severe Storms Laboratory as a replacement to the Stage IV product. The Multi-Radar Multi-Sensor (MRMS; formerly known as the National Mosaic and multi-sensor Quantitative precipitation estimate) product has full CONUS coverage at higher-resolution, thereby providing better coverage and greater detail than that of the Stage IV product. This paper will describe the expanded/upgraded SPoRT-LIS, present comparisons between the original and upgraded SPoRT-LIS, and discuss the path forward for future collaboration opportunities with SPoRT partners in the NWS.

Abscopal Effects With Hypofractionated Schedules Extending Into the Effector Phase of the Tumor-Specific T-Cell Response.

PubMed

Zhang, Xuanwei; Niedermann, Gabriele

2018-05-01

Hypofractionated radiation therapy (hRT) combined with immune checkpoint blockade can induce T-cell-mediated local and abscopal antitumor effects. We had previously observed peak levels of tumor-infiltrating lymphocytes (TILs) between days 5 and 8 after hRT. Because TILs are regarded as radiosensitive, hRT schedules extending into this period might be less immunogenic, prompting us to compare clinically relevant, short and extended schedules with equivalent biologically effective doses combined with anti-programmed cell death 1 (PD1) antibody treatment. In mice bearing 2 B16-CD133 melanoma tumors, the primary tumor was irradiated with 3 × 9.18 Gy in 3 or 5 days or with 5 × 6.43 Gy in 10 days; an anti-PD1 antibody was given weekly. The mice were monitored for tumor growth and survival. T-cell responses were determined on days 8 and 15 of treatment. The role of regional lymph nodes was studied by administering FTY720, which blocks lymph node egress of activated T cells. Tumor growth measurements after combination treatment using short or extended hRT and control treatment were also performed in the wild-type B16 melanoma and 4T1 breast carcinoma models. In the B16-CD133 model, growth inhibition of irradiated primary and nonirradiated secondary tumors and overall survival were similar with all 3 hRT/anti-PD1 combinations, superior to hRT and anti-PD1 monotherapy, and was strongly dependent on CD8 + T cells. TIL infiltration and local and systemic tumor-specific CD8 + T-cell responses were also similar, regardless of whether short or extended hRT was used. Administration of FTY720 accelerated growth of both primary and secondary tumors, strongly reduced their TIL infiltration, and increased tumor-specific CD8 + T cells in the lymph nodes draining the irradiated tumor. In the 4T1 model, local and abscopal tumor control was also similar, regardless of whether short or extended hRT was used, although the synergy between hRT and anti-PD1 was weaker. No synergies were found in the B16 wild-type model lacking an exogenous antigen. Our data suggest that combination therapy with hRT schedules extending into the period during which treatment-induced T cells infiltrate the irradiated tumor can provoke local and systemic antitumor effects similar to those with therapy using shorter schedules, if the regional lymph nodes supply sufficient tumor-specific T cells. This has implications for planning clinical RT/immune checkpoint blockade trials. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Comparative evaluation of polarimetric and bi-spectral cloud microphysics retrievals: Retrieval closure experiments and comparisons based on idealized and LES case studies

NASA Astrophysics Data System (ADS)

Miller, D. J.; Zhang, Z.; Ackerman, A. S.; Platnick, S. E.; Cornet, C.

2016-12-01

A remote sensing cloud retrieval simulator, created by coupling an LES cloud model with vector radiative transfer (RT) models is the ideal framework for assessing cloud remote sensing techniques. This simulator serves as a tool for understanding bi-spectral and polarimetric retrievals by comparing them directly to LES cloud properties (retrieval closure comparison) and for comparing the retrieval techniques to one another. Our simulator utilizes the DHARMA LES [Ackerman et al., 2004] with cloud properties based on marine boundary layer (MBL) clouds observed during the DYCOMS-II and ATEX field campaigns. The cloud reflectances are produced by the vectorized RT models based on polarized doubling adding and monte carlo techniques (PDA, MCPOL). Retrievals are performed utilizing techniques as similar as possible to those implemented on their corresponding well known instruments; polarimetric retrievals are based on techniques implemented for polarimeters (POLDER, AirMSPI, and RSP) and bi-spectral retrievals are performed using the Nakajima-King LUT method utilized on a number of spectral instruments (MODIS and VIIRS). Retrieval comparisons focus on cloud droplet effective radius (re), effective variance (ve), and cloud optical thickness (τ). This work explores the sensitivities of these two retrieval techniques to various observation limitations, such as spatial resolution/cloud inhomogeneity, impact of 3D radiative effects, and angular resolution requirements. With future remote sensing missions like NASA's Aerosols/Clouds/Ecosystems (ACE) planning to feature advanced polarimetric instruments it is important to understand how these retrieval techniques compare to one another. The cloud retrieval simulator we've developed allows us to probe these important questions in a realistically relevant test bed.

Radiation Therapy Noncompliance and Clinical Outcomes in an Urban Academic Cancer Center

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

Ohri, Nitin; Rapkin, Bruce D.; Guha, Chandan

Purpose: To examine associations between radiation therapy (RT) noncompliance and clinical outcomes. Methods and Materials: We reviewed all patients who completed courses of external beam RT with curative intent in our department from the years 2007 to 2012 for cancers of the head and neck, breast, lung, cervix, uterus, or rectum. Patients who missed 2 or more scheduled RT appointments (excluding planned treatment breaks) were deemed noncompliant. Univariate, multivariable, and propensity-matched analyses were performed to examine associations between RT noncompliance and clinical outcomes. Results: Of 1227 patients, 266 (21.7%) were noncompliant. With median follow-up of 50.9 months, 108 recurrences (8.8%) and 228more » deaths (18.6%) occurred. In univariate analyses, RT noncompliance was associated with increased recurrence risk (5-year cumulative incidence 16% vs 7%, P<.001), inferior recurrence-free survival (5-year actuarial rate 63% vs 79%, P<.001), and inferior overall survival (5-year actuarial rate 72% vs 83%, P<.001). In multivariable analyses that were adjusted for disease site and stage, comorbidity score, gender, ethnicity, race, and socioeconomic status (SES), RT noncompliance was associated with inferior recurrence, recurrence-free survival, and overall survival rates. Propensity score–matched models yielded results nearly identical to those seen in univariate analyses. Low SES was associated with RT noncompliance and was associated with inferior clinical outcomes in univariate analyses, but SES was not associated with inferior outcomes in multivariable models. Conclusion: For cancer patients being treated with curative intent, RT noncompliance is associated with inferior clinical outcomes. The magnitudes of these effects demonstrate that RT noncompliance can serve as a behavioral biomarker to identify high-risk patients who require additional interventions. Treatment compliance may mediate the associations that have been observed linking SES and clinical outcomes.« less

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.

Comparing efficacy of reduced-toxicity allogeneic hematopoietic cell transplantation with conventional chemo-(immuno) therapy in patients with relapsed or refractory CLL: a Markov decision analysis.

PubMed

Kharfan-Dabaja, M A; Pidala, J; Kumar, A; Terasawa, T; Djulbegovic, B

2012-09-01

Despite therapeutic advances, relapsed/refractory CLL, particularly after fludarabine-based regimens, remains a major challenge for which optimal therapy is undefined. No randomized comparative data exist to suggest the superiority of reduced-toxicity allogeneic hematopoietic cell transplantation (RT-allo-HCT) over conventional chemo-(immuno) therapy (CCIT). By using estimates from a systematic review and by meta-analysis of available published evidence, we constructed a Markov decision model to examine these competing modalities. Cohort analysis demonstrated superior outcome for RT-allo-HCT, with a 10-month overall life expectancy (and 6-month quality-adjusted life expectancy (QALE)) advantage over CCIT. Although the model was sensitive to changes in base-case assumptions and transition probabilities, RT-allo-HCT provided superior overall life expectancy through a range of values supported by the meta-analysis. QALE was superior for RT-allo-HCT compared with CCIT. This conclusion was sensitive to change in the anticipated state utility associated with the post-allogeneic HCT state; however, RT-allo-HCT remained the optimal strategy for values supported by existing literature. This analysis provides a quantitative comparison of outcomes between RT-allo-HCT and CCIT for relapsed/refractory CLL in the absence of randomized comparative trials. Confirmation of these findings requires a prospective randomized trial, which compares the most effective RT-allo-HCT and CCIT regimens for relapsed/refractory CLL.

Characterizing the utility of the TMPA real-time product for hydrologic predictions over global river basins across scales

NASA Astrophysics Data System (ADS)

Gao, H.; Zhang, S.; Nijssen, B.; Zhou, T.; Voisin, N.; Sheffield, J.; Lee, K.; Shukla, S.; Lettenmaier, D. P.

2017-12-01

Despite its errors and uncertainties, the Tropical Rainfall Measuring Mission (TRMM) Multi-satellite Precipitation Analysis real-time product (TMPA-RT) has been widely used for hydrological monitoring and forecasting due to its timely availability for real-time applications. To evaluate the utility of TMPA-RT in hydrologic predictions, many studies have compared modeled streamflows driven by TMPA-RT against gauge data. However, because of the limited availability of streamflow observations in data sparse regions, there is still a lack of comprehensive comparisons for TMPA-RT based hydrologic predictions at the global scale. Furthermore, it is expected that its skill is less optimal at the subbasin scale than the basin scale. In this study, we evaluate and characterize the utility of the TMPA-RT product over selected global river basins during the period of 1998 to 2015 using the TMPA research product (TMPA-RP) as a reference. The Variable Infiltration Capacity (VIC) model, which was calibrated and validated previously, is adopted to simulate streamflows driven by TMPA-RT and TMPA-RP, respectively. The objective of this study is to analyze the spatial and temporal characteristics of the hydrologic predictions by answering the following questions: (1) How do the precipitation errors associated with the TMPA-RT product transform into streamflow errors with respect to geographical and climatological characteristics? (2) How do streamflow errors vary across scales within a basin?

Comparative lytic efficacy of rt-PA and ultrasound in porcine versus human clots.

PubMed

Huang, Shenwen; Shekhar, Himanshu; Holland, Christy K

2017-01-01

Porcine thrombi are employed routinely in preclinical models of ischemic stroke. In this study, we examined the differential lytic susceptibility of porcine and human whole blood clots with and without the use of microbubbles and ultrasound (US) as an adjuvant. An in vitro system equipped with time-lapse microscopy was used to evaluate recombinant tissue-plasminogen activator (rt-PA) lysis of porcine and human clots in the same species or cross species plasma. Human and porcine whole blood clots were treated with rt-PA and an echo contrast agent, Definity®, and exposed to intermittent 120 kHz US. The rt-PA lytic efficacy observed for porcine clots in porcine plasma was 22 times lower than for human clots in human plasma reported previously. Further, porcine clots did not exhibit increased lysis with adjuvant Definity® and US exposure. However, the rt-PA lytic susceptibility of the porcine clots in human plasma was similar to that of human clots in human plasma. Human clots perfused with porcine plasma did not respond to rt-PA, but adjuvant use of Definity® and US enhanced lysis. These results reveal considerable differences in lytic susceptibility of porcine clots and human clots to rt-PA. The use of porcine clot models to test new human thrombolytic therapies may necessitate modulation of coagulation and thrombolytic factors to reflect human hemostasis accurately.

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.

Significant inconsistency of vegetation carbon density in CMIP5 Earth system models against observational data

NASA Astrophysics Data System (ADS)

Song, Xia; Hoffman, Forrest M.; Iversen, Colleen M.; Yin, Yunhe; Kumar, Jitendra; Ma, Chun; Xu, Xiaofeng

2017-09-01

Earth system models (ESMs) have been widely used for projecting global vegetation carbon dynamics, yet how well ESMs performed for simulating vegetation carbon density remains untested. We compiled observational data of vegetation carbon density from literature and existing data sets to evaluate nine ESMs at site, biome, latitude, and global scales. Three variables—root (including fine and coarse roots), total vegetation carbon density, and the root:total vegetation carbon ratios (R/T ratios), were chosen for ESM evaluation. ESM models performed well in simulating the spatial distribution of carbon densities in root (r = 0.71) and total vegetation (r = 0.62). However, ESM models had significant biases in simulating absolute carbon densities in root and total vegetation biomass across the majority of land ecosystems, especially in tropical and arctic ecosystems. Particularly, ESMs significantly overestimated carbon density in root (183%) and total vegetation biomass (167%) in climate zones of 10°S-10°N. Substantial discrepancies between modeled and observed R/T ratios were found: the R/T ratios from ESMs were relatively constant, approximately 0.2 across all ecosystems, along latitudinal gradients, and in tropic, temperate, and arctic climatic zones, which was significantly different from the observed large variations in the R/T ratios (0.1-0.8). There were substantial inconsistencies between ESM-derived carbon density in root and total vegetation biomass and the R/T ratio at multiple scales, indicating urgent needs for model improvements on carbon allocation algorithms and more intensive field campaigns targeting carbon density in all key vegetation components.

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.

Radiation-induced erectile dysfunction using prostate-confined modern radiotherapy in a rat model.

PubMed

Kimura, Masaki; Yan, Hui; Rabbani, Zahid; Satoh, Takefumi; Baba, Shiro; Yin, Fang-fang; Polascik, Thomas J; Donatucci, Craig F; Vujaskovic, Zeljko; Koontz, Bridget F

2011-08-01

The mechanisms of radiation-induced erectile dysfunction (ED) are unclear, as clinical studies are limited, and previous animal models were based on wide-field irradiation, which does not model current radiotherapy (RT) techniques. To perform functional and morphological analyses of erectile function (EF) utilizing image-guided stereotactic prostate-confined RT in a rat model. Sixty young adult male rats aged 10-12 weeks old were divided into age-matched sham and RT groups. A single 20-Gy fraction to the prostate was delivered to RT animals. Penile bulb, shaft, and testes were excluded from treatment fields. Bioassay and intracavernous pressure (ICP) measurements were conducted at 2, 4, and 9 weeks following RT. Perfusion analysis of the corpora cavernosa (CC) was conducted using Hoechst injected prior to sacrifice. Penile shaft and cavernous nerve (CN) were evaluated by immunohistochemistry. Plasma testosterone level was analyzed using a testosterone enzyme-linked immunosorbent assay (ELISA) assay kit. Irradiated animals demonstrated statistically significant time-dependent functional impairment of EF by bioassay and ICP measurement from 4 weeks. Neuronal nitric oxide synthase (NOS) expression was decreased in CN by 4 weeks. In CC, expression levels of anti-alpha smooth muscle actin and endothelial NOS were significantly decreased at 9 weeks. In penile dorsal vessels, smooth muscle/collagen ratio was significantly decreased at 4 and 9 weeks. Additionally, Hoechst perfusion showed time-dependent decrease in CC of RT animals, whereas CD31 expression was not affected. No toxicities were noted; testosterone levels were similar in both groups. We demonstrated time-dependent ED following image-guided stereotactic RT. Our results imply that reduction of neuronal NOS expression in cavernous nerve could trigger consecutive reduction of smooth muscle content as well as blood perfusion in CC that resulted in corporal veno-occlusive dysfunction. Present study could be a cornerstone to future research that may bring comprehensive scientific understanding of radiation-induced ED. © 2011 International Society for Sexual Medicine.

Locally targeted delivery of a micron-size radiation therapy source using temperature-sensitive hydrogel.

PubMed

Kim, Yusung; Seol, Dong Rim; Mohapatra, Sucheta; Sunderland, John J; Schultz, Michael K; Domann, Frederick E; Lim, Tae-Hong

2014-04-01

To propose a novel radiation therapy (RT) delivery modality: locally targeted delivery of micron-size RT sources by using temperature-sensitive hydrogel (RT-GEL) as an injectable vehicle. Hydrogel is a water-like liquid at room temperature but gels at body temperature. Two US Food and Drug Administration-approved polymers were synthesized. Indium-111 (In-111) was used as the radioactive RT-GEL source. The release characteristics of In-111 from polymerized RT-GEL were evaluated. The injectability and efficacy of RT-GEL delivery to human breast tumor were tested using animal models with control datasets of RT-saline injection. As proof-of-concept studies, a total of 6 nude mice were tested by injecting 4 million tumor cells into their upper backs after a week of acclimatization. Three mice were injected with RT-GEL and 3 with RT-saline. Single-photon emission computed tomography (SPECT) and CT scans were performed on each mouse at 0, 24, and 48 h after injection. The efficacy of RT-GEL was determined by comparison with that of the control datasets by measuring kidney In-111 accumulation (mean nCi/cc), representing the distant diffusion of In-111. RT-GEL was successfully injected into the tumor by using a 30-gauge needle. No difficulties due to polymerization of hydrogel during injection and intratumoral pressure were observed during RT-GEL injection. No back flow occurred for either RT-GEL or RT-saline. The residual tumor activities of In-111 were 49% at 24 h (44% at 48 h, respectively) for RT-GEL and 29% (22%, respectively) for RT-saline. Fused SPECT-CT images of RT-saline showed considerable kidney accumulation of In-111 (2886%, 261%, and 262% of RT-GEL at 0, 24, and 48 h, respectively). RT-GEL was successfully injected and showed much higher residual tumor activity: 170% (200%, respectively), than that of RT-saline at 24 h (48 h, respectively) after injection with a minimal accumulation of In-111 to the kidneys. Preliminary data of RT-GEL as a delivery modality of a radiation source to a local tumor are promising. Published by Elsevier Inc.

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

Son, Christina H.; Law, Ethel; Oh, Jung Hun

Purpose: Although vaginal stenosis (VS) is a recognized toxicity in women who receive pelvic radiation therapy (RT), the relationship between RT dose and the volume and extent of toxicity has not been analyzed. We modeled this relationship to identify predictors of VS. Methods and Materials: We evaluated 54 women, aged 29 to 78 years, who underwent pelvic RT for rectal or anal cancer during 2008 to 2011 and were enrolled in a prospective study evaluating vaginal dilator use. Maximum dilator size was measured before RT (baseline) and 1 month and 12 months after RT. Dilator use was initiated at 1 month. The difference (D)more » in dilator size before and after RT was recorded. Those with D ≤−1 were classified as having VS (n=35); those with D ≥0 were classified as having no VS (n=19 at 1 month). Dose-volume parameters were extracted, and the generalized equivalent uniform dose (gEUD) was used to build a predictive model. Results: The mean vaginal doses were 50.0 Gy and 36.8 Gy for anal and rectal cancer patients, respectively. One month after RT, a gEUD model using a wide range of a values suggests that sparing of vaginal volume to a low dose may be important. When gEUD (a = −1) was <35 Gy and the mean vaginal dose was <43 Gy, severe VS was reduced (P=.02). A 1-year analysis suggests increasingly negative D values with increasing mean dose. However, patients with compliance <40% were more likely to have toxicity. Conclusions: Vaginal stenosis is influenced by multiple RT dose-volume characteristics. Mean dose and gEUD constraints together may reduce the risk of severe VS. Patients receiving higher mean vaginal doses should have greater compliance with dilator therapy to minimize risk of toxicity. Further validation with independent datasets is needed.« less

A Combination Microbicide Gel Protects Macaques Against Vaginal Simian Human Immunodeficiency Virus-Reverse Transcriptase Infection, But Only Partially Reduces Herpes Simplex Virus-2 Infection After a Single High-Dose Cochallenge

PubMed Central

Hsu, Mayla; Aravantinou, Meropi; Menon, Radhika; Seidor, Samantha; Goldman, Daniel; Kenney, Jessica; Derby, Nina; Gettie, Agegnehu; Blanchard, James; Piatak, Michael; Lifson, Jeffrey D.; Fernández-Romero, Jose A.; Zydowsky, Thomas M.

2014-01-01

Abstract Herpes simplex virus-2 (HSV-2) infection increases HIV susceptibility. We previously established a rhesus macaque model of vaginal HSV-2 preexposure followed by cochallenge with HSV-2 and simian/human immunodeficiency virus-reverse transcriptase (SHIV-RT). Using this model, we showed that a gel containing the nonnucleoside reverse transcriptase inhibitor (NNRTI) MIV-150 in carrageenan (CG) reduced SHIV-RT infection. To evaluate the efficacy of new generation microbicides against both viruses, we first established dual infection after single vaginal cochallenge with SHIV-RT and HSV-2 in HSV-2-naive macaques. All animals (6/6) became HSV-2 infected, with 4/6 coinfected with SHIV-RT. In a control group cochallenged with SHIV-RT and UV-inactivated HSV-2, 2/4 became SHIV-RT infected, and none had detectable HSV-2. Low-level HSV-2-specific antibody and T cell responses were detected in some HSV-2-infected animals. To test a CG gel containing MIV-150 and zinc acetate (MZC), which provided naive animals full protection from SHIV-RT for at least 8 h, MZC (vs. CG) was applied daily for 14 days followed by cochallenge 8 h later. MZC prevented SHIV-RT infection (0/9 infected, p=0.04 vs. 3/6 in CG controls), but only reduced HSV-2 infection by 20% (6/9 infected vs. 5/6 in CG, p=0.6). In HSV-2-infected animals, none of the gel-treated animals seroconverted, and only the CG controls had measurable HSV-2-specific T cell responses. This study shows the promise of MZC to prevent immunodeficiency virus infection (even in the presence of HSV-2) and reduce HSV-2 infection after exposure to a high-dose inoculum. Additionally, it demonstrates the potential of a macaque coinfection model to evaluate broad-spectrum microbicides. PMID:24117013

A combination microbicide gel protects macaques against vaginal simian human immunodeficiency virus-reverse transcriptase infection, but only partially reduces herpes simplex virus-2 infection after a single high-dose cochallenge.

PubMed

Hsu, Mayla; Aravantinou, Meropi; Menon, Radhika; Seidor, Samantha; Goldman, Daniel; Kenney, Jessica; Derby, Nina; Gettie, Agegnehu; Blanchard, James; Piatak, Michael; Lifson, Jeffrey D; Fernández-Romero, Jose A; Zydowsky, Thomas M; Robbiani, Melissa

2014-02-01

Herpes simplex virus-2 (HSV-2) infection increases HIV susceptibility. We previously established a rhesus macaque model of vaginal HSV-2 preexposure followed by cochallenge with HSV-2 and simian/human immunodeficiency virus-reverse transcriptase (SHIV-RT). Using this model, we showed that a gel containing the nonnucleoside reverse transcriptase inhibitor (NNRTI) MIV-150 in carrageenan (CG) reduced SHIV-RT infection. To evaluate the efficacy of new generation microbicides against both viruses, we first established dual infection after single vaginal cochallenge with SHIV-RT and HSV-2 in HSV-2-naive macaques. All animals (6/6) became HSV-2 infected, with 4/6 coinfected with SHIV-RT. In a control group cochallenged with SHIV-RT and UV-inactivated HSV-2, 2/4 became SHIV-RT infected, and none had detectable HSV-2. Low-level HSV-2-specific antibody and T cell responses were detected in some HSV-2-infected animals. To test a CG gel containing MIV-150 and zinc acetate (MZC), which provided naive animals full protection from SHIV-RT for at least 8 h, MZC (vs. CG) was applied daily for 14 days followed by cochallenge 8 h later. MZC prevented SHIV-RT infection (0/9 infected, p=0.04 vs. 3/6 in CG controls), but only reduced HSV-2 infection by 20% (6/9 infected vs. 5/6 in CG, p=0.6). In HSV-2-infected animals, none of the gel-treated animals seroconverted, and only the CG controls had measurable HSV-2-specific T cell responses. This study shows the promise of MZC to prevent immunodeficiency virus infection (even in the presence of HSV-2) and reduce HSV-2 infection after exposure to a high-dose inoculum. Additionally, it demonstrates the potential of a macaque coinfection model to evaluate broad-spectrum microbicides.

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.

Four years comparative follow-up evaluation of community-based, step-down, and residential specialist psychodynamic programmes for personality disorders.

PubMed

Chiesa, Marco; Cirasola, Antonella; Fonagy, Peter

2017-11-01

Although the fulcrum of service provision for personality disorder (PD) has shifted from hospital-based to psychodynamically- and cognitively-oriented outpatient programmes, very few studies have attempted to compare specialist moderate intensity outpatient programmes with specialist high-intensity residential models, or to explore whether a period of inpatient treatment may be necessary to improve outcome and prognosis. In this article, we prospectively compare changes over a 4-year period in 3 groups of patients with personality disorders (N = 162) treated in a specialist community-based (CBP, N = 30), a step-down (RT-CBP, N = 87), and a specialist residential programme (RT, N = 45) in psychiatric distress, deliberate self-injury, and suicide attempt using multilevel modelling and multivariate logistic regression analyses. The results showed that percentages of early-dropout were significantly different (p = .0001) for the 3 programmes (CBP = 13.4%, RT-CBP = 10.2%, and RT = 41.4%). A significant interaction between treatment model and time was found for psychiatric distress (p = .001), with CBP and RT-CBP achieving more marked changes (g = 1.20 and g = 0.68, respectively) compared to RT (g = 0.30) at 48-month follow-up. CBP and RT-CBP were found to significantly reduce impulsive behaviour (deliberate self-injury and suicide attempt) compared to RT. Severity of presentation was not found to be a significant predictor of outcome. Long-term RT showed no advantage over long-term CBP, either as stand-alone or as step-down treatment. Replication may be needed to confirm generalizability of results, and a number of limitations in the study design may moderate the inferences that can be drawn from the results. Copyright © 2017 John Wiley & Sons, Ltd.

Rayleigh-Taylor instability in an equal mass plasma

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

Adak, Ashish, E-mail: ashish-adak@yahoo.com; Ghosh, Samiran, E-mail: sran-g@yahoo.com; Chakrabarti, Nikhil, E-mail: nikhil.chakrabarti@saha.ac.in

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

Effects of urban microcellular environments on ray-tracing-based coverage predictions.

PubMed

Liu, Zhongyu; Guo, Lixin; Guan, Xiaowei; Sun, Jiejing

2016-09-01

The ray-tracing (RT) algorithm, which is based on geometrical optics and the uniform theory of diffraction, has become a typical deterministic approach of studying wave-propagation characteristics. Under urban microcellular environments, the RT method highly depends on detailed environmental information. The aim of this paper is to provide help in selecting the appropriate level of accuracy required in building databases to achieve good tradeoffs between database costs and prediction accuracy. After familiarization with the operating procedures of the RT-based prediction model, this study focuses on the effect of errors in environmental information on prediction results. The environmental information consists of two parts, namely, geometric and electrical parameters. The geometric information can be obtained from a digital map of a city. To study the effects of inaccuracies in geometry information (building layout) on RT-based coverage prediction, two different artificial erroneous maps are generated based on the original digital map, and systematic analysis is performed by comparing the predictions with the erroneous maps and measurements or the predictions with the original digital map. To make the conclusion more persuasive, the influence of random errors on RMS delay spread results is investigated. Furthermore, given the electrical parameters' effect on the accuracy of the predicted results of the RT model, the dielectric constant and conductivity of building materials are set with different values. The path loss and RMS delay spread under the same circumstances are simulated by the RT prediction model.

Use of alternative alkali chlorides in RT and PCR of polynucleotides containing G quadruplex structures.

PubMed

Ramos-Alemán, Fabiola; González-Jasso, Eva; Pless, Reynaldo C

2018-02-15

Several alkali chlorides were compared for their use in reverse transcription (RT) and PCR of different types of nucleic acid templates. On a test region of biological DNA incapable of forming G quadruplex (G4) structures, Taq DNA polymerase showed similar PCR performance with 50 mM KCl, CsCl, LiCl, and NaCl. In contrast, on a synthetic model polydeoxyribonucleotide prone to G4 formation, good PCR amplification was obtained with 50 mM CsCl, but little or none with LiCl or KCl. Similarly, in RT of a G4-prone model polyribonucleotide, MMLV reverse transcriptase produced a good yield with 50 mM CsCl, mediocre yields with LiCl or without added alkali chloride, and a poor yield with 50 mM KCl. The full RT-PCR assay starting from the G4-prone polyribonucleotide, showed good results with CsCl in both stages, poor results with LiCl, and no product formation with KCl. The model polynucleotides showed fast G quadruplex formation under PCR or RT conditions with 50 mM KCl, but not with CsCl or LiCl. The results argue for the use of CsCl instead of KCl for RT and PCR of G4-prone sequences. No advantage was observed when using the 7-deaza type nucleotide analog c 7 dGTP in PCR amplification of the G4-prone polydeoxyribonucleotide. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Dose-Dependent Cortical Thinning After Partial Brain Irradiation in High-Grade Glioma

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

Karunamuni, Roshan; Bartsch, Hauke; White, Nathan S.

Purpose: Radiation-induced cognitive deficits may be mediated by tissue damage to cortical regions. Volumetric changes in cortex can be reliably measured using high-resolution magnetic resonance imaging (MRI). We used these methods to study the association between radiation therapy (RT) dose and change in cortical thickness in high-grade glioma (HGG) patients. Methods and Materials: We performed a voxel-wise analysis of MRI from 15 HGG patients who underwent fractionated partial brain RT. Three-dimensional MRI was acquired pre- and 1 year post RT. Cortex was parceled with well-validated segmentation software. Surgical cavities were censored. Each cortical voxel was assigned a change in cortical thicknessmore » between time points, RT dose value, and neuroanatomic label by lobe. Effects of dose, neuroanatomic location, age, and chemotherapy on cortical thickness were tested using linear mixed effects (LME) modeling. Results: Cortical atrophy was seen after 1 year post RT with greater effects at higher doses. Estimates from LME modeling showed that cortical thickness decreased by −0.0033 mm (P<.001) for every 1-Gy increase in RT dose. Temporal and limbic cortex exhibited the largest changes in cortical thickness per Gy compared to that in other regions (P<.001). Age and chemotherapy were not significantly associated with change in cortical thickness. Conclusions: We found dose-dependent thinning of the cerebral cortex, with varying neuroanatomical regional sensitivity, 1 year after fractionated partial brain RT. The magnitude of thinning parallels 1-year atrophy rates seen in neurodegenerative diseases and may contribute to cognitive decline following high-dose RT.« less

Annual Research Review: Reaction time variability in ADHD and autism spectrum disorders: measurement and mechanisms of a proposed trans-diagnostic phenotype

PubMed Central

Karalunas, Sarah L.; Geurts, Hilde M.; Konrad, Kerstin; Bender, Stephan; Nigg, Joel T.

2014-01-01

Background Intraindividual variability in reaction time (RT) has received extensive discussion as an indicator of cognitive performance, a putative intermediate phenotype of many clinical disorders, and a possible trans-diagnostic phenotype that may elucidate shared risk factors for mechanisms of psychiatric illnesses. Scope and Methodology Using the examples of attention deficit hyperactivity disorder (ADHD) and autism spectrum disorders (ASD), we discuss RT variability. We first present a new meta-analysis of RT variability in ASD with and without comorbid ADHD. We then discuss potential mechanisms that may account for RT variability and statistical models that disentangle the cognitive processes affecting RTs. We then report a second meta-analysis comparing ADHD and non-ADHD children on diffusion model parameters. We consider how findings inform the search for neural correlates of RT variability. Findings Results suggest that RT variability is increased in ASD only when children with comorbid ADHD are included in the sample. Furthermore, RT variability in ADHD is explained by moderate to large increases (d = 0.63–0.99) in the ex-Gaussian parameter τ and the diffusion parameter drift rate, as well as by smaller differences (d = 0.32) in the diffusion parameter of nondecision time. The former may suggest problems in state regulation or arousal and difficulty detecting signal from noise, whereas the latter may reflect contributions from deficits in motor organization or output. The neuroimaging literature converges with this multicomponent interpretation and also highlights the role of top-down control circuits. Conclusion We underscore the importance of considering the interactions between top-down control, state regulation (e.g. arousal), and motor preparation when interpreting RT variability and conclude that decomposition of the RT signal provides superior interpretive power and suggests mechanisms convergent with those implicated using other cognitive paradigms. We conclude with specific recommendations for the field for next steps in the study of RT variability in neurodevelopmental disorders. PMID:24628425

A Ballistic Model of Choice Response Time

ERIC Educational Resources Information Center

Brown, Scott; Heathcote, Andrew

2005-01-01

Almost all models of response time (RT) use a stochastic accumulation process. To account for the benchmark RT phenomena, researchers have found it necessary to include between-trial variability in the starting point and/or the rate of accumulation, both in linear (R. Ratcliff & J. N. Rouder, 1998) and nonlinear (M. Usher & J. L. McClelland, 2001)…

Enceladus-Mimas paradox: a result of different early evolutions of satellites?

NASA Astrophysics Data System (ADS)

Czechowski, Leszek; Witek, Piotr

2015-04-01

Summary: Thermal history of Mimas and Enceladus is investigated from the beginning of accretion to 400 Myr. The following heat sources are included: short lived and long lived radioactive isotopes, accretion, serpentinization, and phase changes. We find that temperature of Mimas' interior was significantly lower than of Enceladus. Comparison of thermal models of Mimas and Enceladus indicates that conditions favorable for starting tidal heating lasted for short time (~107yr) in Mimas and for ~108 yr in Enceladus. This could explain Mimas-Enceladus paradox. 1. Numerical model: In our calculations we use numerical model developed by Czechowski (2012) (see e.g. description in [1]). The model is based on parameterized theory of convection combined with 1-dimensional equation of the heat transfer in spherical coordinates: δT(r,t)- ρcp δt = div(k(r,T ) gradT (r,t))+ Q(r,T), where r is the radial distance (spherical coordinate), ρ is the density [kg m-3], cp [J kg1 K-1 ] is the specific heat, Q [W kg-1] is the heating rate, and k[W m-1 K-1] is the thermal conductivity. Q(r,t) includes sources and sinks of the heat. The equation is solved in time dependent region [0, R(t)]. During accretion the radius R(t) increases in time according to formula: R(t) = atfor tini tac , i.e. after the accretion (see e.g. [2]), where tinidenotes beginning of accretion and tac denotes duration of this process. If the Rayleigh number in the considered layer exceeds its critical value Racr then convection starts. It leads to effective heat transfer. The full description of convection is given by a velocity field and temperature distribution. However, we are interested in convection as a process of heat transport only. For solid state convection (SSC) heat transport can be described by dimensionless Nusselt number Nu. We use the following definition of the Nu: Nu= (True total surface heat flow)/(Total heat flow without convection). The heat transport by SSC is modelled simply by multiplying the coefficient of the heat conduction in the considered layer, i.e.: kconv =Nu k. This approach is used successfully in parameterized theory of convection for SSC in the Earth and other planets (e.g. [3], [4]). Parameterization of liquid state convection (LSC) is even simpler. Ra in molten region is very high (usually higher than 1016). The LSC could be very intensive resulting in almost adiabatic temperature gradient given by: dT-= gαmT-, dr cpm where αm and cpm are thermal expansion coefficient and specific heat in molten region, g is the local gravity. In Enceladus and Mimas the adiabatic gradient is low and therefore LSC region is almost isothermal. 2. Results: Comparison of thermal models of Mimas and Enceladus indicates that conditions favorable for starting tidal heating (interior hot enough) lasted for short time (~107yr) in Mimas and for ~108 yr in Enceladus. This could explain Mimas-Enceladus paradox. 3. Conclusions: The Mimas-Enceladus paradox is probably the result of short time when Mimas was hot enough to allow for substantial tidal heating. The Mimas-Tethys resonance formed later when Mimas was already cool. (see also [1, 4]) The full text of the paper will be published in Acta Geophysica [5]. Acknowledgements: The research is partly supported by National Science Centre (grant 2011/ 01/ B/ ST10/06653). References : [1] Czechowski, L. (2014) Some remarks on the early evolution of Enceladus. Planet. Sp. Sc. 104, 185-199. [2] Merk, R., Breuer, D., Spohn, T. (2002). Numerical modeling of 26Al induced radioactive melting of asteroids concerning accretion. Icarus 199, 183-191. [3] Sharpe, H.N., Peltier, W.R., (1978) Parameterized mantle convection and the Earth's thermal history. Geophys. Res. Lett. 5, 737-740. [4] Czechowski, L. (2006) Parameterized model of convection driven by tidal and radiogenic heating. Adv. Space Res. 38, 788-793. [5] Czechowski, L., Witek, P. (2015) Comparisons of early evolutions of Mimas and Enceladus. Submitted to Acta Geophysica.

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.

Massive star formation at high spatial resolution

NASA Astrophysics Data System (ADS)

Pascucci, Ilaria

2004-05-01

This thesis studies the early phases of massive stars and their impact on the surrounding. The capabilities of continuum radiative transfer (RT) codes to interpret the observations are also investigated. The main results of this work are: 1) Two massive star-forming regions are observed in the infrared. The thermal emission from the ultra-compact H II regions is resolved and the spectral type of the ionizing stars is estimated. The hot cores are not detected thus implying line-of-sight extinction larger than 200 visual magnitude. 2) The first mid-infrared interferometric measurements towards a young massive star resolve thermal emission on scales of 30-50 AU probing the size of the predicted disk. The visibility curve differs from those of intermediate-mass stars. 3) The close vicinity of Θ1C Ori are imaged using the NACO adaptive optics system. The binary proplyd Orion 168-326 and its interaction with the wind from Θ1C Ori are resolved. A proplyd uniquely seen face-on is also identified. 4) Five RT codes are compared in a disk configuration. The solutions provide the first 2D benchmark and serve to test the reliability of other RT codes. The images/visibilities from two RT codes are compared for a distorted disk. The parameter range in which such a distortion is detectable with MIDI is explored.

Laboratory demonstrations of superconducting gravity and inertial sensors for space and airborne gravity measurements

NASA Technical Reports Server (NTRS)

Paik, Ho J.; Canavan, Edgar R.; Kong, Qin; Moody, M. V.

1992-01-01

The paper describes the superconducting gravity gradiometers (SGGs) and superconducting accelerometers being developed at the University of Maryland, which take advantage of many exotic properties of superconductivity to obtain the required low noise, high stability, and large dynamic range. Results of laboratory demonstrations of some of these instruments are presented together with the design and operating principles. Particular attention is given to the three-axis Model II SGG and a six-axis superconducting accelerometer model (Model I SSA). Model II SGG, after a residual common-mode balance, exhibited a noise level of 0.05/sq rt Hz above 0.1 Hz and a 1/f-squared noise below 0.1 Hz. All six channels of Model I SSA operated simultaneously with linear and angular acceleration noise levels of 3 x 10 exp -10 g(E)/sq rt Hz and 5 x 10 exp -8 rad/sec per sec per sq rt Hz, respectively.

The structure and health correlates of trait repetitive thought in older adults.

PubMed

Segerstrom, Suzanne C; Roach, Abbey R; Evans, Daniel R; Schipper, Lindsey J; Darville, Audrey K

2010-09-01

Repetitive thought (RT) involves frequent or prolonged thoughts about oneself and one's world, encompassing discrete forms such as trait worry, rumination, processing, and reminiscing. These forms of RT can be described using 3 basic, underlying qualities: total propensity for RT of all types, valence (positive vs. negative content), and purpose (searching or uncertainty vs. solving or certainty). The adaptiveness of discrete forms with regard to health is likely to be related to these qualities, particularly valence and total propensity. The present study confirmed the model and identified the relationship of these qualities of RT to subjective psychological, physical, and cognitive health in older adults aged 60-94 (N = 179). As predicted, more negatively valenced trait RT was associated with worse psychological, physical, and cognitive health. More total propensity for RT was associated only with worse psychological health. Searching purpose was associated only with worse cognitive health. In turn, negatively valenced RT was predicted by poorer executive functions, suggesting that such functions may be important for directing this quality of RT. The valence of older adults' RT is important insofar as it may contribute to their sense of good or ill health. However, the propensity for all kinds of RT to associate with poorer psychological health may reflect the co-occurrence of negative and positive RT, such as rumination and emotional processing. Although RT has not been extensively investigated in older adults, it appears to play an important role in their subjective health. (c) 2010 APA, all rights reserved.

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.

Identification of rhizome-specific genes by genome-wide differential expression analysis in Oryza longistaminata.

PubMed

Hu, Fengyi; Wang, Di; Zhao, Xiuqin; Zhang, Ting; Sun, Haixi; Zhu, Linghua; Zhang, Fan; Li, Lijuan; Li, Qiong; Tao, Dayun; Fu, Binying; Li, Zhikang

2011-01-24

Rhizomatousness is a key component of perenniality of many grasses that contribute to competitiveness and invasiveness of many noxious grass weeds, but can potentially be used to develop perennial cereal crops for sustainable farmers in hilly areas of tropical Asia. Oryza longistaminata, a perennial wild rice with strong rhizomes, has been used as the model species for genetic and molecular dissection of rhizome development and in breeding efforts to transfer rhizome-related traits into annual rice species. In this study, an effort was taken to get insights into the genes and molecular mechanisms underlying the rhizomatous trait in O. longistaminata by comparative analysis of the genome-wide tissue-specific gene expression patterns of five different tissues of O. longistaminata using the Affymetrix GeneChip Rice Genome Array. A total of 2,566 tissue-specific genes were identified in five different tissues of O. longistaminata, including 58 and 61 unique genes that were specifically expressed in the rhizome tips (RT) and internodes (RI), respectively. In addition, 162 genes were up-regulated and 261 genes were down-regulated in RT compared to the shoot tips. Six distinct cis-regulatory elements (CGACG, GCCGCC, GAGAC, AACGG, CATGCA, and TAAAG) were found to be significantly more abundant in the promoter regions of genes differentially expressed in RT than in the promoter regions of genes uniformly expressed in all other tissues. Many of the RT and/or RI specifically or differentially expressed genes were located in the QTL regions associated with rhizome expression, rhizome abundance and rhizome growth-related traits in O. longistaminata and thus are good candidate genes for these QTLs. The initiation and development of the rhizomatous trait in O. longistaminata are controlled by very complex gene networks involving several plant hormones and regulatory genes, different members of gene families showing tissue specificity and their regulated pathways. Auxin/IAA appears to act as a negative regulator in rhizome development, while GA acts as the activator in rhizome development. Co-localization of the genes specifically expressed in rhizome tips and rhizome internodes with the QTLs for rhizome traits identified a large set of candidate genes for rhizome initiation and development in rice for further confirmation.

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

Numerical modelling of phase-change material used for PV panels cooling

NASA Astrophysics Data System (ADS)

Sellami, Assia; Elotmani, Rabie; Kandoussi, Khalid; Eljouad, Mohamed; Hajjaji, Abdelowahed; Boutaous, M'Hamed

2017-12-01

Passive cooling of a PV solar panel using phase-change material (PCM) may play an important role in increasing efficiency of PV cells. Because it does not need a maintenance and does not release greenhouses gases, PCM seems to be a good way to decrease the among of overheating of PV cell. The aims of this paper describes a detailed multiphysical issue in order to understand the effect of PCM (RT25) in keeping PV cell temperature close to ambient. The study is focused on modeling the heat and mass transfer in a PCM domain by modifying the buoyancy term in momentum equation. Due to a phase-change and free convection, transient incompressible flow is taken into account to explain the dynamic variations of the velocity profile and viscosity distribution. With standard condition of irradiation and heat flux on both sides of the PV panel, a melt front has been tracked by the energy equation, which gives a good argument for the temperature evolution during phase-change.

Cell-phone vs microphone recordings: Judging emotion in the voice.

PubMed

Green, Joshua J; Eigsti, Inge-Marie

2017-09-01

Emotional states can be conveyed by vocal cues such as pitch and intensity. Despite the ubiquity of cellular telephones, there is limited information on how vocal emotional states are perceived during cell-phone transmissions. Emotional utterances (neutral, happy, angry) were elicited from two female talkers and simultaneously recorded via microphone and cell-phone. Ten-step continua (neutral to happy, neutral to angry) were generated using the straight algorithm. Analyses compared reaction time (RT) and emotion judgment as a function of recording type (microphone vs cell-phone). Logistic regression revealed no judgment differences between recording types, though there were interactions with emotion type. Multi-level model analyses indicated that RT data were best fit by a quadratic model, with slower RT at the middle of each continuum, suggesting greater ambiguity, and slower RT for cell-phone stimuli across blocks. While preliminary, results suggest that critical acoustic cues to emotion are largely retained in cell-phone transmissions, though with effects of recording source on RT, and support the methodological utility of collecting speech samples by phone.

Prostate Cancer Radiation Therapy and Risk of Thromboembolic Events

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

Bosco, Cecilia, E-mail: Cecilia.t.bosco@kcl.ac.uk; Garmo, Hans; Regional Cancer Centre, Uppsala, Akademiska Sjukhuset, Uppsala

Purpose: To investigate the risk of thromboembolic disease (TED) after radiation therapy (RT) with curative intent for prostate cancer (PCa). Patients and Methods: We identified all men who received RT as curative treatment (n=9410) and grouped according to external beam RT (EBRT) or brachytherapy (BT). By comparing with an age- and county-matched comparison cohort of PCa-free men (n=46,826), we investigated risk of TED after RT using Cox proportional hazard regression models. The model was adjusted for tumor characteristics, demographics, comorbidities, PCa treatments, and known risk factors of TED, such as recent surgery and disease progression. Results: Between 2006 and 2013, 6232more » men with PCa received EBRT, and 3178 underwent BT. A statistically significant association was found between EBRT and BT and risk of pulmonary embolism in the crude analysis. However, upon adjusting for known TED risk factors these associations disappeared. No significant associations were found between BT or EBRT and deep venous thrombosis. Conclusion: Curative RT for prostate cancer using contemporary methodologies was not associated with an increased risk of TED.« less

Generation and Characterization of Transgenic Mice Expressing Mouse Ins1 Promoter for Pancreatic β-Cell-Specific Gene Overexpression and Knockout.

PubMed

Cheng, Yulong; Su, Yutong; Shan, Aijing; Jiang, Xiuli; Ma, Qinyun; Wang, Weiqing; Ning, Guang; Cao, Yanan

2015-07-01

The technologies for pancreatic β-cell-specific gene overexpression or knockout are fundamental for investigations of functional genes in vivo. Here we generated the Ins1-Cre-Dsred and Ins1-rtTA mouse models, which expressed the Cre recombinase or reverse tetracycline regulatable transactivator (rtTA) without hGH minigene under the control of mouse Ins1 promoter. Our data showed that the Cre-mediated recombination and rtTA-mediated activation could be efficiently detected at embryonic day 13.5 when these models were crossed with the reporter mice (ROSA(mT/mG) or tetO-HIST1H2BJ/GFP). The Cre and rtTA expression was restricted to β-cells without leakage in the brain and other tissues. Moreover, both the transgenic lines showed normal glucose tolerance and insulin secretion. These results suggested that the Ins1-Cre-Dsred and Ins1-rtTA mice could be used to knock out or overexpress target genes in embryos and adults to facilitate β-cell researches.

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.

Management Trends and Outcomes for Stage I to II Mantle Cell Lymphoma Using the National Cancer Data Base: Ascertaining the Ideal Treatment Paradigm

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

Gill, Beant S.; Vargo, John A.; Pai, Sarah S.

Purpose: Mantle cell lymphoma (MCL) is a rare, albeit aggressive subset of non-Hodgkin lymphoma, resulting in varied treatment approaches. Given the paucity of data defining the optimal management for early-stage MCL, we conducted an analysis using the National Cancer Data Base (NCDB) to identify practice patterns and outcomes. Methods and Materials: The NCDB was queried for patients with stage I to II MCL diagnosed from 1998 to 2012 receiving chemotherapy (CT) or radiation therapy (RT), or both (CT+RT). Univariate and multivariable analyses for factors associated with treatment selection were completed using logistic regression. Propensity scores with inverse probability treatment weightingmore » (IPTW) were calculated based on the conditional probability of receiving CT+RT. The log-rank test and Cox proportional hazards modeling with IPTW adjustment were conducted for the survival analyses. Results: In total, 2539 patients were identified. The key characteristics were as follows: 69% were male, 71% were aged ≥60 years, 28% had extranodal involvement, and 51% had stage I disease. Of the 2539 patients, 70% underwent CT, 11% underwent RT, and 19% underwent CT+RT. The use of CT+RT decreased from 23.1% to 14.1% in 1998 to 2002 and 2010 to 2012 (P<.001). CT+RT usage was lower for patients with the following characteristics: age ≥60 years, female sex, stage II disease, and the presence of B symptoms. With a median follow-up period of 42.8 months, the unadjusted 3-year overall survival estimates for patients receiving CT, RT, or CT+RT were 67.8%, 72.4%, and 79.8%, respectively (P<.001). After correcting for indication bias through IPTW-adjusted modeling, CT+RT reduced the risk of overall mortality compared with monotherapy (hazard ratio 0.65, P=.029). Conclusions: Although uncommon, patients with stage I-II MCL can have favorable outcomes. Despite a continued decline in the usage of consolidative RT, combined modality therapy improves survival in this cohort compared with monotherapy.« less

A domestic porcine model for studying the effects of radiation on head and neck cancers.

PubMed

Arnold, Christoph R; Kloss, Frank; Singh, Sarvpreet; Vasiljevic, Danijela; Stigler, Robert; Auberger, Thomas; Wenzel, Volker; Klima, Günter; Lukas, Peter; Lepperdinger, Günter; Gassner, Robert

2017-05-01

Radiation therapy (RT) of the head and neck region is often accompanied by serious side effects. Research in this area is needed to improve treatment outcomes and ameliorate therapy tolerance. Laboratory rodents are barely matching today's clinical standards in RT research. Yet domestic swine (Sus scrofa domestica) have previously proved suitable for various advanced tests in clinical research and training. We therefore investigated whether S. scrofa domestica is also appropriate for irradiation of the mandible. A common scheme for irradiation treatment of S. scrofa domestica mandibles in a split-mouth design was acquired by applying computed tomography (CT) scanning under sedation. Basing on close anatomic resemblance, a standard treatment plan comprising 2 opposed irradiation fields could be accomplished. RT was carried out in a clinical environment with 2 × 9 Gy. The resulting operating procedure facilitated complication-free sedation, transport, positioning, CT scanning, and effective irradiation. Based on common standards applied for RT in humans, domestic pigs can be employed to progress RT clinical research. Due to their human-like anatomy, physiology, size, and weight, the swine model is expedient for advancing experimental RT of the head and neck area. Copyright © 2016 Elsevier Inc. All rights reserved.

NASA SPoRT Initialization Datasets for Local Model Runs in the Environmental Modeling System

NASA Technical Reports Server (NTRS)

Case, Jonathan L.; LaFontaine, Frank J.; Molthan, Andrew L.; Carcione, Brian; Wood, Lance; Maloney, Joseph; Estupinan, Jeral; Medlin, Jeffrey M.; Blottman, Peter; Rozumalski, Robert A.

2011-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center has developed several products for its National Weather Service (NWS) partners that can be used to initialize local model runs within the Weather Research and Forecasting (WRF) Environmental Modeling System (EMS). These real-time datasets consist of surface-based information updated at least once per day, and produced in a composite or gridded product that is easily incorporated into the WRF EMS. The primary goal for making these NASA datasets available to the WRF EMS community is to provide timely and high-quality information at a spatial resolution comparable to that used in the local model configurations (i.e., convection-allowing scales). The current suite of SPoRT products supported in the WRF EMS include a Sea Surface Temperature (SST) composite, a Great Lakes sea-ice extent, a Greenness Vegetation Fraction (GVF) composite, and Land Information System (LIS) gridded output. The SPoRT SST composite is a blend of primarily the Moderate Resolution Imaging Spectroradiometer (MODIS) infrared and Advanced Microwave Scanning Radiometer for Earth Observing System data for non-precipitation coverage over the oceans at 2-km resolution. The composite includes a special lake surface temperature analysis over the Great Lakes using contributions from the Remote Sensing Systems temperature data. The Great Lakes Environmental Research Laboratory Ice Percentage product is used to create a sea-ice mask in the SPoRT SST composite. The sea-ice mask is produced daily (in-season) at 1.8-km resolution and identifies ice percentage from 0 100% in 10% increments, with values above 90% flagged as ice.

Operations research for resource planning and -use in radiotherapy: a literature review.

PubMed

Vieira, Bruno; Hans, Erwin W; van Vliet-Vroegindeweij, Corine; van de Kamer, Jeroen; van Harten, Wim

2016-11-25

The delivery of radiotherapy (RT) involves the use of rather expensive resources and multi-disciplinary staff. As the number of cancer patients receiving RT increases, timely delivery becomes increasingly difficult due to the complexities related to, among others, variable patient inflow, complex patient routing, and the joint planning of multiple resources. Operations research (OR) methods have been successfully applied to solve many logistics problems through the development of advanced analytical models for improved decision making. This paper presents the state of the art in the application of OR methods for logistics optimization in RT, at various managerial levels. A literature search was performed in six databases covering several disciplines, from the medical to the technical field. Papers included in the review were published in peer-reviewed journals from 2000 to 2015. Data extraction includes the subject of research, the OR methods used in the study, the extent of implementation according to a six-stage model and the (potential) impact of the results in practice. From the 33 papers included in the review, 18 addressed problems related to patient scheduling (of which 12 focus on scheduling patients on linear accelerators), 8 focus on strategic decision making, 5 on resource capacity planning, and 2 on patient prioritization. Although calculating promising results, none of the papers reported a full implementation of the model with at least a thorough pre-post performance evaluation, indicating that, apart from possible reporting bias, implementation rates of OR models in RT are probably low. The literature on OR applications in RT covers a wide range of approaches from strategic capacity management to operational scheduling levels, and shows that considerable benefits in terms of both waiting times and resource utilization are likely to be achieved. Various fields can be further developed, for instance optimizing the coordination between the available capacity of different imaging devices or developing scheduling models that consider the RT chain of operations as a whole rather than the treatment machines alone.

Evidence of common and separate eye and hand accumulators underlying flexible eye-hand coordination

PubMed Central

Jana, Sumitash; Gopal, Atul

2016-01-01

Eye and hand movements are initiated by anatomically separate regions in the brain, and yet these movements can be flexibly coupled and decoupled, depending on the need. The computational architecture that enables this flexible coupling of independent effectors is not understood. Here, we studied the computational architecture that enables flexible eye-hand coordination using a drift diffusion framework, which predicts that the variability of the reaction time (RT) distribution scales with its mean. We show that a common stochastic accumulator to threshold, followed by a noisy effector-dependent delay, explains eye-hand RT distributions and their correlation in a visual search task that required decision-making, while an interactive eye and hand accumulator model did not. In contrast, in an eye-hand dual task, an interactive model better predicted the observed correlations and RT distributions than a common accumulator model. Notably, these two models could only be distinguished on the basis of the variability and not the means of the predicted RT distributions. Additionally, signatures of separate initiation signals were also observed in a small fraction of trials in the visual search task, implying that these distinct computational architectures were not a manifestation of the task design per se. Taken together, our results suggest two unique computational architectures for eye-hand coordination, with task context biasing the brain toward instantiating one of the two architectures. NEW & NOTEWORTHY Previous studies on eye-hand coordination have considered mainly the means of eye and hand reaction time (RT) distributions. Here, we leverage the approximately linear relationship between the mean and standard deviation of RT distributions, as predicted by the drift-diffusion model, to propose the existence of two distinct computational architectures underlying coordinated eye-hand movements. These architectures, for the first time, provide a computational basis for the flexible coupling between eye and hand movements. PMID:27784809

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

Swanson, K; Corwin, D; Rockne, R

Purpose: To demonstrate a method of generating patient-specific, biologically-guided radiation therapy (RT) plans and to quantify and predict response to RT in glioblastoma. We investigate the biological correlates and imaging physics driving T2-MRI based response to radiation therapy using an MRI simulator. Methods: We have integrated a patient-specific biomathematical model of glioblastoma proliferation, invasion and radiotherapy with a multiobjective evolutionary algorithm for intensity-modulated RT optimization to construct individualized, biologically-guided plans. Patient-individualized simulations of the standard-of-care and optimized plans are compared in terms of several biological metrics quantified on MRI. An extension of the PI model is used to investigate themore » role of angiogenesis and its correlates in glioma response to therapy with the Proliferation-Invasion-Hypoxia- Necrosis-Angiogenesis model (PIHNA). The PIHNA model is used with a brain tissue phantom to predict tumor-induced vasogenic edema, tumor and tissue density that is used in a multi-compartmental MRI signal equation for generation of simulated T2- weighted MRIs. Results: Applying a novel metric of treatment response (Days Gained) to the patient-individualized simulation results predicted that the optimized RT plans would have a significant impact on delaying tumor progression, with Days Gained increases from 21% to 105%. For the T2- MRI simulations, initial validation tests compared average simulated T2 values for white matter, tumor, and peripheral edema to values cited in the literature. Simulated results closely match the characteristic T2 value for each tissue. Conclusion: Patient-individualized simulations using the combination of a biomathematical model with an optimization algorithm for RT generated biologically-guided doses that decreased normal tissue dose and increased therapeutic ratio with the potential to improve survival outcomes for treatment of glioblastoma. Simulated T2-MRI is shown to be consistent with known physics of MRI and can be used to further investigate biological drivers of imaging-based response to RT.« less

Modeling Individual Differences in Response Time and Accuracy in Numeracy

PubMed Central

Ratcliff, Roger; Thompson, Clarissa A.; McKoon, Gail

2015-01-01

In the study of numeracy, some hypotheses have been based on response time (RT) as a dependent variable and some on accuracy, and considerable controversy has arisen about the presence or absence of correlations between RT and accuracy, between RT or accuracy and individual differences like IQ and math ability, and between various numeracy tasks. In this article, we show that an integration of the two dependent variables is required, which we accomplish with a theory-based model of decision making. We report data from four tasks: numerosity discrimination, number discrimination, memory for two-digit numbers, and memory for three-digit numbers. Accuracy correlated across tasks, as did RTs. However, the negative correlations that might be expected between RT and accuracy were not obtained; if a subject was accurate, it did not mean that they were fast (and vice versa). When the diffusion decision-making model was applied to the data (Ratcliff, 1978), we found significant correlations across the tasks between the quality of the numeracy information (drift rate) driving the decision process and between the speed/ accuracy criterion settings, suggesting that similar numeracy skills and similar speed-accuracy settings are involved in the four tasks. In the model, accuracy is related to drift rate and RT is related to speed-accuracy criteria, but drift rate and criteria are not related to each other across subjects. This provides a theoretical basis for understanding why negative correlations were not obtained between accuracy and RT. We also manipulated criteria by instructing subjects to maximize either speed or accuracy, but still found correlations between the criteria settings between and within tasks, suggesting that the settings may represent an individual trait that can be modulated but not equated across subjects. Our results demonstrate that a decision-making model may provide a way to reconcile inconsistent and sometimes contradictory results in numeracy research. PMID:25637690

Significant inconsistency of vegetation carbon density in CMIP5 Earth system models against observational data: Vegetation Carbon Density in ESMs

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

Song, Xia; Hoffman, Forrest M.; Iversen, Colleen M.

Earth system models (ESMs) have been widely used for projecting global vegetation carbon dynamics, yet how well ESMs performed for simulating vegetation carbon density remains untested. Here we have compiled observational data of vegetation carbon density from literature and existing data sets to evaluate nine ESMs at site, biome, latitude, and global scales. Three variables—root (including fine and coarse roots), total vegetation carbon density, and the root:total vegetation carbon ratios (R/T ratios), were chosen for ESM evaluation. ESM models performed well in simulating the spatial distribution of carbon densities in root (r = 0.71) and total vegetation (r = 0.62).more » However, ESM models had significant biases in simulating absolute carbon densities in root and total vegetation biomass across the majority of land ecosystems, especially in tropical and arctic ecosystems. Particularly, ESMs significantly overestimated carbon density in root (183%) and total vegetation biomass (167%) in climate zones of 10°S–10°N. Substantial discrepancies between modeled and observed R/T ratios were found: the R/T ratios from ESMs were relatively constant, approximately 0.2 across all ecosystems, along latitudinal gradients, and in tropic, temperate, and arctic climatic zones, which was significantly different from the observed large variations in the R/T ratios (0.1–0.8). There were substantial inconsistencies between ESM-derived carbon density in root and total vegetation biomass and the R/T ratio at multiple scales, indicating urgent needs for model improvements on carbon allocation algorithms and more intensive field campaigns targeting carbon density in all key vegetation components.« less

Significant inconsistency of vegetation carbon density in CMIP5 Earth system models against observational data: Vegetation Carbon Density in ESMs

DOE PAGES

Song, Xia; Hoffman, Forrest M.; Iversen, Colleen M.; ...

2017-09-09

Earth system models (ESMs) have been widely used for projecting global vegetation carbon dynamics, yet how well ESMs performed for simulating vegetation carbon density remains untested. Here we have compiled observational data of vegetation carbon density from literature and existing data sets to evaluate nine ESMs at site, biome, latitude, and global scales. Three variables—root (including fine and coarse roots), total vegetation carbon density, and the root:total vegetation carbon ratios (R/T ratios), were chosen for ESM evaluation. ESM models performed well in simulating the spatial distribution of carbon densities in root (r = 0.71) and total vegetation (r = 0.62).more » However, ESM models had significant biases in simulating absolute carbon densities in root and total vegetation biomass across the majority of land ecosystems, especially in tropical and arctic ecosystems. Particularly, ESMs significantly overestimated carbon density in root (183%) and total vegetation biomass (167%) in climate zones of 10°S–10°N. Substantial discrepancies between modeled and observed R/T ratios were found: the R/T ratios from ESMs were relatively constant, approximately 0.2 across all ecosystems, along latitudinal gradients, and in tropic, temperate, and arctic climatic zones, which was significantly different from the observed large variations in the R/T ratios (0.1–0.8). There were substantial inconsistencies between ESM-derived carbon density in root and total vegetation biomass and the R/T ratio at multiple scales, indicating urgent needs for model improvements on carbon allocation algorithms and more intensive field campaigns targeting carbon density in all key vegetation components.« less

Comparative lytic efficacy of rt-PA and ultrasound in porcine versus human clots

PubMed Central

Shekhar, Himanshu; Holland, Christy K.

2017-01-01

Introduction Porcine thrombi are employed routinely in preclinical models of ischemic stroke. In this study, we examined the differential lytic susceptibility of porcine and human whole blood clots with and without the use of microbubbles and ultrasound (US) as an adjuvant. Materials and methods An in vitro system equipped with time-lapse microscopy was used to evaluate recombinant tissue-plasminogen activator (rt-PA) lysis of porcine and human clots in the same species or cross species plasma. Human and porcine whole blood clots were treated with rt-PA and an echo contrast agent, Definity®, and exposed to intermittent 120 kHz US. Results and conclusions The rt-PA lytic efficacy observed for porcine clots in porcine plasma was 22 times lower than for human clots in human plasma reported previously. Further, porcine clots did not exhibit increased lysis with adjuvant Definity® and US exposure. However, the rt-PA lytic susceptibility of the porcine clots in human plasma was similar to that of human clots in human plasma. Human clots perfused with porcine plasma did not respond to rt-PA, but adjuvant use of Definity® and US enhanced lysis. These results reveal considerable differences in lytic susceptibility of porcine clots and human clots to rt-PA. The use of porcine clot models to test new human thrombolytic therapies may necessitate modulation of coagulation and thrombolytic factors to reflect human hemostasis accurately. PMID:28545055

Response to Intervention (RtI) in the Social, Emotional, and Behavioral Domains: Current Challenges and Emerging Possibilities

ERIC Educational Resources Information Center

Saeki, Elina; Jimerson, Shane R.; Earhart, James; Hart, Shelley R.; Renshaw, Tyler; Singh, Renee D.; Stewart, Kaitlyn

2011-01-01

As many schools move toward a three-tier model that incorporates a Response to Intervention (RtI) service delivery model in the social, emotional, and behavioral domains, school psychologists may provide leadership. The decision-making process for filtering students through multiple tiers of support and intervention and examining change is an area…

Clot retraction affects the extent of ultrasound-enhanced thrombolysis in an ex vivo porcine thrombosis model.

PubMed

Sutton, Jonathan T; Ivancevich, Nikolas M; Perrin, Stephen R; Vela, Deborah C; Holland, Christy K

2013-05-01

We investigated ultrasound-enhanced thrombolysis in two whole-blood clot models using a Food and Drug Administration-approved contrast agent (Definity, Lantheus Medical Imaging; Billerica, MA USA) and thrombolytic drug (recombinant tissue-type plasminogen activator [rt-PA]) (Genentech; South San Francisco, CA USA). Porcine venous blood was collected from donor hogs and coagulated in vials made of two different materials. This method produced clots with differing compositional properties, as determined by routine scanning electron microscopy and histology. Clots were deployed in an ex vivo porcine thrombosis model, and exposed to an intermittent ultrasound scheme previously developed to maximize stable cavitation while acoustic emissions were detected. Exposure to 3.15 μg/mL rt-PA promoted lysis in both clot models, compared with exposure to plasma alone. However, only unretracted clots experienced significant enhancement of thrombolysis in the presence of rt-PA, Definity, and ultrasound, compared with treatment with rt-PA. In these clots, microscopy revealed loose erythrocyte aggregates, a significantly less extensive fibrin network and a higher porosity, which may facilitate increased penetration of thrombolytics by cavitation. Copyright © 2013 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Inhibition by TNF-alpha and IL-4 of cationic lipid mediated gene transfer in cystic fibrosis tracheal gland cells.

PubMed

Bastonero, Sonia; Gargouri, Myriem; Ortiou, Sandrine; Guéant, Jean-Louis; Merten, Marc D

2005-11-01

In vivo, tracheal gland serous cells highly express the cystic fibrosis transmembrane conductance regulator (cftr) gene. This gene is mutated in the lethal monogenic disease cystic fibrosis (CF). Clinical trials in which the human CFTR cDNA was delivered to the respiratory epithelia of CF patients have resulted in weak and transient gene expression. As CF is characterized by mucus inspissation, airway infection, and severe inflammation, we tested the hypothesis that inflammation and especially two cytokines involved in the Th1/Th2 inflammatory response, interleukin 4 (IL-4) and TNFalpha, could inhibit gene transfer efficiency using a model of human CF tracheal gland cells (CF-KM4) and Lipofectamine reagent as a transfection reagent. The specific secretory defects of CF-KM4 cells were corrected by Lipofectamine-mediated human CFTR gene transfer. However, this was altered when cells were pre-treated with IL-4 and TNFalpha. Inhibition of luciferase reporter gene expression by IL-4 and TNFalpha pre-treated CF-KM4 cells was measured by activity and real-time RT-PCR. Both cytokines induced similar and synergistic inhibition of transgene expression and activity. This cytokine-mediated inhibition could be prevented by anti-inflammatory agents such as glucocorticoids but not by non-steroidal (NSAI) agents. This data suggests that an inflammatory context generated by IL-4 and TNFalpha can inhibit human CFTR gene transfer in CF tracheal gland cells and that glucocorticoids may have a protecting action. Copyright (c) 2005 John Wiley & Sons, Ltd.

Stability issues of nonlocal gravity during primordial inflation

NASA Astrophysics Data System (ADS)

Belgacem, Enis; Cusin, Giulia; Foffa, Stefano; Maggiore, Michele; Mancarella, Michele

2018-01-01

We study the cosmological evolution of some nonlocal gravity models, when the initial conditions are set during a phase of primordial inflation. We examine in particular three models, the so-called RT, RR and Δ4 models, previously introduced by our group. We find that, during inflation, the RT model has a viable background evolution, but at the level of cosmological perturbations develops instabilities that make it nonviable. In contrast, the RR and Δ4 models have a viable evolution even when their initial conditions are set during a phase of primordial inflation.

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

Recent Upgrades to NASA SPoRT Initialization Datasets for the Environmental Modeling System

NASA Technical Reports Server (NTRS)

Case, Jonathan L.; Lafontaine, Frank J.; Molthan, Andrew L.; Zavodsky, Bradley T.; Rozumalski, Robert A.

2012-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center has developed several products for its NOAA/National Weather Service (NWS) partners that can initialize specific fields for local model runs within the NOAA/NWS Science and Training Resource Center Environmental Modeling System (EMS). The suite of SPoRT products for use in the EMS consists of a Sea Surface Temperature (SST) composite that includes a Lake Surface Temperature (LST) analysis over the Great Lakes, a Great Lakes sea-ice extent within the SST composite, a real-time Green Vegetation Fraction (GVF) composite, and NASA Land Information System (LIS) gridded output. This paper and companion poster describe each dataset and provide recent upgrades made to the SST, Great Lakes LST, GVF composites, and the real-time LIS runs.

Early thermal history of Rhea: the role of serpentinization and liquid state convection

NASA Astrophysics Data System (ADS)

Czechowski, Leszek; Losiak, Anna

2015-04-01

Intorduction: Thermal history of Rhea from the beginning of accretion is investigated. The numerical model of convection combined with the parameterized theory is developed. Melting of the satellite's matter, gravitational differentiation and serpentinization of silicates are included. The role of the following parameters of the model is investigated: time of beginning of accretion, duration of accretion, viscosity of ice close to the melting point, activation energy in the formula for viscosity E, thermal conductivity of silicate component, ammonia content X, and energy of serpentinization. 1. Numerical model: In our calculations we use numerical model developed by Czechowski (2012) (see e.g. description in [1]). The model is based on parameterized theory of convection combined with 1-dimensional equation of the heat transfer in spherical coordinates: δT(r,t)- ρcp δt = div(k(r,T ) gradT (r,t))+ Q(r,T), where r is the radial distance (spherical coordinate), ρ is the density [kg m-3], cp [J kg1 K-1 ] is the specific heat, Q [W kg-1] is the heating rate, and k[W m-1 K-1] is the thermal conductivity. Q(r,t) includes sources and sinks of the heat. The equation is solved in time dependent region [0, R(t)]. During accretion the radius R(t) increases in time according to formula: R(t) = atfor tini tac , i.e. after the accretion (see e.g. [2]), where tinidenotes beginning of accretion and tac denotes duration of this process. If the Rayleigh number in the considered layer exceeds its critical value Racr then convection starts. It leads to effective heat transfer. The full description of convection is given by a velocity field and temperature distribution. However, we are interested in convection as a process of heat transport only. For solid state convection (SSC) heat transport can be described by dimensionless Nusselt number Nu. We use the following definition of the Nu: Nu= (True total surface heat flow)/(Total heat flow without convection). The heat transport by SSC is modelled simply by multiplying the coefficient of the heat conduction in the considered layer, i.e.: kconv =Nu k. This approach is used successfully in parameterized theory of convection for SSC in the Earth and other planets (e.g. [3], [4]). Parameterization of liquid state convection (LSC) is even simpler. Ra in molten region is very high (usually higher than 1016). The LSC could be very intensive resulting in almost adiabatic temperature gradient given by: dT-= gαmT-, dr cpm where αm and cpm are thermal expansion coefficient and specific heat in molten region, g is the local gravity. In Enceladus and Mimas the adiabatic gradient is low and therefore LSC region is almost isothermal. 2. Results: 1. We found that time of beginning of accretion and duration of accretion are crucial for early evolution, especially for differentiation. 2. Viscosity of ice close to melting point, activation energy in formula for viscosity E, and ammonia content X are very important for evolution, but not dramatic differences are found if realistic values are considered. 3. The energy of serpentinization is important for evolution, but its role is also not dominant. 4. LSC operating in molten part could delay the differentiation and the core formation for a few hundreds Myr. 5. The gravity data could be interpreted that Rhea is fully differentiated only if its core has high porosity and low density ~1300 kg m-3. In fact, there is not mechanism that could remove the water from molten core and the core of Rhea is probably porous. Acknowledgements: The research is partly supported by National Science Centre (grant 2011/ 01/ B/ ST10/06653). References : [1] Czechowski, L. (2014) Some remarks on the early evolution of Enceladus. Planet. Sp. Sc. 104, 185-199. [2] Merk, R., Breuer, D., Spohn, T. (2002). Numerical modeling of 26Al induced radioactive melting of asteroids concerning accretion. Icarus 199, 183-191. [3] Sharpe, H.N., Peltier, W.R., (1978) Parameterized mantle convection and the Earth's thermal history. Geophys. Res. Lett. 5, 737-740.

Coupled retrieval of water cloud and above-cloud aerosol properties using the Airborne Multiangle SpectroPolarimetric Imager (AirMSPI)

NASA Astrophysics Data System (ADS)

Xu, F.; van Harten, G.; Diner, D. J.; Rheingans, B. E.; Tosca, M.; Seidel, F. C.; Bull, M. A.; Tkatcheva, I. N.; McDuffie, J. L.; Garay, M. J.; Davis, A. B.; Jovanovic, V. M.; Brian, C.; Alexandrov, M. D.; Hostetler, C. A.; Ferrare, R. A.; Burton, S. P.

2017-12-01

The Airborne Multiangle SpectroPolarimetric Imager (AirMSPI) has been flying aboard the NASA ER-2 high altitude aircraft since October 2010. AirMSPI acquires radiance and polarization data in bands centered at 355, 380, 445, 470*, 555, 660*, 865*, and 935 nm (*denotes polarimetric bands). In sweep mode, georectified images cover an area of 80-100 km (along track) by 10-25 km (across track) between ±66° off nadir, with a map-projected spatial resolution of 25 meters. An efficient and flexible retrieval algorithm has been developed using AirMSPI polarimetric bands for simultaneous retrieval of cloud and above-cloud aerosol microphysical properties. We design a three-step retrieval approach, namely 1) estimating effective droplet size distribution using polarimetric cloudbow observations and using it as initial guess for Step 2; 2) combining water cloud and aerosol above cloud retrieval by fitting polarimetric signals at all scattering angles (e.g. from 80° to 180°); and 3) constructing a lookup table of radiance for a set of cloud optical depth grids using aerosol and cloud information retrieved from Step 2 and then estimating pixel-scale cloud optical depth based on 1D radiative transfer (RT) theory by fitting the AirMSPI radiance. Retrieval uncertainty is formulated by accounting for instrumental errors and constraints imposed on spectral variations of aerosol and cloud droplet optical properties. As the forward RT model, a hybrid approach is developed to combine the computational strengths of Markov-chain and adding-doubling methods to model polarized RT in a coupled aerosol, Rayleigh and cloud system. Our retrieval approach is tested using 134 AirMSPI datasets acquired during NASA ORACLES field campaign in 09/2016, with low to high aerosol loadings. For validation, the retrieved aerosol optical depths and cloud-top heights are compared to coincident High Spectral Resolution Lidar-2 (HSRL-2) data, and the droplet size parameters including effective radius and effective variance and cloud optical thickness are compared to coincident Research Scanning Polarimeter (RSP) data.

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.

Blind estimation of reverberation time

NASA Astrophysics Data System (ADS)

Ratnam, Rama; Jones, Douglas L.; Wheeler, Bruce C.; O'Brien, William D.; Lansing, Charissa R.; Feng, Albert S.

2003-11-01

The reverberation time (RT) is an important parameter for characterizing the quality of an auditory space. Sounds in reverberant environments are subject to coloration. This affects speech intelligibility and sound localization. Many state-of-the-art audio signal processing algorithms, for example in hearing-aids and telephony, are expected to have the ability to characterize the listening environment, and turn on an appropriate processing strategy accordingly. Thus, a method for characterization of room RT based on passively received microphone signals represents an important enabling technology. Current RT estimators, such as Schroeder's method, depend on a controlled sound source, and thus cannot produce an online, blind RT estimate. Here, a method for estimating RT without prior knowledge of sound sources or room geometry is presented. The diffusive tail of reverberation was modeled as an exponentially damped Gaussian white noise process. The time-constant of the decay, which provided a measure of the RT, was estimated using a maximum-likelihood procedure. The estimates were obtained continuously, and an order-statistics filter was used to extract the most likely RT from the accumulated estimates. The procedure was illustrated for connected speech. Results obtained for simulated and real room data are in good agreement with the real RT values.

Online estimation of room reverberation time

NASA Astrophysics Data System (ADS)

Ratnam, Rama; Jones, Douglas L.; Wheeler, Bruce C.; Feng, Albert S.

2003-04-01

The reverberation time (RT) is an important parameter for characterizing the quality of an auditory space. Sounds in reverberant environments are subject to coloration. This affects speech intelligibility and sound localization. State-of-the-art signal processing algorithms for hearing aids are expected to have the ability to evaluate the characteristics of the listening environment and turn on an appropriate processing strategy accordingly. Thus, a method for the characterization of room RT based on passively received microphone signals represents an important enabling technology. Current RT estimators, such as Schroeder's method or regression, depend on a controlled sound source, and thus cannot produce an online, blind RT estimate. Here, we describe a method for estimating RT without prior knowledge of sound sources or room geometry. The diffusive tail of reverberation was modeled as an exponentially damped Gaussian white noise process. The time constant of the decay, which provided a measure of the RT, was estimated using a maximum-likelihood procedure. The estimates were obtained continuously, and an order-statistics filter was used to extract the most likely RT from the accumulated estimates. The procedure was illustrated for connected speech. Results obtained for simulated and real room data are in good agreement with the real RT values.

Bioconjugation of recombinant tissue plasminogen activator to magnetic nanocarriers for targeted thrombolysis

PubMed Central

Yang, Hung-Wei; Hua, Mu-Yi; Lin, Kun-Ju; Wey, Shiaw-Pyng; Tsai, Rung-Ywan; Wu, Siao-Yun; Lu, Yi-Ching; Liu, Hao-Li; Wu, Tony; Ma, Yunn-Hwa

2012-01-01

Low-toxicity magnetic nanocarriers (MNCs) composed of a shell of poly [aniline-co-N-(1-one-butyric acid) aniline] over a Fe3O4 magnetic nanoparticle core were developed to carry recombinant tissue plasminogen activator (rtPA) in MNC-rtPA for targeted thrombolysis. With an average diameter of 14.8 nm, the MNCs exerted superparamagnetic properties. Up to 276 μg of active rtPA was immobilized per mg of MNCs, and the stability of the immobilized rtPA was greatly improved during storage at 4°C and 25°C. In vitro thrombolysis testing with a tubing system demonstrated that magnet-guided MNC-rtPA showed significantly improved thrombolysis compared with free rtPA and reduced the clot lysis time from 39.2 ± 3.2 minutes to 10.8 ± 4.2 minutes. In addition, magnet-guided MNC-rtPA at 20% of the regular rtPA dose restored blood flow within 15–25 minutes of treatment in a rat embolism model without triggering hematological toxicity. In conclusion, this improved system is based on magnetic targeting accelerated thrombolysis and is potentially amenable to therapeutic applications in thromboembolic diseases. PMID:23055728

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.

Using Lunar Impact Basin Relaxation to Test Impact Flux Models

NASA Astrophysics Data System (ADS)

Nimmo, F.; Conrad, J. W.; Neumann, G. A.; Kamata, S.; Fassett, C.

2017-12-01

Gravity data obtained by the GRAIL mission [1] has constrained the number and distribution of lunar impact basins [2]. We analyzed crater densities for newly-proposed basins to assign relative ages. The extent to which a basin is relaxed is calculated using GRAIL-derived crustal thickness models [3] by comparing the mantle uplift under basins to the surrounding region. With our catalog we can investigate the distribution of basin properties through relative time. We identify a relaxation state transition (RT) around the pre-Nectarian 4 relative age group for basins with diameters > 450 km, similar to previous results using a pre-GRAIL basin catalog [4]. This RT likely signals a change in the global thermal state of the crust, representing the time at which the lunar moho temperature fell below 1400 K [4]. This transition happens 50-100 million years (Myr) after the lunar magma ocean (LMO) solidifies [4]. Based on models and inferences of LMO solidification [5, 6] the RT is expected to occur at 4.25-4.50 Ga, depending on the rate of cooling once a crustal lid has formed [5] and the amount of tidal heating in the early crust [6]. Monotonically declining impact flux models, such as [7] and [8] predict a younger RT; 4.07-4.08 and 4.24-4.27 Ga respectively. A scaled-down version of [8] can fit the RT but fails to match the observed number of younger, unrelaxed basins. Models that invoke a later transient increase in impact flux can reproduce the inferred RT time; for instance, the model of [9] gives a RT age of 4.43-4.46 Ga. This model matches the number of younger basins and implies that basin preservation started at 4.49 Ga, likely before the LMO completely solidified. [1] Zuber M.T. et al. (2013) Science, 339, 668-671. [2] Neumann G.A. et al. (2015) Science Advances, 1, e1500852. [3] Wieczorek M.A. (2013) Science, 339, 671-675. [4] Kamata S. et al. (2015) Icarus, 250, 492-504. [5] Elkins-Tanton L.T. et al. (2011) Earth Planet. Sci. Lett., 304, 326-336. [6] Meyer, J. et al. (2010) Icarus, 208, 1-10. [7] Robbins S.J. (2014) Earth Planet. Sci. Lett., 403, 188-198. [8] Neukum G. et al. (2001) Space Sci. Rev., 96, 55-86. [9] Morbidelli A. et al. (2012) Earth Planet. Sci. Lett., 355, 144-151.

Modelling endurance and resumption times for repetitive one-hand pushing.

PubMed

Rose, Linda M; Beauchemin, Catherine A A; Neumann, W Patrick

2018-07-01

This study's objective was to develop models of endurance time (ET), as a function of load level (LL), and of resumption time (RT) after loading as a function of both LL and loading time (LT) for repeated loadings. Ten male participants with experience in construction work each performed 15 different one-handed repetaed pushing tasks at shoulder height with varied exerted force and duration. These data were used to create regression models predicting ET and RT. It is concluded that power law relationships are most appropriate to use when modelling ET and RT. While the data the equations are based on are limited regarding number of participants, gender, postures, magnitude and type of exerted force, the paper suggests how this kind of modelling can be used in job design and in further research. Practitioner Summary: Adequate muscular recovery during work-shifts is important to create sustainable jobs. This paper describes mathematical modelling and presents models for endurance times and resumption times (an aspect of recovery need), based on data from an empirical study. The models can be used to help manage fatigue levels in job design.

In Vitro and In Vivo Enhancement of Chemoradiation Using the Oral PARP Inhibitor ABT-888 in Colorectal Cancer Cells

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

Shelton, Joseph W., E-mail: jwshelt@emory.edu; Waxweiler, Timothy V.; Landry, Jerome

2013-07-01

Purpose: Poly(ADP-ribose) polymerase plays a critical role in the recognition and repair of DNA single-strand breaks and double-strand breaks (DSBs). ABT-888 is an orally available inhibitor of this enzyme. This study seeks to evaluate the use of ABT-888 combined with chemotherapy and radiation therapy (RT) in colorectal carcinoma models. Methods and Materials: RT clonogenic assays were performed on HCT116 and HT29 cells treated with 5-fluorouracil, irinotecan, or oxaliplatin with or without ABT. The surviving fraction at 2 Gy and dose-modifying factor at 10% survival were analyzed. Synergism was assessed by isobologram analysis for combination therapies. γH2AX and neutral comet assaysmore » were performed to assess the effect of therapy on DSB formation/repair. In vivo assessments were made by use of HCT116 cells in a xenograft mouse model. Tumor growth delay was measured at a volume of 500 mm{sup 3}. Results: Both lines were radiosensitized by ABT alone, and ABT further increased chemotherapy dose-modifying factors to the 1.6 to 1.8 range. All combinations were synergistic (combination indices <0.9). ABT treatment significantly increased DSB after RT (γH2AX, 69% vs 43%; P=.017) and delayed repair. We found tumor growth delays of 7.22 days for RT; 11.90 days for RT and ABT; 13.5 days for oxaliplatin, RT, and ABT; 14.17 days for 5-fluorouracil, RT, and ABT; and 23.81 days for irinotecan, RT, and ABT. Conclusion: ABT-888 radiosensitizes at similar or higher levels compared with classic chemotherapies and acts synergistically with these chemotherapies to enhance RT effects. In vivo confirmation of these results indicates a potential role for combining its use with existing chemoradiation regimens.« less

Economic consequence of local control with radiotherapy: Cost analysis of internal mammary and medial supraclavicular lymph node radiotherapy in breast cancer

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

Lievens, Yolande; Kesteloot, Katrien; Bogaert, Walter van den

2005-11-15

Purpose: To investigate the financial implications of radiotherapy (RT) to the internal mammary and medial supraclavicular lymph node chain (IM-MS) in postoperative breast cancer. Methods and Materials: A cost-effectiveness and cost-utility analysis were performed, using Markov models, comparing the early and delayed costs and effects of IM-MS during a 20-year time span from a societal viewpoint. The outcome estimates were based on Level I evidence from postoperative RT literature and the cost estimates on the standard practice of the Leuven University Hospitals, with the RT costs derived from an activity-based costing program developed in the department. Results: On the basismore » of the assumptions of the model and seen during a 20-year time span, primary treatment including IM-MS RT results in a cost savings (approximately EURO 10,000) compared with a strategy without RT. Because IM-MS RT also results in better clinical effectiveness and greater quality of life, the treatment with IM-MS dominates the approach without IM-MS. Sensitivity analyses confirmed the robustness of these results in all tested circumstances. Although threshold values were found for the cost of IM-MS, the cost at relapse, and the quality of life after treatment, these were substantially different from the baseline estimates, indicating that it is very unlikely that omitting IM-MS would become superior. Conclusion: This ex-ante cost evaluation of IM-MS RT showed that the upfront costs of locoregional RT are easily compensated for by avoiding the costs of treating locoregional and distant relapse at a later stage. The cost-sparing effect of RT should, however, be evaluated for a sufficiently long time span and is most specifically found in tumors with a rather slow natural history and a multitude of available systemic treatments at relapse, such as breast cancer.« less

The microRNA-let-7b-mediated attenuated strain of influenza A (H1N1) virus in a mouse model.

PubMed

Tan, Mingming; Sun, Wenkui; Feng, Chunlai; Xia, Di; Shen, Xiaoyue; Ding, Yuan; Liu, Zhicheng; Xing, Zheng; Su, Xin; Shi, Yi

2016-09-30

Evaluating the attenuation of influenza viruses in animal studies is important in developing safe and effective vaccines. This study aimed to demonstrate that the microRNA (miRNA)-let-7b-mediated attenuated influenza viruses (miRT-H1N1) are sufficiently attenuated and safe in mice. The pathogenicity of the miRT-H1N1virus was investigated in a mouse model, evaluated with median lethal dose (LD50). The replicative dynamics of the miRT-H1N1, wild type (wt)-H1N1, and scramble (scbl)-H1N1 viruses in the lungs of infected mice were compared. The degrees of lesions and the expression levels of IL-6, TNF-α, and IFN-β in the lungs of mice infected with different viruses were also analyzed. In miRT-H1N1 virus-infected mice, 100% of mice survived, and a lower pathogenicity was characterized with non-significant weight loss when compared to mice infected with the control wt virus. The miRT-H1N1 virus was not fatal for mice, even at the highest dose administered. The viral load in the lungs of miRT-H1N1-infected mice was significantly lower than that of the wild-type virus-infected mice. Fewer pulmonary lesions and lower levels of selected pro-inflammatory cytokines in the lungs of the mice infected with the miRT-H1N1 virus were also observed. The virulence of the miRT-H1N1 virus reduced significantly, suggesting that the miRT-H1N1 virus was safe for mice. Our study demonstrated that the miRNA-mediated gene silencing is an alternative approach to attenuating the pathogenicity of wt influenza viruses that have potential in the development of influenza vaccines.

TU-C-17A-03: An Integrated Contour Evaluation Software Tool Using Supervised Pattern Recognition for Radiotherapy

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

Chen, H; Tan, J; Kavanaugh, J

Purpose: Radiotherapy (RT) contours delineated either manually or semiautomatically require verification before clinical usage. Manual evaluation is very time consuming. A new integrated software tool using supervised pattern contour recognition was thus developed to facilitate this process. Methods: The contouring tool was developed using an object-oriented programming language C# and application programming interfaces, e.g. visualization toolkit (VTK). The C# language served as the tool design basis. The Accord.Net scientific computing libraries were utilized for the required statistical data processing and pattern recognition, while the VTK was used to build and render 3-D mesh models from critical RT structures in real-timemore » and 360° visualization. Principal component analysis (PCA) was used for system self-updating geometry variations of normal structures based on physician-approved RT contours as a training dataset. The inhouse design of supervised PCA-based contour recognition method was used for automatically evaluating contour normality/abnormality. The function for reporting the contour evaluation results was implemented by using C# and Windows Form Designer. Results: The software input was RT simulation images and RT structures from commercial clinical treatment planning systems. Several abilities were demonstrated: automatic assessment of RT contours, file loading/saving of various modality medical images and RT contours, and generation/visualization of 3-D images and anatomical models. Moreover, it supported the 360° rendering of the RT structures in a multi-slice view, which allows physicians to visually check and edit abnormally contoured structures. Conclusion: This new software integrates the supervised learning framework with image processing and graphical visualization modules for RT contour verification. This tool has great potential for facilitating treatment planning with the assistance of an automatic contour evaluation module in avoiding unnecessary manual verification for physicians/dosimetrists. In addition, its nature as a compact and stand-alone tool allows for future extensibility to include additional functions for physicians’ clinical needs.« less

Making the Right Choice: Optimizing rt-PA and eptifibatide lysis, an in vitro study

PubMed Central

Shaw, George J.; Meunier, Jason M.; Lindsell, Christopher J.; Pancioli, Arthur M.; Holland, Christy K.

2010-01-01

Introduction Recombinant tissue plasminogen activator (rt-PA) is the only FDA approved lytic therapy for acute ischemic stroke. However, there can be complications such as intra-cerebral hemorrhage. This has led to interest in adjuncts such as GP IIb-IIIa inhibitors. However, there is little data on combined therapies. Here, we measure clot lysis for rt-PA and eptifibatide in an in vitro human clot model, and determine the drug concentrations maximizing lysis. A pharmacokinetic model is used to compare drug concentrations expected in clinical trials with those used here. The hypothesis is that there is a range of rt-PA and eptifibatide concentrations that maximize in vitro clot lysis. Materials and Methods Whole blood clots were made from blood obtained from 28 volunteers, after appropriate institutional approval. Sample clots were exposed to rt-PA and eptifibatide in human fresh-frozen plasma; rt-PA concentrations were 0, 0.5, 1, and 3.15 μg/ml, and eptifibatide concentrations were 0, 0.63, 1.05, 1.26 and 2.31 μg/ml. All exposures were for 30 minutes at 37 C. Clot width was measured using a microscopic imaging technique and mean fractional clot loss (FCL) at 30 minutes was used to determine lytic efficacy. On average, 28 clots (range: 6-148) from 6 subjects (3-24) were used in each group. Results and Conclusions FCL for control clots was 14% (95% Confidence Interval: 13-15%). FCL was 58% (55-61%) for clots exposed to both drugs at all concentrations, except those at an rt-PA concentration of 3.15 μg/ml, and eptifibatide concentrations of 1.26 μg/ml (Epf) or 2.31 μg/ml. Here, FCL was 43% (36-51) and 35% (32-38) respectively. FCL is maximized at moderate rt-PA and eptifibatide concentration; these values may approximate the average concentrations used in some rt-PA and eptifibatide treatments. PMID:20813398

The Impact of Adjuvant Radiation Therapy for High-Grade Gliomas by Histology in the United States Population

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

Rusthoven, Chad G., E-mail: Chad.Rusthoven@ucdenver.edu; Carlson, Julie A.; Waxweiler, Timothy V.

Purpose: To compare the survival impact of adjuvant external beam radiation therapy (RT) for malignant gliomas of glioblastoma (GBM), anaplastic astrocytoma (AA), anaplastic oligodendroglioma (AO), and mixed anaplastic oligoastrocytoma (AOA) histology. Methods and Materials: The Surveillance, Epidemiology, and End Results (SEER) database was queried from 1998 to 2007 for patients aged ≥18 years with high-grade gliomas managed with upfront surgical resection, treated with and without adjuvant RT. Results: The primary analysis totaled 14,461 patients, with 12,115 cases of GBM (83.8%), 1312 AA (9.1%), 718 AO (4.9%), and 316 AOA (2.2%). On univariate analyses, adjuvant RT was associated with significantly improved overallmore » survival (OS) for GBMs (2-year OS, 17% vs 7%, p<.001), AAs (5-year OS, 38% vs 24%, p<.001), and AOAs (5-year OS, 55% vs 44%, p=.026). No significant differences in OS were observed for AOs (5-year OS, with RT 50% vs 56% without RT, p=.277). In multivariate Cox proportional hazards models accounting for extent of resection, age, sex, race, year, marital status, and tumor registry, RT was associated with significantly improved OS for both GBMs (HR, 0.52; 95% CI, 0.50-0.55; P<.001) and AAs (HR, 0.57; 95% CI, 0.48-0.68; P<.001) but only a trend toward improved OS for AOAs (HR, 0.70; 95% CI, 0.45-1.09; P=.110). Due to the observation of nonproportional hazards, Cox regressions were not performed for AOs. A significant interaction was observed between the survival impact of RT and histology overall (interaction P<.001) and in a model limited to the anaplastic (WHO grade 3) histologies. (interaction P=.024), characterizing histology as a significant predictive factor for the impact of RT. Subgroup analyses demonstrated greater hazard reductions with RT among patients older than median age for both GBMs and AAs (all interaction P≤.001). No significant interactions were observed between RT and extent of resection. Identical patterns of significance were observed for cause-specific survival and OS across analyses. Conclusions: In this large population-based cohort, glioma histology represented a significant predictor for the survival impact of RT. Adjuvant RT was associated with improved survival for AAs, with benefits comparable to those observed for GBMs over the same 10-year interval. No survival advantage was observed with adjuvant RT for AOs.« less

HIF-2α-induced chemokines stimulate motility of fibroblast-like synoviocytes and chondrocytes into the cartilage-pannus interface in experimental rheumatoid arthritis mouse models.

PubMed

Huh, Yun Hyun; Lee, Gyuseok; Lee, Keun-Bae; Koh, Jeong-Tae; Chun, Jang-Soo; Ryu, Je-Hwang

2015-10-29

Pannus formation and resulting cartilage destruction during rheumatoid arthritis (RA) depends on the migration of synoviocytes to cartilage tissue. Here, we focused on the role of hypoxia-inducible factor (HIF)-2α-induced chemokines by chondrocytes in the regulation of fibroblast-like synoviocyte (FLS) migration into the cartilage-pannus interface and cartilage erosion. Collagen-induced arthritis (CIA), K/BxN serum transfer, and tumor necrosis factor-α transgenic mice were used as experimental RA models. Expression patterns of HIF-2α and chemokines were determined via immunostaining, Western blotting and RT-PCR. FLS motility was evaluated using transwell migration and invasion assays. The specific role of HIF-2α was determined via local deletion of HIF-2α in joint tissues or using conditional knockout (KO) mice. Cartilage destruction, synovitis and pannus formation were assessed via histological analysis. HIF-2α and various chemokines were markedly upregulated in degenerating cartilage and pannus of RA joints. HIF-2α induced chemokine expression by chondrocytes in both primary culture and cartilage tissue. HIF-2α -induced chemokines by chondrocytes regulated the migration and invasion of FLS. Local deletion of HIF-2α in joint tissues inhibited pannus formation adjacent to cartilage tissue and cartilage destruction caused by K/BxN serum transfer. Furthermore, conditional knockout of HIF-2α in cartilage blocked pannus formation in adjacent cartilage but not bone tissue, along with inhibition of cartilage erosion caused by K/BxN serum transfer. Our findings suggest that chemokines induced by IL-1β or HIF-2α in chondrocytes regulate pannus expansion by stimulating FLS migration and invasion, leading to cartilage erosion during RA pathogenesis.

Persistence, immune specificity, and functional ability of murine mutant ras epitope-specific CD4(+) and CD8(+) T lymphocytes following in vivo adoptive transfer.

PubMed

Bristol, J A; Schlom, J; Abrams, S I

1999-05-25

Adoptive T-cell transfer has been shown to be a potentially effective strategy for cellular immunotherapy in some murine models of disease. However, several issues remain unresolved regarding some of the basic features involved in effective adoptive transfer, such as the influence of specific peptide antigen (Ag) boost after T-cell transfer, the addition of IL-2 post-T-cell transfer, the trafficking of transferred T cells to lymphoid and nonlymphoid tissues, and the functional stability of recoverable CD4(+) and CD8(+) T cells. We investigated several of these parameters, particularly as they relate to the persistence and maintenance of effector functions of murine CD4(+) and/or CD8(+) T lymphocytes after adoptive cellular transfer into partially gamma-irradiated syngeneic hosts. Our laboratory previously identified murine (H-2(d)) immunogenic CD4(+) and CD8(+) T-cell peptide epitopes reflecting codon 12 ras mutations as tumor-specific Ag. Therefore, the model system chosen here employed epitope-specific MHC class II-restricted CD4(+) T cells and MHC class I-restricted CD8(+) T cells produced from previously immunized BALB/c mice. Between 2 and 7 days after T-cell transfer, recipient mice received various combinations of peptide boosts and/or IL-2 treatments. At different times after the T-cell transfer, spleen and lung tissues were analyzed phenotypically to monitor the persistence of the immune T cells and functionally (via proliferation or cytotoxicity assays) to assess the maintenance of peptide specificity. The results showed that immune donor T lymphocytes (uncultured immune T cells or cloned T cells) were recoverable from the spleens and lungs of recipient mice after transfer. The recovery of Ag-specific T-cell responses was greatest from recipient mice that received peptide boosts and IL-2 treatment. However, mice that received a peptide boost without IL-2 treatment responded nearly as well, which suggested that including a peptide boost after T-cell transfer was more obligatory than exogenous IL-2 treatment to sustain adoptively transferred T cells in vivo. Ag-specific T-cell responses were weak in mice that either received IL-2 alone or did not receive the cognate peptide boost after T-cell transfer. The T-cell clones were also monitored by flow cytometry or RT-PCR based on expression of the T-cell receptor Vbeta-chain, which was previously characterized. Ag-specific T cells were recovered from both spleens and lungs of recipient mice, demonstrating that the T-cell clones could localize to both lymphoid and nonlymphoid tissues. This study demonstrates that both uncultured and in vitro-cloned T lymphocytes can migrate to lymphoid tissues and nonlymphoid (e.g., lung) tissues in recipient hosts and that their functional activities can be maintained at these sites after transfer, if they are exposed to peptide Ag in vivo. Copyright 1999 Academic Press.

Predicting High Health Care Resource Utilization in a Single-payer Public Health Care System: Development and Validation of the High Resource User Population Risk Tool (HRUPoRT).

PubMed

Rosella, Laura C; Kornas, Kathy; Yao, Zhan; Manuel, Douglas G; Bornbaum, Catherine; Fransoo, Randall; Stukel, Therese

2017-11-17

A large proportion of health care spending is incurred by a small proportion of the population. Population-based health planning tools that consider both the clinical and upstream determinants of high resource users (HRU) of the health system are lacking. To develop and validate the High Resource User Population Risk Tool (HRUPoRT), a predictive model of adults that will become the top 5% of health care users over a 5-year period, based on self-reported clinical, sociodemographic, and health behavioral predictors in population survey data. The HRUPoRT model was developed in a prospective cohort design using the combined 2005 and 2007/2008 Canadian Community Health Surveys (CCHS) (N=58,617), and validated using the external 2009/2010 CCHS cohort (N=28,721). Health care utilization for each of the 5 years following CCHS interview date were determined by applying a person-centered costing algorithm to the linked health administrative databases. Discrimination and calibration of the model were assessed using c-statistic and Hosmer-Lemeshow (HL) χ statistic. The best prediction model for 5-year transition to HRU status included 12 predictors and had good discrimination (c-statistic=0.8213) and calibration (HL χ=18.71) in the development cohort. The model performed similarly in the validation cohort (c-statistic=0.8171; HL χ=19.95). The strongest predictors in the HRUPoRT model were age, perceived general health, and body mass index. HRUPoRT can accurately project the proportion of individuals in the population that will become a HRU over 5 years. HRUPoRT can be applied to inform health resource planning and prevention strategies at the community level.This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal. http://creativecommons.org/licenses/by-nc-nd/4.0/.

Establishing Cost-Effective Allocation of Proton Therapy for Breast Irradiation

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

Mailhot Vega, Raymond B.; Ishaq, Omar; Raldow, Ann

Purpose: Cardiac toxicity due to conventional breast radiation therapy (RT) has been extensively reported, and it affects both the life expectancy and quality of life of affected women. Given the favorable oncologic outcomes in most women irradiated for breast cancer, it is increasingly paramount to minimize treatment side effects and improve survivorship for these patients. Proton RT offers promise in limiting heart dose, but the modality is costly and access is limited. Using cost-effectiveness analysis, we provide a decision-making tool to help determine which breast cancer patients may benefit from proton RT referral. Methods and Materials: A Markov cohort model wasmore » constructed to compare the cost-effectiveness of proton versus photon RT for breast cancer management. The model was analyzed for different strata of women based on age (40 years, 50 years, and 60 years) and the presence or lack of cardiac risk factors (CRFs). Model entrants could have 1 of 3 health states: healthy, alive with coronary heart disease (CHD), or dead. Base-case analysis assumed CHD was managed medically. No difference in tumor control was assumed between arms. Probabilistic sensitivity analysis was performed to test model robustness and the influence of including catheterization as a downstream possibility within the health state of CHD. Results: Proton RT was not cost-effective in women without CRFs or a mean heart dose (MHD) <5 Gy. Base-case analysis noted cost-effectiveness for proton RT in women with ≥1 CRF at an approximate minimum MHD of 6 Gy with a willingness-to-pay threshold of $100,000/quality-adjusted life-year. For women with ≥1 CRF, probabilistic sensitivity analysis noted the preference of proton RT for an MHD ≥5 Gy with a similar willingness-to-pay threshold. Conclusions: Despite the cost of treatment, scenarios do exist whereby proton therapy is cost-effective. Referral for proton therapy may be cost-effective for patients with ≥1 CRF in cases for which photon plans are unable to achieve an MHD <5 Gy.« less

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.

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.

4-1BB Aptamer-Based Immunomodulation Enhances the Therapeutic Index of Radiation Therapy in Murine Tumor Models

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

Benaduce, Ana Paula; Brenneman, Randall; Schrand, Brett

Purpose: To report a novel strategy using oligonucleotide aptamers to 4-1BB as an alternate method for costimulation, and show that combinatorial therapy with radiation improves the therapeutic ratio over equivalent monoclonal antibodies. Methods and Materials: Subcutaneous 4T1 (mouse mammary carcinoma) tumors were established (approximately 100 mm{sup 3}), and a radiation therapy (RT) dose/fractionation schedule that optimally synergizes with 4-1BB monoclonal antibody (mAb) was identified. Comparable tumor control and animal survival was observed when either 4-1BB antibody or aptamer were combined with RT using models of breast cancer and melanoma (4T1 and B16-F10). Off-target CD8{sup +} T-cell toxicity was evaluated by quantification ofmore » CD8{sup +} T cells in livers and spleens of treated animals. Results: When combined with 4-1BB mAb, significant differences in tumor control were observed by varying RT dose and fractionation schedules. Optimal synergy between RT and 4-1BB mAb was observed at 5 Gy × 6. Testing 4-1BB mAb and aptamer independently using the optimal RT (5 Gy × 6 for 4T1/Balb/c and 12 Gy × 1 for B16/C57BL6J mouse models) revealed equivalent tumor control using 4-1BB aptamer and 4-1BB mAb. 4-1BB mAb, but not 4-1BB aptamer-treated animals, exhibited increased lymphocytic liver infiltrates and increased splenic and liver CD8{sup +} T cells. Conclusions: Radiation therapy synergizes with 4-1BB mAb, and this effect is dependent on RT dose and fractionation. Tumor control by 4-1BB aptamer is equivalent to 4-1BB mAb when combined with optimal RT dose, without eliciting off-target liver and spleen CD8{sup +} expansion. 4-1BB aptamer-based costimulation affords a comparable and less toxic strategy to augment RT-mediated tumor control.« less

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

Clinical radiobiology of stage T2-T3 bladder cancer.

PubMed

Majewski, Wojciech; Maciejewski, Boguslaw; Majewski, Stanislaw; Suwinski, Rafal; Miszczyk, Leszek; Tarnawski, Rafal

2004-09-01

To evaluate the relationship between total radiation dose and overall treatment time (OTT) with the treatment outcome, with adjustment for selected clinical factors, in patients with Stage T2-T3 bladder cancer treated with curative radiotherapy (RT). The analysis was based on 480 patients with Stage T2-T3 bladder cancer who were treated at the Center of Oncology in Gliwice between 1975 and 1995. The mean total radiation dose was 65.5 Gy, and the mean OTT was 51 days. In 261 patients (54%), planned and unplanned gaps occurred during RT. Four fractionation schedules were used: (1) conventional fractionation (once daily, 1.8-2.5 Gy/fraction); (2) protracted fractionation (pelvic RT, once daily, 1.6-1.7 Gy/fraction, boost RT, once daily, 2.0 Gy/fraction); (3) accelerated hyperfractionated boost (pelvic RT, once daily, 2.0 Gy/fraction; boost RT, twice daily, 1.3-1.4 Gy/fraction); and (4) accelerated hyperfractionation (pelvic and boost RT, twice daily, 1.2-1.5 Gy/fraction). In all fractionation schedules, the total radiation dose was similar (average 65.5 Gy), but the OTT was different (mean 53 days for conventional fractionation, 62 days for protracted fractionation, 45 days for accelerated hyperfractionated boost, and 41 days for accelerated hyperfractionation). A Cox proportional hazard model and maximum likelihood logistic model were used to evaluate the relationship between the treatment-related parameters (total radiation dose, dose per fraction, and OTT) and clinical factors (clinical T stage, hemoglobin level and bladder capacity before RT) and treatment outcome. With a median follow-up of 76 months, the actuarial 5-year local control rate was 47%, and the overall survival rate was 40%. The logistic analysis, which included the total dose, OTT, and T stage, revealed that all of these factors were significantly related to tumor control probability (p = 0.021 for total radiation dose, p = 0.038 for OTT, and p = 0.00068 for T stage). A multivariate Cox model, which included the treatment-related parameters and other clinical factors, revealed that the hemoglobin level and bladder capacity before RT and T-stage were statistically significant factors determining local control and overall survival. The total radiation dose was of borderline statistical significance for overall survival (p = 0.087), and OTT did not reach statistical significance. The results of our study showed that the treatment outcome after RT for bladder cancer depends mainly on clinical factors: hemoglobin level and bladder capacity before RT, and clinical T stage. An increase in the total radiation dose seemed to be associated with a better treatment outcome. The effect of the OTT was difficult to define, because it was influenced by other prognostic factors.

A novel predictive pharmacokinetic/pharmacodynamic model of repolarization prolongation derived from the effects of terfenadine, cisapride and E-4031 in the conscious chronic av node--ablated, His bundle-paced dog.

PubMed

Nolan, Emily R; Feng, Meihua Rose; Koup, Jeffrey R; Liu, Jing; Turluck, Daniel; Zhang, Yiqun; Paulissen, Jerome B; Olivier, N Bari; Miller, Teresa; Bailie, Marc B

2006-01-01

Terfenadine, cisapride, and E-4031, three drugs that prolong ventricular repolarization, were selected to evaluate the sensitivity of the conscious chronic atrioventricular node--ablated, His bundle-paced Dog for defining drug induced cardiac repolarization prolongation. A novel predictive pharmacokinetic/pharmacodynamic model of repolarization prolongation was generated from these data. Three male beagle dogs underwent radiofrequency AV nodal ablation, and placement of a His bundle-pacing lead and programmable pacemaker under anesthesia. Each dog was restrained in a sling for a series of increasing dose infusions of each drug while maintained at a constant heart rate of 80 beats/min. RT interval, a surrogate for QT interval in His bundle-paced dogs, was recorded throughout the experiment. E-4031 induced a statistically significant RT prolongation at the highest three doses. Cisapride resulted in a dose-dependent increase in RT interval, which was statistically significant at the two highest doses. Terfenadine induced a dose-dependent RT interval prolongation with a statistically significant change occurring only at the highest dose. The relationship between drug concentration and RT interval change was described by a sigmoid E(max) model with an effect site. Maximum RT change (E(max)), free drug concentration at half of the maximum effect (EC(50)), and free drug concentration associated with a 10 ms RT prolongation (EC(10 ms)) were estimated. A linear correlation between EC(10 ms) and HERG IC(50) values was identified. The conscious dog with His bundle-pacing detects delayed cardiac repolarization related to I(Kr) inhibition, and detects repolarization change induced by drugs with activity at multiple ion channels. A clinically relevant sensitivity and a linear correlation with in vitro HERG data make the conscious His bundle-paced dog a valuable tool for detecting repolarization effect of new chemical entities.

Optimal location of radiation therapy centers with respect to geographic access.

PubMed

Santibáñez, Pablo; Gaudet, Marc; French, John; Liu, Emma; Tyldesley, Scott

2014-07-15

To develop a framework with which to evaluate locations of radiation therapy (RT) centers in a region based on geographic access. Patient records were obtained for all external beam radiation therapy started in 2011 for the province of British Columbia, Canada. Two metrics of geographic access were defined. The primary analysis was percentage of patients (coverage) within a 90-minute drive from an RT center (C90), and the secondary analysis was the average drive time (ADT) to an RT center. An integer programming model was developed to determine optimal center locations, catchment areas, and capacity required under different scenarios. Records consisted of 11,096 courses of radiation corresponding to 161,616 fractions. Baseline geographic access was estimated at 102.5 minutes ADT (each way, per fraction) and 75.9% C90. Adding 2 and 3 new centers increased C90 to 88% and 92%, respectively, and decreased ADT by between 43% and 61%, respectively. A scenario in which RT was provided in every potential location that could support at least 1 fully utilized linear accelerator resulted in 35.3 minutes' ADT and 93.6% C90. The proposed framework and model provide a data-driven means to quantitatively evaluate alternative configurations of a regional RT system. Results suggest that the choice of location for future centers can significantly improve geographic access to RT. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

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

Mouth opening in patients irradiated for head and neck cancer: a prospective repeated measures study.

PubMed

Kamstra, J I; Dijkstra, P U; van Leeuwen, M; Roodenburg, J L N; Langendijk, J A

2015-05-01

Aims of this prospective cohort study were (1) to analyze the course of mouth opening up to 48months post-radiotherapy (RT), (2) to assess risk factors predicting decrease in mouth opening, and (3) to develop a multivariable prediction model for change in mouth opening in a large sample of patients irradiated for head and neck cancer. Mouth opening was measured prior to RT (baseline) and at 6, 12, 18, 24, 36, and 48months post-RT. The primary outcome variable was mouth opening. Potential risk factors were entered into a linear mixed model analysis (manual backward-stepwise elimination) to create a multivariable prediction model. The interaction terms between time and risk factors that were significantly related to mouth opening were explored. The study population consisted of 641 patients: 70.4% male, mean age at baseline 62.3years (sd 12.5). Primary tumors were predominantly located in the oro- and nasopharynx (25.3%) and oral cavity (20.6%). Mean mouth opening at baseline was 38.7mm (sd 10.8). Six months post-RT, mean mouth opening was smallest, 36.7mm (sd 10.0). In the linear mixed model analysis, mouth opening was statistically predicted by the location of the tumor, natural logarithm of time post-RT in months (Ln (months)), gender, baseline mouth opening, and baseline age. All main effects interacted with Ln (months). The mean mouth opening decreased slightly over time. Mouth opening was predicted by tumor location, time, gender, baseline mouth opening, and age. The model can be used to predict mouth opening. Copyright © 2015 Elsevier Ltd. All rights reserved.

Molecular docking of (5E)-3-(2-aminoethyl)-5-(2- thienylmethylene)-1, 3-thiazolidine-2, 4-dione on HIV-1 reverse transcriptase: novel drug acting on enzyme.

PubMed

Seniya, Chandrabhan; Yadav, Ajay; Uchadia, Kuldeep; Kumar, Sanjay; Sagar, Nitin; Shrivastava, Priyanka; Shrivastava, Shilpi; Wadhwa, Gulshan

2012-01-01

The study of Human immunodeficiency virus (HIV) in humans and animal models in last 31 years suggested that it is a causative agent of AIDS. This causes serious pandemic public health concern globally. It was reported that the HIV-1 reverse transcriptase (RT) played a critical role in the life cycle of HIV. Therefore, inhibition of HIV-1RT enzyme is one of the major and potential targets in the treatment of AIDS. The enzyme (HIV-1RT) was successfully targeted by non nucleotide reverse transcriptase inhibitors (NNRTIs). But frequent application of NNRTIs led drug resistance mutation on HIV infections. Therefore, there is a need to search new NNRTIs with appropriate pharmacophores. For the purpose, a virtually screened 3D model of unliganded HIV-1RT (1DLO) was explored. The unliganded HIV-1RT (1DLO) was docked with 4-thiazolidinone and its derivatives (ChemBank Database) by using AutoDock4. The best seven docking solutions complex were selected and analyzed by Ligplot. The analysis showed that derivative (5E)-3-(2- aminoethyl)-5-(2- thienylmethylene)-1, 3-thiazolidine-2, 4-dione (CID 3087795) has maximum potential against unliganded HIV-1RT (1DLO). The analysis was done on the basis of scoring and binding ability. The derivative (5E)-3-(2- aminoethyl)-5-(2- thienylmethylene)-1, 3-thiazolidine-2, 4-dione (CID 3087795) indicated minimum energy score and highest number of interactions with active site residue and could be a promising inhibitor for HIV-1 RT as Drug target.

ULTRASOUND-ENHANCED rt-PA THROMBOLYSIS IN AN EX VIVO PORCINE CAROTID ARTERY MODEL

PubMed Central

Hitchcock, Kathryn E.; Ivancevich, Nikolas M.; Haworth, Kevin J.; Caudell Stamper, Danielle N.; Vela, Deborah C.; Sutton, Jonathan T.; Pyne-Geithman, Gail J.; Holland, Christy K.

2014-01-01

Ultrasound is known to enhance recombinant tissue plasminogen activator (rt-PA) thrombolysis. In this study, occlusive porcine whole blood clots were placed in flowing plasma within living porcine carotid arteries. Ultrasonically induced stable cavitation was investigated as an adjuvant to rt-PA thrombolysis. Aged, retracted clots were exposed to plasma alone, plasma containing rt-PA (7.1 ± 3.8 μg/mL) or plasma with rt-PA and Definity® ultrasound contrast agent (0.79 ± 0.47 μL/mL) with and without 120-kHz continuous wave ultrasound at a peak-to-peak pressure amplitude of 0.44 MPa. An insonation scheme was formulated to promote and maximize stable cavitation activity by incorporating ultrasound quiescent periods that allowed for the inflow of Definity®-rich plasma. Cavitation was measured with a passive acoustic detector throughout thrombolytic treatment. Thrombolytic efficacy was measured by comparing clot mass before and after treatment. Average mass loss for clots exposed to rt-PA and Definity® without ultrasound (n = 7) was 34%, and with ultrasound (n = 6) was 83%, which constituted a significant difference (p < 0.0001). Without Definity® there was no thrombolytic enhancement by ultrasound exposure alone at this pressure amplitude (n = 5, p < 0.0001). In the low-oxygen environment of the ischemic artery, significant loss of endothelium occurred but no correlation was observed between arterial tissue damage and treatment type. Acoustic stable cavitation nucleated by an infusion of Definity® enhances rt-PA thrombolysis without apparent treatment-related damage in this ex vivo porcine carotid artery model. PMID:21723448

USE IT OR LOSE IT: EAT AND EXERCISE DURING RADIOTHERAPY OR CHEMORADIOTHERAPY FOR PHARYNGEAL CANCERS

PubMed Central

Hutcheson, Katherine A.; Bhayani, Mihir K.; Beadle, Beth M.; Gold, Kathryn A.; Shinn, Eileen H.; Lai, Stephen Y.; Lewin, Jan

2014-01-01

Objective Proactive swallowing therapy promotes ongoing use of the swallowing mechanism during radiotherapy through 2 goals: eat and exercise. The purpose of this study was to evaluate the independent effects of maintaining oral intake throughout treatment and preventive swallowing exercise. Design Retrospective observational study. Setting The University of Texas MD Anderson Cancer Center, Houston. Patients The study included 497 patients treated with definitive radiotherapy (RT) or chemoradiation (CRT) for pharyngeal cancer (458 oropharynx, 39 hypopharynx) between 2002 and 2008. Main Outcome Measures Swallowing-related endpoints were: final diet after RT/CRT and length of gastrostomy-dependence. Primary independent variables included per oral (PO) status at the end of RT/CRT (nothing per oral [NPO], partial PO, 100% PO) and swallowing exercise adherence. Multiple linear regression and ordered logistic regression models were analyzed. Results At the conclusion of RT/CRT, 131 (26%) were NPO, 74% were PO (167 [34%] partial, 199 [40%] full). Fifty-eight percent (286/497) reported adherence to swallowing exercises. Maintenance of PO intake during RT/CRT and swallowing exercise adherence were independently associated (p<0.05) with better long-term diet after RT/CRT and shorter length of gastrostomy dependence in models adjusted for tumor and treatment burden. Conclusions Data indicate independent, positive associations between maintenance of PO intake throughout RT/CRT and swallowing exercise adherence with long-term swallowing outcomes. Patients who either eat or exercise fare better than those who do neither. Patients who both eat and exercise have the highest return to a regular diet and shortest gastrostomy dependence. PMID:24051544

Enhanced Motor Recovery After Stroke With Combined Cortical Stimulation and Rehabilitative Training Is Dependent on Infarct Location.

PubMed

Boychuk, Jeffery A; Schwerin, Susan C; Thomas, Nagheme; Roger, Alexandra; Silvera, Geoffrey; Liverpool, Misha; Adkins, DeAnna L; Kleim, Jeffrey A

2016-02-01

Cortical electrical stimulation of the motor cortex in combination with rehabilitative training (CS/RT) has been shown to enhance motor recovery in animal models of focal cortical stroke, yet in clinical trials, the effects are much less robust. The variability of stroke location in human patient populations that include both cortical and subcortical brain regions may contribute to the failure to find consistent effects clinically. This study sought to determine whether infarct location influences the enhanced motor recovery previously observed in response to CS/RT. The efficacy of CS/RT to promote improvements in motor function was examined in 2 different rat models of stroke that varied the amount and location of cortical and subcortical damage. Ischemic infarctions were induced by injecting the vasoconstricting peptide endothelin-1 either (1) onto the middle cerebral artery (MCA) producing damage to the frontal cortex and lateral striatum or (2) into a subcortical region producing damage to the posterior thalamus and internal capsule (subcortical capsular ischemic injury [SCII]). Daily CS/RT or RT alone was then given for 20 days, during which time performance on a skilled reaching task was assessed. Animals with MCA occlusion infarctions exhibited enhanced improvements on a skilled reaching task in response to CS/RT relative to RT alone. No such enhancement was observed in animals with SCII infarctions across the 20 days of treatment. The efficacy of CS for enhancing motor recovery after stroke may depend in part on the extent and location of the ischemic infarct. © The Author(s) 2015.

Evaluation of the preventive effect of dexpanthenol in radiation injury by lung perfusion scintigraphy: a preclinical experimental model of radiation injury.

PubMed

Koç, Zehra P; İn, Erdal; Karslioğlu, İhsan; Üçer, Özlem; Canpolat, Sinan

2015-12-01

The aim of this study was to show the preventative effects of dexpanthenol in radiation injuries caused by radiotherapy (RT) through the use of lung perfusion scintigraphy in the pre-RT and post-RT periods. Six male New Zealand rabbits (5-6 months of age and ∼2.5-3 kg in weight) were the used in this study. The animals were subjected to Tc-macroaggregated albumin lung perfusion scintigraphy in the pre-RT and post-RT (i.e. 2 weeks after treatment) periods. The scintigraphies were performed with the same dose by the same staff and the methodology used the same acquisition parameters. The rabbits were divided into two groups: group I (administered RT only) and group II (also administered intramuscular 500 mg dexpanthenol injections for 14 consecutive days after RT). Quantification was performed to compare the groups and the quantification variables were compared using a paired samples t-test, with P value less than 0.05 considered to be statistically significant. Histopathological analysis was also carried out. The post-RT scintigraphies indicated a decrease in the counts in both lungs, suggesting early post-RT injury. The difference between the counts obtained from both lungs in groups I and II was significantly different and favoured group II. Histopathological results confirmed the scintigraphy results. It is possible to estimate post-RT changes in the early period (in contrast to previous data) by lung perfusion scintigraphy. Dexpanthenol may also reduce the effects of RT to a degree. Although this is the first study to report the preventive effects of dexpanthenol on RT injuries, further studies are warranted in this area.

Evaluating the 4-hour and 30-minute rules: effects of room temperature exposure on red blood cell quality and bacterial growth.

PubMed

Ramirez-Arcos, Sandra; Mastronardi, Cherie; Perkins, Heather; Kou, Yuntong; Turner, Tracey; Mastronardi, Emily; Hansen, Adele; Yi, Qi-Long; McLaughlin, Natasha; Kahwash, Eiad; Lin, Yulia; Acker, Jason

2013-04-01

A 30-minute rule was established to limit red blood cell (RBC) exposure to uncontrolled temperatures during storage and transportation. Also, RBC units issued for transfusion should not remain at room temperature (RT) for more than 4 hours (4-hour rule). This study was aimed at determining if single or multiple RT exposures affect RBC quality and/or promote bacterial growth. Growth and RT exposure experiments were performed in RBCs inoculated with Serratia liquefaciens and Serratia marcescens. RBCs were exposed once to RT for 5 hours (S. liquefaciens) or five times to RT for 30 minutes (S. marcescens) with periodic sampling for bacterial counts. Noncontaminated units were exposed to RT once (5 hr) or five times (30 min each) and sampled to measure in vitro quality variables. RBC core temperature was monitored using mock units with temperature loggers. Growth and RT exposure experiments were repeated three and at least six times, respectively. Statistical analysis was done using mixed-model analysis. RBC core temperature ranged from 7.3 to 11.6°C during 30-minute RT exposures and the time to reach 10°C varied from 22 to 55 minutes during 5-hour RT exposures. RBC quality was preserved after single or multiple RT exposures. Increased growth of S. liquefaciens was only observed after 2 hours of continuous RT exposure. S. marcescens concentration increased significantly in multiple-exposed units compared to the controls but did not reach clinically important levels. Single or multiple RT exposures did not affect RBC quality but slightly promoted bacterial growth in contaminated units. The clinical significance of these results remains unclear and needs further investigation. © 2012 American Association of Blood Banks.

The effects of aerobic, resistance, and combination training on insulin sensitivity and secretion in overweight adults from STRRIDE AT/RT: a randomized trial.

PubMed

AbouAssi, Hiba; Slentz, Cris A; Mikus, Catherine R; Tanner, Charles J; Bateman, Lori A; Willis, Leslie H; Shields, A Tamlyn; Piner, Lucy W; Penry, Lorrie E; Kraus, Erik A; Huffman, Kim M; Bales, Connie W; Houmard, Joseph A; Kraus, William E

2015-06-15

Most health organizations recommend a combination of aerobic training (AT) and resistance training (RT), yet few studies have compared their acute (within 24 h of the last exercise bout) and sustained (after 14 days of no exercise training) effects alone and in combination on glucose metabolism. The present study (Studies Targeting Risk Reduction Interventions through Defined Exercise-Aerobic Training and/or Resistance Training) compared the effects of AT, RT, and the combination (AT/RT) on insulin action at both acute and sustained phases. Subjects (N = 196) were 18-70 yr old (mean age = 50 yr), overweight (mean body mass index = 30 kg/m2), sedentary with moderate dyslipidemia, and were randomized into one of three 8-mo exercise groups: 1) RT: 3 days/wk, 8 exercises, 3 sets/exercise, 8-12 repetitions/set; 2) AT: equivalent to ∼19.2 km/wk (12 miles/wk) at 75% peak O2 consumption; 3) AT/RT: the combination of AT and RT. One hundred forty-four subjects completed the intervention. Eighty-eight subjects completed all pre- and postintervention testing visits. Insulin sensitivity, glucose effectiveness, and disposition index were measured via a frequently sampled intravenous glucose tolerance test with subsequent minimal model analyses. AT/RT resulted in greater improvements in insulin sensitivity, β-cell function (disposition index), and glucose effectiveness than either AT or RT alone (all P < 0.05). Approximately 52% of the improvement in insulin sensitivity by AT/RT was retained 14 days after the last exercise training bout. Neither AT or RT led to acute or chronic improvement in sensitivity index. In summary, only AT/RT (which required twice as much time as either alone) led to significant acute and sustained benefits in insulin sensitivity

Adverse Outcomes After Palliative Radiation Therapy for Uncomplicated Spine Metastases: Role of Spinal Instability and Single-Fraction Radiation Therapy

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

Lam, Tai-Chung, E-mail: lamtaichung@gmail.com; Uno, Hajime; Krishnan, Monica

2015-10-01

Purpose: Level I evidence demonstrates equivalent pain response after single-fraction (SF) or multifraction (MF) radiation therapy (RT) for bone metastases. The purpose of this study is to provide additional data to inform the incidence and predictors of adverse outcomes after RT for spine metastases. Methods and Materials: At a single institution, 299 uncomplicated spine metastases (without cord compression, prior RT, or surgery) treated with RT from 2008 to 2013 were retrospectively reviewed. The spinal instability neoplastic score (SINS) was used to assess spinal instability. The primary outcome was time to first spinal adverse event (SAE) at the site, including symptomaticmore » vertebral fracture, hospitalization for site-related pain, salvage surgery, interventional procedure, new neurologic symptoms, or cord compression. Fine and Gray's multivariable model assessed associations of the primary outcome with SINS, SF RT, and other significant baseline factors. Propensity score matched analysis further assessed the relationship of SF RT to first SAEs. Results: The cumulative incidence of first SAE after SF RT (n=66) was 6.8% at 30 days, 16.9% at 90 days, and 23.6% at 180 days. For MF RT (n=233), the incidence was 3.5%, 6.4%, and 9.2%, respectively. In multivariable analysis, SF RT (hazard ratio [HR] = 2.8, 95% confidence interval [CI] 1.5-5.2, P=.001) and SINS ≥11 (HR=2.5 , 95% CI 1.3-4.9, P=.007) were predictors of the incidence of first SAE. In propensity score matched analysis, first SAEs had developed in 22% of patients with SF RT versus 6% of those with MF RT cases (HR=3.9, 95% CI 1.6-9.6, P=.003) at 90 days after RT. Conclusion: In uncomplicated spinal metastases treated with RT alone, spinal instability with SINS ≥11 and SF RT were associated with a higher rate of SAEs.« less

Combination therapy of intravenously injected microglia and radiotherapy prolongs survival in a rat model of spontaneous malignant glioma.

PubMed

Okonogi, Noriyuki; Suzuki, Yoshiyuki; Sato, Hiro; Oike, Takahiro; Yoshimoto, Yuya; Mimura, Kousaku; Noda, Shin-Ei; Okamoto, Masahiko; Tamaki, Tomoaki; Morokoshi, Yukie; Hasegawa, Sumitaka; Ohgaki, Hiroko; Yokoo, Hideaki; Nakano, Takashi

2018-06-18

The aim of this study was to investigate the efficacy of combination therapy with intravenously injected microglia (MI) and radiotherapy (RT) for rat malignant glioma. Transgenic rats expressing v-erbB and spontaneously developing malignant glioma were used. The rats were divided into four groups: control (n = 19), RT alone (n = 10), MI alone (n = 9), and combination of MI and RT (MI+RT) (n = 10). Cranial X-ray irradiation (8 Gy per fraction; once per week) was performed at 50 and 51 weeks of age. Cultured rat microglial cells (5 × 10 6 cells/rat) were intravenously injected via the tail vein within 30 minutes after RT. No evidence of side effects including thrombosis or graft-versus-host disease was noted. Rats treated with RT alone, MI alone, MI+RT, and control survived 60.9, 56.3, 66.0, and 56.1 weeks, respectively. The survival period of MI+RT was significantly longer than that of control (p = 0.014), MI alone (p = 0.027), and RT alone (p = 0.049). Immunohistochemical analysis showed significantly higher number of tumor-infiltrated microglia in the RT alone (p = 0.041) and MI+RT groups (p = 0.014) compared with the control. Significantly more CD8-positive lymphocytes were observed in the MI+RT group (p = 0.049) compared with the control. A positive correlation was found between the number of microglia and CD8-positive lymphocytes (R 2 = 0.556). A positive correlation was also found between CD8-positive lymphocytes and survival periods (R 2 = 0.460). MI+RT increased infiltrated microglia and CD8-positive T cells and prolonged the survival in transgenic rats spontaneously developing malignant glioma. Combined immunocellular therapy and RT may provide a novel treatment strategy for malignant glioma. Copyright © 2018. Published by Elsevier Inc.

Radiocurability by Targeting Tumor Necrosis Factor-{alpha} Using a Bispecific Antibody in Carcinoembryonic Antigen Transgenic Mice

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

Larbouret, Christel; Robert, Bruno; Linard, Christine

2007-11-15

Purpose: Tumor necrosis factor-{alpha} (TNF-{alpha}) enhances radiotherapy (RT) killing of tumor cells in vitro and in vivo. To overcome systemic side effects, we used a bispecific antibody (BsAb) directed against carcinoembryonic antigen (CEA) and TNF-{alpha} to target this cytokine in a CEA-expressing colon carcinoma. We report the evaluation of this strategy in immunocompetent CEA-transgenic mice. Methods and Materials: The murine CEA-transfected colon carcinoma MC-38 was used for all experiments. In vitro, clonogenic assays were performed after RT alone, TNF-{alpha} alone, and RT plus TNF-{alpha}. In vivo, the mice were randomly assigned to treatment groups: control, TNF-{alpha}, BsAb, BsAb plus TNF-{alpha},more » RT, RT plus TNF-{alpha}, and RT plus BsAb plus TNF-{alpha}. Measurements of endogenous TNF-{alpha} mRNA levels and evaluation of necrosis (histologic evaluation) were assessed per treatment group. Results: In vitro, combined RT plus TNF-{alpha} resulted in a significant decrease in the survival fraction at 2 Gy compared with RT alone (p < 0.00001). In vivo, we observed a complete response in 5 (50%) of 10, 2 (20%) of 10, 2 (18.2%) of 11, and 0 (0%) of 12 treated mice in the RT plus BsAb plus TNF-{alpha}, RT plus TNF-{alpha}, RT alone, and control groups, respectively. This difference was statistically significant when TNF-{alpha} was targeted with the BsAb (p = 0.03). The addition of exogenous TNF-{alpha} to RT significantly increased the endogenous TNF-{alpha} mRNA level, particularly when TNF-{alpha} was targeted with BsAb (p < 0.01). The percentages of necrotic area were significantly augmented in the RT plus BsAb plus TNF-{alpha} group. Conclusion: These results suggest that targeting TNF-{alpha} with the BsAb provokes RT curability in a CEA-expressing digestive tumor syngenic model and could be considered as a solid rationale for clinical trials.« less

Revealing the drug-resistant mechanism for diarylpyrimidine analogue inhibitors of HIV-1 reverse transcriptase.

PubMed

Zhang, Hao; Qin, Fang; Ye, Wei; Li, Zeng; Ma, Songyao; Xia, Yan; Jiang, Yi; Zhu, Jiayi; Li, Yixue; Zhang, Jian; Chen, Hai-Feng

2011-09-01

Diaryltriazine (DATA) and diarylpyrimidine (DAPY) were two category inhibitors with highly potent activity for wild type (wt) and four principal mutant types (L100I, K103N, Y181C and Y188L) of HIV-1 reverse transcriptase (RT). We had revealed the drug-resistant mechanism of DATA analogue inhibitors with molecular dynamics simulation and three-dimensional quantitative structure-activity relationship (3D-QSAR) methods. In this work, we investigated the drug-resistant mechanism of DAPY analogue inhibitors. It was found that DAPY analogue inhibitors form more hydrogen bonds and hydrophobic contacts with wild type and mutants of HIV-1 RT than DATA inhibitors. This could explain that DAPY analogue inhibitors are more potent than DATA for the wild type and mutants of HIV-1 RT. Then, 3D-QSAR models were constructed for these inhibitors of wild type and four principal mutant types HIV-1 RT and evaluated by test set compounds. These combined models can be used to design new chemical entities and make quantitative prediction of the bioactivities for HIV-1 RT inhibitors before resorting to in vitro and in vivo experiment. © 2011 John Wiley & Sons A/S.

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

The discovery of student experiences using the Frayer model map as a Tier 2 intervention in secondary science

NASA Astrophysics Data System (ADS)

Miller, Cory D.

The purpose of this study was to discover the student experiences of using the Frayer model map as a Tier 2 intervention in science. As a response to the criticized discrepancy model and the mandates contained in NCLB and the IDEA, response to intervention (RtI) has been implemented in education to increase achievement for all students and to discover what students need further interventions. Based on Cronbach's (1957) aptitude X treatment interaction theory, RtI assumes that progress over time can be measured when interventions are applied. While RtI has been actively implemented in reading and math, it has not been implemented in science. Therefore, it was not known what the experiences of students are using the Frayer model map as a Tier 2 intervention to impact science achievement. The multiple case study used a qualitative methodology that included pre-intervention and post-intervention web-based surveys, field notes during observations, and student work that were collected during the course of the study. The population that was studied was seventh- and eighth-grade students considered at-risk and attend a Title I school in Florida. The sample of the studied population was purposively selected according to a set of criteria similar to Tier 2 selection in RtI. The research question was, "What are the experiences of middle grades students using the Frayer model map as an instructional intervention in science?" The answer to the research question was that the experiences of students using the Frayer model map as a Tier 2 intervention in secondary science can be described as participants perceived the Frayer model map as use as a tool to organize tasks and create meaning while they completed the work independently and with accuracy. Even though there were limitations to quantity of data, the research question was adequately answered. Overall, the study fills a gap in the literature related to RtI and science education.

Radiation Therapy Versus No Radiation Therapy to the Neo-breast Following Skin-Sparing Mastectomy and Immediate Autologous Free Flap Reconstruction for Breast Cancer: Patient-Reported and Surgical Outcomes at 1 Year-A Mastectomy Reconstruction Outcomes Consortium (MROC) Substudy.

PubMed

Cooke, Andrew L; Diaz-Abele, Julian; Hayakawa, Tom; Buchel, Ed; Dalke, Kimberly; Lambert, Pascal

2017-09-01

To determine whether adjuvant radiation therapy (RT) is associated with adverse patient-reported outcomes and surgical complications 1 year after skin-sparing mastectomy and immediate autologous free flap reconstruction for breast cancer. We compared 24 domains of patient-reported outcome measures 1 year after autologous reconstruction between patients who received adjuvant RT and those who did not. A total of 125 patients who underwent surgery between 2012 and 2015 at our institution were included from the Mastectomy Reconstruction Outcomes Consortium study database. Adjusted multivariate models were created incorporating RT technical data, age, cancer stage, estrogen receptor, chemotherapy, breast size, body mass index, and income to determine whether RT was associated with outcomes. At 1 year after surgery, European Organisation for Research and Treatment of Cancer (EORTC) Breast Cancer-Specific Quality of Life Questionnaire breast symptoms were significantly greater in 64 patients who received RT (8-point difference on 100-point ordinal scale, P<.0001) versus 61 who did not receive RT in univariate and multivariate models. EORTC arm symptoms (20-point difference on 100-point ordinal scale, P=.0200) differed on univariate analysis but not on multivariate analysis. All other outcomes-including Numerical Pain Rating Scale, BREAST-Q (Post-operative Reconstruction Module), Patient-Report Outcomes Measurement Information System Profile 29, McGill Pain Questionnaire-Short Form (MPQ-SF) score, Generalized Anxiety Disorder Scale, and Patient Health Questionnaire-were not statistically different between groups. Surgical complications were uncommon and did not differ by treatment. RT to the neo-breast compared with no RT following immediate autologous free flap reconstruction for breast cancer is well tolerated at 1 year following surgery despite patients undergoing RT also having a higher cancer stage and more intensive surgical and systemic treatment. Neo-breast symptoms are more common in patients receiving RT by the EORTC Breast Cancer-Specific Quality of Life Questionnaire but not by the BREAST-Q. Patient-reported results at 1 year after surgery suggest RT following immediate autologous free flap breast reconstruction is well tolerated. Copyright © 2017 Elsevier Inc. All rights reserved.

Synergistically combining Optical and Thermal radiative transfer modelswithin the EO-LDAS data assimilation framework to estimate land surfaceand component temperatures from MODIS and Sentinel-3

NASA Astrophysics Data System (ADS)

Timmermans, J.; Gomez-Dans, J. L.; Verhoef, W.; Tol, C. V. D.; Lewis, P.

2017-12-01

Evapotranspiration (ET) cannot be directly measured from space. Instead it relies on modelling approaches that use several land surface parameters (LSP), LAI and LST, in conjunction with meteorological parameters. Such a modelling approach presents two caveats: the validity of the model, and the consistency between the different input parameters. Often this second step is not considered, ignoring that without good inputs no decent output can provided. When LSP- dynamics contradict each other, the output of the model cannot be representative of reality. At present however, the LSPs used in large scale ET estimations originate from different single-sensor retrieval-approaches and even from different satellite sensors. In response, the Earth Observation Land Data Assimilation System (EOLDAS) was developed. EOLDAS uses a multi-sensor approach to couple different satellite observations/types to radiative transfer models (RTM), consistently. It is therefore capable of synergistically estimating a variety of LSPs. Considering that ET is most sensitive to the temperatures of the land surface (components), the goal of this research is to expand EOLDAS to the thermal domain. This research not only focuses on estimating LST, but also on retrieving (soil/vegetation, Sunlit/shaded) component temperatures, to facilitate dual/quad-source ET models. To achieve this, The Soil Canopy Observations of Photosynthesis and Energy (SCOPE) model was integrated into EOLDAS. SCOPE couples key-parameters to key-processes, such as photosynthesis, ET and optical/thermal RT. In this research SCOPE was also coupled to MODTRAN RTM, in order to estimate BOA component temperatures directly from TOA observations. This paper presents the main modelling steps of integrating these complex models into an operational platform. In addition it highlights the actual retrieval using different satellite observations, such as MODIS and Sentinel-3, and meteorological variables from the ERA-Interim.

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

Qin, Rosie; Olson, Adam; Singh, Bhavana

Purpose: Ipilimumab and radiation therapy (RT) are standard treatments for advanced melanoma; preclinical models suggest the potential for synergy. However, limited clinical information exists regarding safety and optimal timing of the combination. Methods and Materials: We reviewed the records of consecutive patients with unresectable stage 3 or 4 melanoma treated with ipilimumab. Patients were categorized as having received RT or not. Differences were estimated between these 2 cohorts. Results: We identified 88 patients treated with ipilimumab. At baseline, the ipilimumab-plus-RT group (n=44) had more unfavorable characteristics. Despite this, overall survival, progression-free survival, and both immune-related and non–immune-related toxicity were notmore » statistically different (P=.67). Patients who received ipilimumab before RT had an increased duration of irradiated tumor response compared with patients receiving ipilimumab after RT (74.7% vs 44.8% at 12 months; P=.01, log-rank test). In addition, patients receiving ablative RT had non–statistically significantly improved median overall survival (19.6 vs 10.2 months), as well as 6-month (95.1% vs 72.7%) and 12-month (79.7% vs 48.5%) survival rates, compared with those treated with conventionally fractionated RT. Conclusions: We found that both ablative and conventionally fractionated RT can be safely administered with ipilimumab without a clinically apparent increase in toxicity. Patients who received ipilimumab before RT had an increased duration of irradiated tumor response.« less

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

Sanchez-Nieto, Beatriz, E-mail: bsanchez@fis.puc.cl; Goset, Karen C.; Caviedes, Ivan

Purpose: To propose multivariate predictive models for changes in pulmonary function tests ({Delta}PFTs) with respect to preradiotherapy (pre-RT) values in patients undergoing RT for breast cancer and lymphoma. Methods and Materials: A prospective study was designed to measure {Delta}PFTs of patients undergoing RT. Sixty-six patients were included. Spirometry, lung capacity (measured by helium dilution), and diffusing capacity of carbon monoxide tests were used to measure lung function. Two lung definitions were considered: paired lung vs. irradiated lung (IL). Correlation analysis of dosimetric parameters (mean lung dose and the percentage of lung volume receiving more than a threshold dose) and {Delta}PFTsmore » was carried out to find the best dosimetric predictor. Chemotherapy, age, smoking, and the selected dose-volume parameter were considered as single and interaction terms in a multivariate analysis. Stability of results was checked by bootstrapping. Results: Both lung definitions proved to be similar. Modeling was carried out for IL. Acute and late damage showed the highest correlations with volumes irradiated above {approx}20 Gy (maximum R{sup 2} = 0.28) and {approx}40 Gy (maximum R{sup 2} = 0.21), respectively. RT alone induced a minor and transitory restrictive defect (p = 0.013). Doxorubicin-cyclophosphamide-paclitaxel (Taxol), when administered pre-RT, induced a late, large restrictive effect, independent of RT (p = 0.031). Bootstrap values confirmed the results. Conclusions: None of the dose-volume parameters was a perfect predictor of outcome. Thus, different predictor models for {Delta}PFTs were derived for the IL, which incorporated other nondosimetric parameters mainly through interaction terms. Late {Delta}PFTs seem to behave more serially than early ones. Large restrictive defects were demonstrated in patients pretreated with doxorubicin-cyclophosphamide-paclitaxel.« less

Real-Time MRI-Guided Endovascular Recanalization of Chronic Total Arterial Occlusion in a Swine Model

PubMed Central

Raval, Amish N.; Karmarkar, Parag V.; Guttman, Michael A.; Ozturk, Cengizhan; Sampath, Smita; DeSilva, Ranil; Aviles, Ronnier J.; Xu, Minnan; Wright, Victor J.; Schenke, William H.; Kocaturk, Ozgur; Dick, Alexander J.; Raman, Venkatesh K.; Atalar, Ergin; McVeigh, Elliot R.; Lederman, Robert J.

2006-01-01

Background Endovascular recanalization (guidewire traversal) of peripheral artery chronic total occlusion (CTO) can be challenging. X-Ray angiography resolves CTO poorly. Virtually “blind” device advancement during X-ray-guided interventions can lead to procedure failure, perforation and hemorrhage. Alternatively, magnetic resonance imaging (MRI) may delineate the artery within the occluded segment to enhance procedural safety and success. We hypothesized that real-time MRI (rtMRI) guided CTO recanalization can be accomplished in an animal model. Methods and Results Carotid artery CTO was created by balloon injury in 19 lipid overfed swine. After 6–8 weeks, two underwent direct necropsy analysis for histology, three underwent primary X-ray-guided CTO recanalization attempts, and the remaining 14 underwent rtMRI-guided recanalization attempts in a 1.5T interventional MRI system. rtMRI intervention used custom CTO catheters and guidewires that incorporated MRI receiver antennae to enhance device visibility. The mean length of the occluded segments was 13.3 ± 1.6cm. rtMRI-guided CTO recanalization was successful in 11/14 swine and only 1/3 swine using X-ray alone. After unsuccessful rtMRI (n = 3), X-ray-guided attempts also were all unsuccessful. Conclusions Recanalization of long CTO is feasible entirely using rtMRI guidance. Low profile clinical-grade devices will be required to translate this experience to humans. Endovascular recanalization of chronic total arterial occlusion (CTO) is challenging under conventional X-ray guidance because devices are advanced almost blindly. MRI can image CTO borders and luminal contents, and could potentially guide these procedures. We test the feasibility of real-time MRI guided wire traversal in a swine model of peripheral artery CTO using custom active MRI catheters. PMID:16490819

Evaluation of bulk heat fluxes from atmospheric datasets

NASA Astrophysics Data System (ADS)

Farmer, Benton

Heat fluxes at the air-sea interface are an important component of the Earth's heat budget. In addition, they are an integral factor in determining the sea surface temperature (SST) evolution of the oceans. Different representations of these fluxes are used in both the atmospheric and oceanic communities for the purpose of heat budget studies and, in particular, for forcing oceanic models. It is currently difficult to quantify the potential impact varying heat flux representations have on the ocean response. In this study, a diagnostic tool is presented that allows for a straightforward comparison of surface heat flux formulations and atmospheric data sets. Two variables, relaxation time (RT) and the apparent temperature (T*), are derived from the linearization of the bulk formulas. They are then calculated to compare three bulk formulae and five atmospheric datasets. Additionally, the linearization is expanded to the second order to compare the amount of residual flux present. It is found that the use of a bulk formula employing a constant heat transfer coefficient produces longer relaxation times and contains a greater amount of residual flux in the higher order terms of the linearization. Depending on the temperature difference, the residual flux remaining in the second order and above terms can reach as much as 40--50% of the total residual on a monthly time scale. This is certainly a non-negligible residual flux. In contrast, a bulk formula using a stability and wind dependent transfer coefficient retains much of the total flux in the first order term, as only a few percent remain in the residual flux. Most of the difference displayed among the bulk formulas stems from the sensitivity to wind speed and the choice of a constant or spatially varying transfer coefficient. Comparing the representation of RT and T* provides insight into the differences among various atmospheric datasets. In particular, the representations of the western boundary current, upwelling, and the Indian monsoon regions of the oceans have distinct characteristics within each dataset. Localized regions, such as the eastern Mexican and Central American coasts, are also shown to have variability among the datasets. The use of this technique for the evaluation of bulk formulae and datasets is an efficient method for identifying the unique characteristics of each. Furthermore, insight into the heat fluxes produced by particular bulk formula or dataset can be gained.

Effect of low frequency ultrasound on combined rt-PA and eptifibatide thrombolysis in human clots.

PubMed

Meunier, Jason M; Holland, Christy K; Pancioli, Arthur M; Lindsell, Christopher J; Shaw, George J

2009-01-01

Fibrinolytics such as recombinant tissue plasminogen activator (rt-PA) are used to treat thrombotic disease such as acute myocardial infarction (AMI) and ischemic stroke. Interest in increasing efficacy and reducing side effects has led to the study of adjuncts such as GP IIb-IIIa inhibitors and ultrasound (US) enhanced thrombolysis. Currently, GP IIb-IIIa inhibitor and fibrinolytic treatment are often used in AMI, and are under investigation for stroke treatment. However, little is known of the efficacy of combined GP IIb-IIIa inhibitor, fibrinolytic and ultrasound treatment. We measure the lytic efficacy of rt-PA, eptifibatide (Epf) and 120 kHz ultrasound treatment in an in-vitro human clot model. Blood was drawn from 15 subjects after IRB approval. Clots were made in 20 microL pipettes, and placed in a water tank for microscopic visualization during lytic treatment. Clots were exposed to control, rt-PA (rt-PA), eptifibatide (Epf), or rt-PA+eptifibatide (rt-PA + Epf), with (+US) or without (-US) ultrasound for 30 minutes at 37 degrees C in human plasma. Clot lysis was measured over time, using a microscopic imaging technique. The fractional clot loss (FCL) and initial lytic rate (LR) were used to quantify lytic efficacy. LR values for (- US) treated clots were 0.8+/-0.1(control), 1.8+/-0.3 (Epf), 1.5+/-0.2 (rt-PA), and 1.3+/-0.4 (rt-PA + Epf) (% clot width/minute) respectively. In comparison, the (+ US) group exhibited LR values of 1.6+/-0.2 (control), 4.3+/-0.4 (Epf), 6.3+/-0.4 (rt-PA), and 4.6+/-0.6 (rt-PA + Epf). For (- US) treated clots, FCL was 6.0+/-0.8 (control), 9.2+/-2.5 (Epf), 15.6+/-1.7 (rt-PA), and 28.0+/-2.2% (rt-PA + Epf) respectively. FCL for (+ US) clots was 13.5+/-2.4 (control), 20.7+/-6.4 (Epf), 44.4+/-3.6 (rt-PA) and 30.3+/-3.6% (rt-PA + Epf) respectively. Although the addition of eptifibatide enhances the in-vitro lytic efficacy of rt-PA in the absence of ultrasound, the efficacy of ultrasound and rt-PA is greater than that of combined ultrasound, rt-PA and eptifibatide exposure.

Effect of Low Frequency Ultrasound on Combined rt-PA and Eptifibatide Thrombolysis in Human Clots

PubMed Central

Meunier, Jason M.; Holland, Christy K.; Pancioli, Arthur M.; Lindsell, Christopher J.; Shaw, George J.

2009-01-01

Introduction Fibrinolytics such as recombinant tissue plasminogen activator (rt-PA) are used to treat thrombotic disease such as acute myocardial infarction (AMI) and ischemic stroke. Interest in increasing efficacy and reducing side effects has led to the study of adjuncts such as GP IIb-IIIa inhibitors and ultrasound (US) enhanced thrombolysis. Currently, GP IIb-IIIa inhibitor and fibrinolytic treatment are often used in AMI, and are under investigation for stroke treatment. However, little is known of the efficacy of combined GP IIb-IIIa inhibitor, fibrinolytic and ultrasound treatment. We measure the lytic efficacy of rt-PA, eptifibatide (Epf) and 120 kHz ultrasound treatment in an in-vitro human clot model. Materials and Methods Blood was drawn from 15 subjects after IRB approval. Clots were made in 20 μL pipettes, and placed in a water tank for microscopic visualization during lytic treatment. Clots were exposed to control, rt-PA (rt-PA), eptifibatide (Epf), or rt-PA+eptifibatide (rt-PA+Epf), with or without ultrasound for 30 minutes at 37°C in human plasma. Clot lysis was measured over time, using a microscopic imaging technique. The fractional clot loss (FCL) and initial lytic rate (LR) were used to quantify lytic efficacy. Results and Conclusions LR values for (−US) treated clots were 0.8±0.1(control), 1.8±0.3 (Epf), 1.5±0.2 (rt-PA), and 1.3±0.4 (rt-PA+Epf) (% clot width/minute) respectively. In comparison, the (+US) group exhibited LR values of 1.6±0.2 (control), 4.3±0.4 (Epf), 6.3±0.4 (rt-PA), and 4.6±0.6 (rt-PA+Epf). For (−US) treated clots, FCL was 6.0±0.8 (control), 9.2±2.5 (Epf), 15.6±1.7 (rt-PA), and 28.0±2.2% (rt-PA+Epf) respectively. FCL for (+US) clots was 13.5±2.4 (control), 20.7±6.4 (Epf), 44.4±3.6 (rt-PA) and 30.3±3.6% (rt-PA+Epf) respectively. Although the addition of eptifibatide enhances the in-vitro lytic efficacy of rt-PA in the absence of ultrasound, the efficacy of ultrasound and rt-PA is greater than that of combined ultrasound, rt-PA and eptifibatide exposure. PMID:18619651

Reaction time in ankle movements: a diffusion model analysis

PubMed Central

Michmizos, Konstantinos P.; Krebs, Hermano Igo

2015-01-01

Reaction time (RT) is one of the most commonly used measures of neurological function and dysfunction. Despite the extensive studies on it, no study has ever examined the RT in the ankle. Twenty-two subjects were recruited to perform simple, 2- and 4-choice RT tasks by visually guiding a cursor inside a rectangular target with their ankle. RT did not change with spatial accuracy constraints imposed by different target widths in the direction of the movement. RT increased as a linear function of potential target stimuli, as would be predicted by Hick–Hyman law. Although the slopes of the regressions were similar, the intercept in dorsal–plantar (DP) direction was significantly smaller than the intercept in inversion–eversion (IE) direction. To explain this difference, we used a hierarchical Bayesian estimation of the Ratcliff's (Psychol Rev 85:59, 1978) diffusion model parameters and divided processing time into cognitive components. The model gave a good account of RTs, their distribution and accuracy values, and hence provided a testimony that the non-decision processing time (overlap of posterior distributions between DP and IE < 0.045), the boundary separation (overlap of the posterior distributions < 0.1) and the evidence accumulation rate (overlap of the posterior distributions < 0.01) components of the RT accounted for the intercept difference between DP and IE. The model also proposed that there was no systematic change in non-decision processing time or drift rate when spatial accuracy constraints were altered. The results were in agreement with the memory drum hypothesis and could be further justified neurophysiologically by the larger innervation of the muscles controlling DP movements. This study might contribute to assessing deficits in sensorimotor control of the ankle and enlighten a possible target for correction in the framework of our on-going effort to develop robotic therapeutic interventions to the ankle of children with cerebral palsy. PMID:25030966

Nomogram Prediction of Overall Survival After Curative Irradiation for Uterine Cervical Cancer

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

Seo, YoungSeok; Yoo, Seong Yul; Kim, Mi-Sook

Purpose: The purpose of this study was to develop a nomogram capable of predicting the probability of 5-year survival after radical radiotherapy (RT) without chemotherapy for uterine cervical cancer. Methods and Materials: We retrospectively analyzed 549 patients that underwent radical RT for uterine cervical cancer between March 1994 and April 2002 at our institution. Multivariate analysis using Cox proportional hazards regression was performed and this Cox model was used as the basis for the devised nomogram. The model was internally validated for discrimination and calibration by bootstrap resampling. Results: By multivariate regression analysis, the model showed that age, hemoglobin levelmore » before RT, Federation Internationale de Gynecologie Obstetrique (FIGO) stage, maximal tumor diameter, lymph node status, and RT dose at Point A significantly predicted overall survival. The survival prediction model demonstrated good calibration and discrimination. The bootstrap-corrected concordance index was 0.67. The predictive ability of the nomogram proved to be superior to FIGO stage (p = 0.01). Conclusions: The devised nomogram offers a significantly better level of discrimination than the FIGO staging system. In particular, it improves predictions of survival probability and could be useful for counseling patients, choosing treatment modalities and schedules, and designing clinical trials. However, before this nomogram is used clinically, it should be externally validated.« less

Modeling aging effects on two-choice tasks: response signal and response time data.

PubMed

Ratcliff, Roger

2008-12-01

In the response signal paradigm, a test stimulus is presented, and then at one of a number of experimenter-determined times, a signal to respond is presented. Response signal, standard response time (RT), and accuracy data were collected from 19 college-age and 19 60- to 75-year-old participants in a numerosity discrimination task. The data were fit with 2 versions of the diffusion model. Response signal data were modeled by assuming a mixture of processes, those that have terminated before the signal and those that have not terminated; in the latter case, decisions are based on either partial information or guessing. The effects of aging on performance in the regular RT task were explained the same way in the models, with a 70- to 100-ms increase in the nondecision component of processing, more conservative decision criteria, and more variability across trials in drift and the nondecision component of processing, but little difference in drift rate (evidence). In the response signal task, the primary reason for a slower rise in the response signal functions for older participants was variability in the nondecision component of processing. Overall, the results were consistent with earlier fits of the diffusion model to the standard RT task for college-age participants and to the data from aging studies using this task in the standard RT procedure. Copyright (c) 2009 APA, all rights reserved.

Modeling Aging Effects on Two-Choice Tasks: Response Signal and Response Time Data

PubMed Central

Ratcliff, Roger

2009-01-01

In the response signal paradigm, a test stimulus is presented, and then at one of a number of experimenter-determined times, a signal to respond is presented. Response signal, standard response time (RT), and accuracy data were collected from 19 college-age and 19 60- to 75-year-old participants in a numerosity discrimination task. The data were fit with 2 versions of the diffusion model. Response signal data were modeled by assuming a mixture of processes, those that have terminated before the signal and those that have not terminated; in the latter case, decisions are based on either partial information or guessing. The effects of aging on performance in the regular RT task were explained the same way in the models, with a 70- to 100-ms increase in the nondecision component of processing, more conservative decision criteria, and more variability across trials in drift and the nondecision component of processing, but little difference in drift rate (evidence). In the response signal task, the primary reason for a slower rise in the response signal functions for older participants was variability in the nondecision component of processing. Overall, the results were consistent with earlier fits of the diffusion model to the standard RT task for college-age participants and to the data from aging studies using this task in the standard RT procedure. PMID:19140659

Factors associated with the rectal temperature of Holstein dairy cows during the first 10 days in milk.

PubMed

Wenz, J R; Moore, D A; Kasimanickam, R

2011-04-01

Daily evaluation of rectal temperature (RT) during the first 10 d in milk (DIM) is used to facilitate the early identification of postpartum complications, particularly metritis in dairy cows. The factors associated with RT of postpartum dairy cows have not been clearly established and the RT threshold used to define fever has been variable. The objectives were to identify factors associated with the RT of postpartum dairy cows and provide descriptive statistics of the RT during the first 10 DIM to clarify the normal range of RT for cows. Daily RT was evaluated from 1 to 10 DIM for all cows calving during 2 consecutive summers on a single 1,500-cow Holstein dairy. Cows were placed into metabolic/digestive (METB), infectious (INF), and no recorded disease (NONE) groups based on disease diagnoses during the first 10 DIM. Cows were grouped based on calving difficulty and parity. Multiple linear regression models with repeated measures were used to evaluate the factors associated with RT. Three hundred and ninety-two cows were evaluated, of which 45% were primiparous and 32% required assistance at calving. No difference was observed in calving assistance by parity. First disease diagnoses peaked in the INF and METB groups at 3 and 1 DIM, respectively. The RT of primiparous cows was 0.1 to 0.2°C higher than that of multiparous cows from 1 to 8 DIM, accounting for calving difficulty, twin births, month of calving, and disease group in the model. The INF group cows had a higher RT than did NONE group cows (38.9±0.04 to 39.2±0.73 vs. 38.7±0.03°C, respectively) on each of the first 10 DIM, which was approximately 0.6°C higher from 3 to 5 DIM. The RT of cows with metritis was at least 0.1°C higher (38.8±0.05°C) than that of NONE group cows beginning 4 d before diagnosis. The mean RT of primiparous, defined healthy (NONE group) cows was 38.8±0.02°C, with an upper normal limit (mean+2 SD) of 39.6°C. The mean RT of multiparous cows in the NONE group during the first 10 DIM was 38.7±0.01°C, with an upper normal limit of 39.5°C. The RT of dairy cattle during the first 10 DIM was associated with parity, month of calving, and an infectious disease diagnosis, particularly the diagnosis of metritis. The normal RT of dairy cattle in the immediate postpartum period, during the warm summer months, is potentially higher than that generally reported. Copyright © 2011 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

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.

Influence of limited proteolysis, detergent treatment and lyophilization on the phenoloxidase activity of Rapana thomasiana hemocyanin.

PubMed

Idakieva, Krassimira; Siddiqui, Nurul Islam; Meersman, Filip; De Maeyer, Marc; Chakarska, Irena; Gielens, Constant

2009-08-01

The intrinsic and inducible phenoloxidase (PO) activity of Rapana thomasiana hemocyanin (RtH) and its substructures were studied. With catechol as substrate, a weak o-diPO activity was measured for the didecameric RtH and its subunits. Some activation of the o-diPO activity of RtH was achieved by limited treatment with subtilisin and by incubation of RtH with 2.9 mM sodium dodecyl sulphate (SDS), suggesting an enhanced substrate access to the active sites. The highest artificial induction of o-diPO activity in RtH, however, was obtained by lyophilization of the protein. This is ascribed to conformational changes during the lyophilization process of the didecameric RtH molecules, affecting the accessibility of the active sites. These conformational changes must be very small, since Fourier-transform infrared and circular dichroism spectroscopies did not reveal any changes in secondary structure of lyophilized RtH. The difference in accessibility of the copper containing active site for substrates between catechol oxidase and functional unit RtH2-e was demonstrated by molecular modeling and surface area accessibility calculations. The low level of intrinsic PO activity in the investigated hemocyanin is related to the inaccessibility of the binuclear copper active sites to the substrates.

Coactivation of response initiation processes with redundant signals.

PubMed

Maslovat, Dana; Hajj, Joëlle; Carlsen, Anthony N

2018-05-14

During reaction time (RT) tasks, participants respond faster to multiple stimuli from different modalities as compared to a single stimulus, a phenomenon known as the redundant signal effect (RSE). Explanations for this effect typically include coactivation arising from the multiple stimuli, which results in enhanced processing of one or more response production stages. The current study compared empirical RT data with the predictions of a model in which initiation-related activation arising from each stimulus is additive. Participants performed a simple wrist extension RT task following either a visual go-signal, an auditory go-signal, or both stimuli with the auditory stimulus delayed between 0 and 125 ms relative to the visual stimulus. Results showed statistical equivalence between the predictions of an additive initiation model and the observed RT data, providing novel evidence that the RSE can be explained via a coactivation of initiation-related processes. It is speculated that activation summation occurs at the thalamus, leading to the observed facilitation of response initiation. Copyright © 2018 Elsevier B.V. All rights reserved.

Is there a general task switching ability?

PubMed

Yehene, Einat; Meiran, Nachshon

2007-11-01

Participants were tested on two analogous task switching paradigms involving Shape/Size tasks and Vertical/Horizontal tasks, respectively, and three measures of psychometric intelligence, tapping fluid, crystallized and perceptual speed abilities. The paradigms produced similar patterns of group mean reaction times (RTs) and the vast majority of the participants showed switching cost (switch RT minus repeat RT), mixing cost (repeat RT minus single-task RT) and congruency effects. The shared intra-individual variance across paradigms and with psychometric intelligence served as criteria for general ability. Structural equations modeling indicated that switching cost with ample preparation ("residual cost") and mixing cost met these criteria. However, switching cost with little preparation and congruency effects were predominantly paradigm specific.

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.

Building a new predictor for multiple linear regression technique-based corrective maintenance turnaround time.

PubMed

Cruz, Antonio M; Barr, Cameron; Puñales-Pozo, Elsa

2008-01-01

This research's main goals were to build a predictor for a turnaround time (TAT) indicator for estimating its values and use a numerical clustering technique for finding possible causes of undesirable TAT values. The following stages were used: domain understanding, data characterisation and sample reduction and insight characterisation. Building the TAT indicator multiple linear regression predictor and clustering techniques were used for improving corrective maintenance task efficiency in a clinical engineering department (CED). The indicator being studied was turnaround time (TAT). Multiple linear regression was used for building a predictive TAT value model. The variables contributing to such model were clinical engineering department response time (CE(rt), 0.415 positive coefficient), stock service response time (Stock(rt), 0.734 positive coefficient), priority level (0.21 positive coefficient) and service time (0.06 positive coefficient). The regression process showed heavy reliance on Stock(rt), CE(rt) and priority, in that order. Clustering techniques revealed the main causes of high TAT values. This examination has provided a means for analysing current technical service quality and effectiveness. In doing so, it has demonstrated a process for identifying areas and methods of improvement and a model against which to analyse these methods' effectiveness.

Phase Measurement of Cognitive Impairment Specific to Radiotherapy

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

Armstrong, Carol L., E-mail: armstrongc@email.chop.edu; Department of Pediatrics, Division of Neuro-Oncology, University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania; Shera, David M.

Purpose: Memory impairment is an early-delayed effect of radiotherapy (RT). The prospective longitudinal measurement of the cognitive phase effects from RT was conducted on treated and untreated brain tumor patients. The study design investigated semantic vs. perceptual and visual vs. verbal memory to determine the most disease-specific measure of RT-related changes and understanding of the neurotoxicity from RT to the brain. Methods and Materials: Tests of memory that had previously shown RT-related phasic changes were compared with experimental tests of memory to test hypotheses about cognition targeted to the neural toxicity of RT. The results from 41 irradiated and 29more » nonirradiated patients with low-grade, supratentorial tumors were analyzed. The methods controlled for comorbid white matter risk, recurrence, interval after treatment, and age (18-69 years). The effects were examined before RT and at three points after RT to 1 year using a mixed effects model that included interval, group, surgical status, medication use, practice, and individual random effects. Four new tests of memory and other candidate cognitive tests were investigated, and a post hoc analysis of a comprehensive battery of tests was performed to identify the cognitive processes most specific to RT. Results: The RT effects on memory were identified in the treated group only; among the new tests of memory and the complete neurocognitive battery, the RT effects were significant only for delayed recall (p < 0.009) and interval to recognize (p < 0.002). Tumor location was not related to the treatment effect. Memory decline was specific to retrieval of semantic memories; a double dissociation of semantic from perceptual visual memory was demonstrated in the RT group. Conclusions: These results implicate memory dependent on the semantic cortex and the hippocampal memory system. A cognitive measurement that is brief but specific to neural mechanisms is effective and feasible for studies of RT damage.« less

Mechanistic Characterization and Molecular Modeling of Hepatitis B Virus Polymerase Resistance to Entecavir

PubMed Central

Walsh, Ann W.; Langley, David R.; Colonno, Richard J.; Tenney, Daniel J.

2010-01-01

Background Entecavir (ETV) is a deoxyguanosine analog competitive inhibitor of hepatitis B virus (HBV) polymerase that exhibits delayed chain termination of HBV DNA. A high barrier to entecavir-resistance (ETVr) is observed clinically, likely due to its potency and a requirement for multiple resistance changes to overcome suppression. Changes in the HBV polymerase reverse-transcriptase (RT) domain involve lamivudine-resistance (LVDr) substitutions in the conserved YMDD motif (M204V/I ± L180M), plus an additional ETV-specific change at residues T184, S202 or M250. These substitutions surround the putative dNTP binding site or primer grip regions of the HBV RT. Methods/Principal Findings To determine the mechanistic basis for ETVr, wildtype, lamivudine-resistant (M204V, L180M) and ETVr HBVs were studied using in vitro RT enzyme and cell culture assays, as well as molecular modeling. Resistance substitutions significantly reduced ETV incorporation and chain termination in HBV DNA and increased the ETV-TP inhibition constant (Ki) for HBV RT. Resistant HBVs exhibited impaired replication in culture and reduced enzyme activity (kcat) in vitro. Molecular modeling of the HBV RT suggested that ETVr residue T184 was adjacent to and stabilized S202 within the LVDr YMDD loop. ETVr arose through steric changes at T184 or S202 or by disruption of hydrogen-bonding between the two, both of which repositioned the loop and reduced the ETV-triphosphate (ETV-TP) binding pocket. In contrast to T184 and S202 changes, ETVr at primer grip residue M250 was observed during RNA-directed DNA synthesis only. Experimentally, M250 changes also impacted the dNTP-binding site. Modeling suggested a novel mechanism for M250 resistance, whereby repositioning of the primer-template component of the dNTP-binding site shifted the ETV-TP binding pocket. No structural data are available to confirm the HBV RT modeling, however, results were consistent with phenotypic analysis of comprehensive substitutions of each ETVr position. Conclusions Altogether, ETVr occurred through exclusion of ETV-TP from the dNTP-binding site, through different, novel mechanisms that involved lamivudine-resistance, ETV-specific substitutions, and the primer-template. PMID:20169198

Mechanistic characterization and molecular modeling of hepatitis B virus polymerase resistance to entecavir.

PubMed

Walsh, Ann W; Langley, David R; Colonno, Richard J; Tenney, Daniel J

2010-02-12

Entecavir (ETV) is a deoxyguanosine analog competitive inhibitor of hepatitis B virus (HBV) polymerase that exhibits delayed chain termination of HBV DNA. A high barrier to entecavir-resistance (ETVr) is observed clinically, likely due to its potency and a requirement for multiple resistance changes to overcome suppression. Changes in the HBV polymerase reverse-transcriptase (RT) domain involve lamivudine-resistance (LVDr) substitutions in the conserved YMDD motif (M204V/I +/- L180M), plus an additional ETV-specific change at residues T184, S202 or M250. These substitutions surround the putative dNTP binding site or primer grip regions of the HBV RT. To determine the mechanistic basis for ETVr, wildtype, lamivudine-resistant (M204V, L180M) and ETVr HBVs were studied using in vitro RT enzyme and cell culture assays, as well as molecular modeling. Resistance substitutions significantly reduced ETV incorporation and chain termination in HBV DNA and increased the ETV-TP inhibition constant (K(i)) for HBV RT. Resistant HBVs exhibited impaired replication in culture and reduced enzyme activity (k(cat)) in vitro. Molecular modeling of the HBV RT suggested that ETVr residue T184 was adjacent to and stabilized S202 within the LVDr YMDD loop. ETVr arose through steric changes at T184 or S202 or by disruption of hydrogen-bonding between the two, both of which repositioned the loop and reduced the ETV-triphosphate (ETV-TP) binding pocket. In contrast to T184 and S202 changes, ETVr at primer grip residue M250 was observed during RNA-directed DNA synthesis only. Experimentally, M250 changes also impacted the dNTP-binding site. Modeling suggested a novel mechanism for M250 resistance, whereby repositioning of the primer-template component of the dNTP-binding site shifted the ETV-TP binding pocket. No structural data are available to confirm the HBV RT modeling, however, results were consistent with phenotypic analysis of comprehensive substitutions of each ETVr position. Altogether, ETVr occurred through exclusion of ETV-TP from the dNTP-binding site, through different, novel mechanisms that involved lamivudine-resistance, ETV-specific substitutions, and the primer-template.

Coupled retrieval of aerosol properties and land surface reflection using the Airborne Multiangle SpectroPolarimetric Imager

NASA Astrophysics Data System (ADS)

Xu, Feng; van Harten, Gerard; Diner, David J.; Kalashnikova, Olga V.; Seidel, Felix C.; Bruegge, Carol J.; Dubovik, Oleg

2017-07-01

The Airborne Multiangle SpectroPolarimetric Imager (AirMSPI) has been flying aboard the NASA ER-2 high-altitude aircraft since October 2010. In step-and-stare operation mode, AirMSPI acquires radiance and polarization data in bands centered at 355, 380, 445, 470*, 555, 660*, 865*, and 935 nm (* denotes polarimetric bands). The imaged area covers about 10 km by 11 km and is typically observed from nine viewing angles between ±66° off nadir. For a simultaneous retrieval of aerosol properties and surface reflection using AirMSPI, an efficient and flexible retrieval algorithm has been developed. It imposes multiple types of physical constraints on spectral and spatial variations of aerosol properties as well as spectral and temporal variations of surface reflection. Retrieval uncertainty is formulated by accounting for both instrumental errors and physical constraints. A hybrid Markov-chain/adding-doubling radiative transfer (RT) model is developed to combine the computational strengths of these two methods in modeling polarized RT in vertically inhomogeneous and homogeneous media, respectively. Our retrieval approach is tested using 27 AirMSPI data sets with low to moderately high aerosol loadings, acquired during four NASA field campaigns plus one AirMSPI preengineering test flight. The retrieval results including aerosol optical depth, single-scattering albedo, aerosol size and refractive index are compared with Aerosol Robotic Network reference data. We identify the best angular combinations for 2, 3, 5, and 7 angle observations from the retrieval quality assessment of various angular combinations. We also explore the benefits of polarimetric and multiangular measurements and target revisits in constraining aerosol property and surface reflection retrieval.

Is organic matter alone sufficient to predict isoproturon sorption in calcareous soils?

PubMed

El Arfaoui, Achouak; Sayen, Stéphanie; Paris, Michaël; Keziou, Amor; Couderchet, Michel; Guillon, Emmanuel

2012-08-15

Eleven soils collected from Champagne-Ardenne area (France) were used to investigate isoproturon sorption in laboratory conditions. Our results identified the organic matter (OM) and the ratio of calcite content to OM content (Rt) as the main two parameters governing isoproturon retention in soils. While organic matter favored pesticide sorption, calcite had an antagonistic effect since it limited isoproturon retention. The Rt ratio of calcite content to organic matter content in soils appeared to be a parameter that should be considered in predictive models in addition to OM in regions presenting calcareous soils. Adsorption of isoproturon as a function of Rt and OM was successfully described through a simple empirical model. Copyright © 2012 Elsevier B.V. All rights reserved.

TMPA Products 3B42RT & 3B42V6: Evaluation and Application in Qinghai-Tibet Plateau

NASA Astrophysics Data System (ADS)

Hao, Z.; Sun, L.; Wang, J.

2012-04-01

Hydrological researchers in Qinghai-Tibet Plateau tend to be haunted by deficiency of station gauged precipitation data for the sparse and uneven distribution of local meteorological stations. Fortunately, alternative data can be obtained from TRMM (Tropic Rainfall Measurement Mission) satellite. Preliminary evaluation and necessary correction of TRMM satellite rainfall products is required for the sake of reliability and suitability considering that TRMM precipitation is unconventional and natural condition in Qinghai-Tibet Plateau is unusually complicated. 3B42RT and 3B42V6 products from TRMM Multisatellite Precipitation Analysis(TMPA) are evaluated in northeast Qinghai-Tibet Plateau with 50 stations quality-controlled gauged daily precipitation as the benchmark precipitation set. It is found that the RT data overestimates the actual precipitation greatly while V6 only overestimates it slightly. RT data shows different seasonal and inter-annual accuracies. Summer and autumn see better accuracies than winter and spring and wet years see higher accuracies than dry years. Latitude is believed to be an important factor that influences the accuracy of satellite precipitation. Both RT and V6 can reflect the general pattern of the spatial distribution of precipitation even though RT overestimates the quantity greatly. A new parameter, accumulated precipitation weight point (APWP), was introduced to describe the temporal-spatial pattern evolution of precipitation. The APWP of both RT and V6 were moving from south to north in the past decade, but they are all in the west of station gauged precipitation APWP(s).V6 APWP track fit gauged precipitation perfectly while RT APWP track has over-exaggerated legs, indicating that spatial distribution of RT precipitation experienced unreasonable sharp changes. A practical and operational procedure to correct satellite precipitation data is developed. For RT, there are two steps. Step 1, the downscaling, original daily precipitation was multiplied by a ratio of its monthly satellite/station precipitation gauged precipitation. Step2, objective analysis, Barnes/Cressman successive correction as well as Optimal Interpolation was applied to refine the processed daily results. Step 1 is unnecessary for V6 correction. The accuracy of RT can be improved significantly and the spatial details of satellite precipitation can be obtained as much as possible while quite little improvement showed in V6 correction. Besides, the iteration of successive correction should not be more than twice and the ideal influence radius for Optimal Interpolation is R=5. The original/corrected RT and V6 data sets were used as precipitation inputs to drive a newly developed hydrological model DHM-SP in the headwater region of the Yellow river so as to assess their applicability in simulating the daily runoff. V6 simulation result is qualified even though it is uncorrected. The bias in RT is too much to make use of RT as model input directly while quite satisfied results can be derived from corrected RT input. The simulation results of corrected RT are even better than that of station gauged and V6.

Rayleigh-Taylor and Richtmyer-Meshkov instability induced flow, turbulence, and mixing. II

NASA Astrophysics Data System (ADS)

Zhou, Ye

2017-12-01

Rayleigh-Taylor (RT) and Richtmyer-Meshkov(RM) instabilities are well-known pathways towards turbulent mixing layers, in many cases characterized by significant mass and species exchange across the mixing layers (Zhou, 2017. Physics Reports, 720-722, 1-136). Mathematically, the pathway to turbulent mixing requires that the initial interface be multimodal, to permit cross-mode coupling leading to turbulence. Practically speaking, it is difficult to experimentally produce a non-multi-mode initial interface. Numerous methods and approaches have been developed to describe the late, multimodal, turbulent stages of RT and RM mixing layers. This paper first presents the initial condition dependence of RT mixing layers, and introduces parameters that are used to evaluate the level of "mixedness" and "mixed mass" within the layers, as well as the dependence on density differences, as well as the characteristic anisotropy of this acceleration-driven flow, emphasizing some of the key differences between the two-dimensional and three-dimensional RT mixing layers. Next, the RM mixing layers are discussed, and differences with the RT mixing layer are elucidated, including the RM mixing layers dependence on the Mach number of the initiating shock. Another key feature of the RM induced flows is its response to a reshock event, as frequently seen in shock-tube experiments as well as inertial confinement events. A number of approaches to modeling the evolution of these mixing layers are then described, in order of increasing complexity. These include simple buoyancy-drag models, Reynolds-averaged Navier-Stokes models of increased complexity, including K- ε, K-L, and K- L- a models, up to full Reynolds-stress models with more than one length-scale. Multifield models and multiphase models have also been implemented. Additional complexities to these flows are examined as well as modifications to the models to understand the effects of these complexities. These complexities include the presence of magnetic fields, compressibility, rotation, stratification and additional instabilities. The complications induced by the presence of converging geometries are also considered. Finally, the unique problems of astrophysical and high-energy-density applications, and efforts to model these are discussed.

A prospective study of cerebral, frontal lobe, and temporal lobe volumes and neuropsychological performance in children with primary brain tumors treated with cranial radiation.

PubMed

Agbahiwe, Harold; Rashid, Arif; Horska, Alena; Mahone, E Mark; Lin, Doris; McNutt, Todd; Cohen, Kenneth; Redmond, Kristin; Wharam, Moody; Terezakis, Stephanie

2017-01-01

Cranial radiation therapy (RT) is an important component in the treatment of pediatric brain tumors. However, it can result in long-term effects on the developing brain. This prospective study assessed the effects of cranial RT on cerebral, frontal lobe, and temporal lobe volumes and their correlation with higher cognitive functioning. Ten pediatric patients with primary brain tumors treated with cranial RT and 14 age- and sex-matched healthy children serving as controls were evaluated. Quantitative magnetic resonance imaging and neuropsychological assessments (language, memory, auditory and visual processing, and vocabulary) were performed at the baseline and 6, 15, and 27 months after RT. The effects of age, the time since RT, and the cerebral RT dose on brain volumes and neuropsychological performance were analyzed with linear mixed effects model analyses. Cerebral volume increased significantly with age in both groups (P = .01); this increase in volume was more pronounced in younger children. Vocabulary performance was found to be significantly associated with a greater cerebral volume (P = .05) and a lower RT dose (P = .003). No relation was observed between the RT dose and the cerebral volume. There was no difference in the corresponding neuropsychological tests between the 2 groups. This prospective study found significant relations among the RT dose, cerebral volumes, and rate of vocabulary development among children receiving RT. The results of this study provide further support for clinical trials aimed at reducing cranial RT doses in the pediatric population. Cancer 2017;161-168. © 2016 American Cancer Society. © 2016 American Cancer Society.

Patterns of care and treatment outcomes of patients with Craniopharyngioma in the national cancer database.

PubMed

Rao, Yuan J; Hassanzadeh, Comron; Fischer-Valuck, Benjamin; Chicoine, Michael R; Kim, Albert H; Perkins, Stephanie M; Huang, Jiayi

2017-03-01

To investigate the patterns of care and outcomes in patients with craniopharyngioma in the National Cancer Data Base (NCDB). This study included 697 patients (166 pediatric and 531 adult cases) treated for craniopharyngioma between 2004 and 2012 in the NCDB. Adjuvant radiotherapy (RT) was defined if within 6 months of surgery. Limited surgery (LS) was defined as biopsy or subtotal resection. Proportional-hazards models were used to evaluate associations between covariates and overall survival (OS). A time-dependent analysis of RT was performed to account for early deaths after surgery. Median follow-up was 46 months. Overall, 21% of patients received adjuvant RT. Of patients with known surgical extent (n = 195), 71% had LS. Utilization of adjuvant RT increased from 18% in 2004-2007 to 24% in 2008-2012. Patterns of care regarding adjuvant RT or LS were not significantly different between adult and pediatric patients. Tumor size, low comorbidity, and LS were associated with increased utilization of adjuvant RT. The 5-year OS among patients treated with LS, LS+RT, and gross total resection were 75, 85, and 82% (p = 0.02). On multivariate analysis of the 195 patients with known surgical extent, LS+RT was associated with improved OS compared to LS (HR 0.22, 95% CI 0.05-0.99, p = 0.04), but was not significant when early deaths (<2 months from surgery) were removed to adjust for immortal-time bias. Medical practice regarding surgical approach and adjuvant RT are similar for pediatric and adult craniopharyngiomas. Immortal-time bias may confound assessment of OS for adjuvant RT. Prospective studies comparing adjuvant RT versus observation after LS are warranted.

The impact of radiation therapy sequencing on survival and cardiopulmonary mortality in the combined modality treatment of patients with esophageal cancer.

PubMed

Wojcieszynski, Andrzej P; Berman, Abigail T; Wan, Fei; Plastaras, John P; Metz, James M; Mitra, Nandita; Apisarnthanarax, Smith

2013-06-01

The addition of chemoradiation (CRT) to surgery has been shown to improve survival in patients with esophageal cancer. In the current study, the authors determined whether the sequencing of CRT has an effect on survival and cardiopulmonary mortality in patients with esophageal cancer. Patients with the following inclusion criteria were identified within 17 Surveillance, Epidemiology, and End Results registries from 1988 through 2007: adenocarcinoma or squamous cell carcinoma of the esophagus and having undergone esophagectomy. Patients who died within 90 days of surgery were excluded. Demographic, tumor, and survival data were compared between patients receiving preoperative and postoperative RT. Cox proportional hazards regression models were calculated to identify parameters associated with cause-specific survival and overall survival. A competing risk analysis was performed to account for death due to esophageal cancer in the calculation of cardiopulmonary mortality. Of 5512 patients, 1881 received preoperative RT, 901 received postoperative RT, and 2730 did not receive RT. Patients receiving preoperative RT had improved 5-year cause-specific survival (41% vs 31%; P < .0001) and overall survival (33% vs 23%; P < .0001) compared with those receiving postoperative RT. No differences in adjusted cardiopulmonary mortality were found between patients who received RT versus those who did not (8% vs 10% at 10 years; hazards ratio [HR], 0.84 [95% confidence interval (95% CI), 0.64-1.12] [P = .24]) or between those treated with preoperative RT versus those treated with postoperative RT (HR, 0.70; 95% CI, 0.46-1.08 [P = .11]). These population-based data support the use of preoperative RT in patients with locally advanced esophageal cancer. RT should not be withheld out of concern for cardiopulmonary mortality. Copyright © 2013 American Cancer Society.

Predicting the 5-Year Risk of Biochemical Relapse After Postprostatectomy Radiation Therapy in ≥PT2, pN0 Patients With a Comprehensive Tumor Control Probability Model

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

Fiorino, Claudio, E-mail: fiorino.claudio@hsr.it; Broggi, Sara; Fossati, Nicola

Purpose: To fit the individual biochemical recurrence-free survival (bRFS) data from patients treated with postprostatectomy radiation therapy (RT) with a comprehensive tumor control probability (TCP) model. Methods and Materials: Considering pre-RT prostate-specific antigen (PSA) as a surrogate of the number of clonogens, bRFS may be expressed as a function of dose-per-fraction–dependent radiosensitivity (α{sub eff}), the number of clonogens for pre-RT PSA = 1 ng/mL (C), and the fraction of patients who relapse because of clonogens outside the treated volume (K), assumed to depend (linearly or exponentially) on pre-RT PSA and Gleason score (GS). Data from 894 node-negative, ≥pT2, pN0 hormone-naive patients treated withmore » adjuvant (n=331) or salvage (n=563) intent were available: 5-year bRFS data were fitted grouping patients according to GS (<7:392, =7:383, >7:119). Results: The median follow-up time, pre-RT PSA, and dose were 72 months, 0.25 ng/mL, and 66.6 Gy (range 59.4-77.4 Gy), respectively. The best-fit values were 0.23 to 0.26 Gy{sup −1} and 10{sup 7} for α{sub eff} and C for the model considering a linear dependence between K and PSA. Calibration plots showed good agreement between expected and observed incidences (slope: 0.90-0.93) and moderately high discriminative power (area under the curve [AUC]: 0.68-0.69). Cross-validation showed satisfactory results (average AUCs in the training/validation groups: 0.66-0.70). The resulting dose-effect curves strongly depend on pre-RT PSA and GS. bRFS rapidly decreases with PSA: the maximum obtainable bRFS (defined as 95% of the maximum) declined by about 2.7% and 4.5% for each increment of 0.1 ng/mL for GS <7 and ≥7, respectively. Conclusions: Individual data were fitted by a TCP model, and the resulting best-fit parameters were radiobiologically consistent. The model suggests that relapses frequently result from clonogens outside the irradiated volume, supporting the choice of lymph-node irradiation, systemic therapy, or both for specific subgroups (GS <7: PSA >0.8-1.0 ng/mL; GS ≥7: PSA >0.3 ng/mL). Early RT should be preferred over delayed RT; the detrimental effect of PSA increase can never be fully compensated by increasing the dose, especially for patients with GS ≥7.« less

Scaling dimensions in spectroscopy of soil and vegetation

NASA Astrophysics Data System (ADS)

Malenovský, Zbyněk; Bartholomeus, Harm M.; Acerbi-Junior, Fausto W.; Schopfer, Jürg T.; Painter, Thomas H.; Epema, Gerrit F.; Bregt, Arnold K.

2007-05-01

The paper revises and clarifies definitions of the term scale and scaling conversions for imaging spectroscopy of soil and vegetation. We demonstrate a new four-dimensional scale concept that includes not only spatial but also the spectral, directional and temporal components. Three scaling remote sensing techniques are reviewed: (1) radiative transfer, (2) spectral (un)mixing, and (3) data fusion. Relevant case studies are given in the context of their up- and/or down-scaling abilities over the soil/vegetation surfaces and a multi-source approach is proposed for their integration. Radiative transfer (RT) models are described to show their capacity for spatial, spectral up-scaling, and directional down-scaling within a heterogeneous environment. Spectral information and spectral derivatives, like vegetation indices (e.g. TCARI/OSAVI), can be scaled and even tested by their means. Radiative transfer of an experimental Norway spruce ( Picea abies (L.) Karst.) research plot in the Czech Republic was simulated by the Discrete Anisotropic Radiative Transfer (DART) model to prove relevance of the correct object optical properties scaled up to image data at two different spatial resolutions. Interconnection of the successive modelling levels in vegetation is shown. A future development in measurement and simulation of the leaf directional spectral properties is discussed. We describe linear and/or non-linear spectral mixing techniques and unmixing methods that demonstrate spatial down-scaling. Relevance of proper selection or acquisition of the spectral endmembers using spectral libraries, field measurements, and pure pixels of the hyperspectral image is highlighted. An extensive list of advanced unmixing techniques, a particular example of unmixing a reflective optics system imaging spectrometer (ROSIS) image from Spain, and examples of other mixture applications give insight into the present status of scaling capabilities. Simultaneous spatial and temporal down-scaling by means of a data fusion technique is described. A demonstrative example is given for the moderate resolution imaging spectroradiometer (MODIS) and LANDSAT Thematic Mapper (TM) data from Brazil. Corresponding spectral bands of both sensors were fused via a pyramidal wavelet transform in Fourier space. New spectral and temporal information of the resultant image can be used for thematic classification or qualitative mapping. All three described scaling techniques can be integrated as the relevant methodological steps within a complex multi-source approach. We present this concept of combining numerous optical remote sensing data and methods to generate inputs for ecosystem process models.

Numerical and experimental study of dissociation in an air-water single-bubble sonoluminescence system.

PubMed

Puente, Gabriela F; Urteaga, Raúl; Bonetto, Fabián J

2005-10-01

We performed a comprehensive numerical and experimental analysis of dissociation effects in an air bubble in water acoustically levitated in a spherical resonator. Our numerical approach is based on suitable models for the different effects considered. We compared model predictions with experimental results obtained in our laboratory in the whole phase parameter space, for acoustic pressures from the bubble dissolution limit up to bubble extinction. The effects were taken into account simultaneously to consider the transition from nonsonoluminescence to sonoluminescence bubbles. The model includes (1) inside the bubble, transient and spatially nonuniform heat transfer using a collocation points method, dissociation of O2 and N2, and mass diffusion of vapor in the noncondensable gases; (2) at the bubble interface, nonequilibrium evaporation and condensation of water and a temperature jump due to the accommodation coefficient; (3) in the liquid, transient and spatially nonuniform heat transfer using a collocation points method, and mass diffusion of the gas in the liquid. The model is completed with a Rayleigh-Plesset equation with liquid compressible terms and vapor mass transfer. We computed the boundary for the shape instability based on the temporal evolution of the computed radius. The model is valid for an arbitrary number of dissociable gases dissolved in the liquid. We also obtained absolute measurements for R(t) using two photodetectors and Mie scattering calculations. The robust technique used allows the estimation of experimental results of absolute R0 and P(a). The technique is based on identifying the bubble dissolution limit coincident with the parametric instability in (P(a),R0) parameter space. We take advantage of the fact that this point can be determined experimentally with high precision and replicability. We computed the equilibrium concentration of the different gaseous species and water vapor during collapse as a function of P(a) and R0. The model obtains from first principles the result that in sonoluminescence the bubble is practically 100% argon for air dissolved in water. Therefore, the dissociation reactions in air bubbles must be taken into account for quantitative computations of maximum temperatures. The agreement found between the numerical and experimental data is very good in the whole parameter space explored. We do not fit any parameter in the model. We believe that we capture all the relevant physics with the model.

Evaluating Model Parameterizations of Submicron Aerosol Scattering and Absorption with in situ Data from ARCTAS 2008

NASA Technical Reports Server (NTRS)

Alvarado, Matthew J.; Lonsdale, Chantelle R.; Macintyre, Helen L.; Bian, Huisheng; Chin, Mian; Ridley, David A.; Heald, Colette L.; Thornhill, Kenneth L.; Anderson, Bruce E.; Cubison, Michael J.;

Reference data on reaction time and aging using the Nintendo Wii Balance Board: A cross-sectional study of 354 subjects from 20 to 99 years of age.

PubMed

Blomkvist, Andreas W; Eika, Fredrik; Rahbek, Martin T; Eikhof, Karin D; Hansen, Mette D; Søndergaard, Malene; Ryg, Jesper; Andersen, Stig; Jørgensen, Martin G

2017-01-01

Falls among older adults is one of the major public health challenges facing the rapidly changing demography. The valid assessment of reaction time (RT) and other well-documented risk factors for falls are mainly restricted to specialized clinics due to the equipment needed. The Nintendo Wii Balance Board has the potential to be a multi-modal test and intervention instrument for these risk factors, however, reference data are lacking. To provide RT reference data and to characterize the age-related changes in RT measured by the Nintendo Wii Balance Board. Healthy participants were recruited at various locations and their RT in hands and feet were tested by six assessors using the Nintendo Wii Balance Board. Reference data were analysed and presented in age-groups, while the age-related change in RT was tested and characterized with linear regression models. 354 participants between 20 and 99 years of age were tested. For both hands and feet, mean RT and its variation increased with age. There was a statistically significant non-linear increase in RT with age. The averaged difference between male and female was significant, with males being faster than females for both hands and feet. The averaged difference between dominant and non-dominant side was non-significant. This study reported reference data with percentiles for a new promising method for reliably testing RT. The RT data were consistent with previously known effects of age and gender on RT.

Symptoms of ADHD Affect Intrasubject Variability in Youths with Autism Spectrum Disorder: An Ex-Gaussian Analysis.

PubMed

Hwang-Gu, Shoou-Lian; Lin, Hsiang-Yuan; Chen, Yu-Chi; Tseng, Yu-Han; Hsu, Wen-Yau; Chou, Miao-Chun; Chou, Wen-Jun; Wu, Yu-Yu; Gau, Susan Shur-Fen

2018-05-30

Increased intrasubject variability in reaction times (RT-ISV) is frequently found in individuals with autism spectrum disorder (ASD). However, how dimensional attention deficit/hyperactivity disorder (ADHD) symptoms impact RT-ISV in individuals with ASD remains elusive. We assessed 97 high-functioning youths with co-occurring ASD and ADHD (ASD+ADHD), 124 high-functioning youths with ASD only, 98 youths with ADHD only, and 249 typically developing youths, 8-18 years of age, using the Conners Continuous Performance Test (CCPT). We compared the conventional CCPT parameters (omission errors, commission errors, mean RT and RT standard error (RTSE) as well as the ex-Gaussian parameters of RT (mu, sigma, and tau) across the four groups. We also conducted regression analyses to assess the relationships between RT indices and symptoms of ADHD and ASD in the ASD group (i.e., the ASD+ADHD and ASD-only groups). The ASD+ADHD and ADHD-only groups had higher RT-ISV than the other two groups. RT-ISV, specifically RTSE and tau, was significantly associated with ADHD symptoms rather than autistic traits in the ASD group. Regression models also revealed that sex partly accounted for RT-ISV variance in the ASD group. A post hoc analysis showed girls with ASD had higher tau and RTSE values than their male counterparts. Our results suggest that RT-ISV is primarily associated with co-occurring ADHD symptoms/diagnosis in children and adolescents with ASD. These results do not support the hypothesis of response variability as a transdiagnostic phenotype for ASD and ADHD and warrant further validation at a neural level.

Reference data on reaction time and aging using the Nintendo Wii Balance Board: A cross-sectional study of 354 subjects from 20 to 99 years of age

PubMed Central

Rahbek, Martin T.; Eikhof, Karin D.; Hansen, Mette D.; Søndergaard, Malene; Ryg, Jesper; Andersen, Stig; Jørgensen, Martin G.

2017-01-01

Background Falls among older adults is one of the major public health challenges facing the rapidly changing demography. The valid assessment of reaction time (RT) and other well-documented risk factors for falls are mainly restricted to specialized clinics due to the equipment needed. The Nintendo Wii Balance Board has the potential to be a multi-modal test and intervention instrument for these risk factors, however, reference data are lacking. Objective To provide RT reference data and to characterize the age-related changes in RT measured by the Nintendo Wii Balance Board. Method Healthy participants were recruited at various locations and their RT in hands and feet were tested by six assessors using the Nintendo Wii Balance Board. Reference data were analysed and presented in age-groups, while the age-related change in RT was tested and characterized with linear regression models. Results 354 participants between 20 and 99 years of age were tested. For both hands and feet, mean RT and its variation increased with age. There was a statistically significant non-linear increase in RT with age. The averaged difference between male and female was significant, with males being faster than females for both hands and feet. The averaged difference between dominant and non-dominant side was non-significant. Conclusion This study reported reference data with percentiles for a new promising method for reliably testing RT. The RT data were consistent with previously known effects of age and gender on RT. PMID:29287063

Morphology and Molecular Mechanisms of Hepatic Injury in Rats under Simulated Weightlessness and the Protective Effects of Resistance Training.

PubMed

Du, Fang; Ding, Ye; Zou, Jun; Li, Zhili; Tian, Jijing; She, Ruiping; Wang, Desheng; Wang, Huijuan; Lv, Dongqiang; Chang, Lingling

2015-01-01

This study investigated the effects of long-term simulated weightlessness on liver morphology, enzymes, glycogen, and apoptosis related proteins by using two-month rat-tail suspension model (TS), and liver injury improvement by rat-tail suspension with resistance training model (TS&RT). Microscopically the livers of TS rats showed massive granular degeneration, chronic inflammation, and portal fibrosis. Mitochondrial and endoplasmic reticulum swelling and loss of membrane integrity were observed by transmission electron microscopy (TEM). The similar, but milder, morphological changes were observed in the livers of TS&RT rats. Serum biochemistry analysis revealed that the levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were significantly higher (p<0.05) in TS rats than in controls. The levels of ALT and AST in TS&RT rats were slightly lower than in RT rats, but they were insignificantly higher than in controls. However, both TS and TS&RT rats had significantly lower levels (p<0.05) of serum glucose and hepatic glycogen than in controls. Immunohistochemistry demonstrated that the expressions of Bax, Bcl-2, and active caspase-3 were higher in TS rats than in TS&RT and control rats. Real-time polymerase chain reaction (real-time PCR) showed that TS rats had higher mRNA levels (P < 0.05) of glucose-regulated protein 78 (GRP78) and caspase-12 transcription than in control rats; whereas mRNA expressions of C/EBP homologous protein (CHOP) and c-Jun N-terminal kinase (JNK) were slightly higher in TS rats. TS&RT rats showed no significant differences of above 4 mRNAs compared with the control group. Our results demonstrated that long-term weightlessness caused hepatic injury, and may trigger hepatic apoptosis. Resistance training slightly improved hepatic damage.

Morphology and Molecular Mechanisms of Hepatic Injury in Rats under Simulated Weightlessness and the Protective Effects of Resistance Training

PubMed Central

Zou, Jun; Li, Zhili; Tian, Jijing; She, Ruiping; Wang, Desheng; Wang, Huijuan; Lv, Dongqiang; Chang, Lingling

2015-01-01

This study investigated the effects of long-term simulated weightlessness on liver morphology, enzymes, glycogen, and apoptosis related proteins by using two-month rat-tail suspension model (TS), and liver injury improvement by rat-tail suspension with resistance training model (TS&RT). Microscopically the livers of TS rats showed massive granular degeneration, chronic inflammation, and portal fibrosis. Mitochondrial and endoplasmic reticulum swelling and loss of membrane integrity were observed by transmission electron microscopy (TEM). The similar, but milder, morphological changes were observed in the livers of TS&RT rats. Serum biochemistry analysis revealed that the levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were significantly higher (p<0.05) in TS rats than in controls. The levels of ALT and AST in TS&RT rats were slightly lower than in RT rats, but they were insignificantly higher than in controls. However, both TS and TS&RT rats had significantly lower levels (p<0.05) of serum glucose and hepatic glycogen than in controls. Immunohistochemistry demonstrated that the expressions of Bax, Bcl-2, and active caspase-3 were higher in TS rats than in TS&RT and control rats. Real-time polymerase chain reaction (real-time PCR) showed that TS rats had higher mRNA levels (P < 0.05) of glucose-regulated protein 78 (GRP78) and caspase-12 transcription than in control rats; whereas mRNA expressions of C/EBP homologous protein (CHOP) and c-Jun N-terminal kinase (JNK) were slightly higher in TS rats. TS&RT rats showed no significant differences of above 4 mRNAs compared with the control group. Our results demonstrated that long-term weightlessness caused hepatic injury, and may trigger hepatic apoptosis. Resistance training slightly improved hepatic damage. PMID:26000905

Ultrasound-enhanced rt-PA thrombolysis in an ex vivo porcine carotid artery model.

PubMed

Hitchcock, Kathryn E; Ivancevich, Nikolas M; Haworth, Kevin J; Caudell Stamper, Danielle N; Vela, Deborah C; Sutton, Jonathan T; Pyne-Geithman, Gail J; Holland, Christy K

2011-08-01

Ultrasound is known to enhance recombinant tissue plasminogen activator (rt-PA) thrombolysis. In this study, occlusive porcine whole blood clots were placed in flowing plasma within living porcine carotid arteries. Ultrasonically induced stable cavitation was investigated as an adjuvant to rt-PA thrombolysis. Aged, retracted clots were exposed to plasma alone, plasma containing rt-PA (7.1 ± 3.8 μg/mL) or plasma with rt-PA and Definity® ultrasound contrast agent (0.79 ± 0.47 μL/mL) with and without 120-kHz continuous wave ultrasound at a peak-to-peak pressure amplitude of 0.44 MPa. An insonation scheme was formulated to promote and maximize stable cavitation activity by incorporating ultrasound quiescent periods that allowed for the inflow of Definity®-rich plasma. Cavitation was measured with a passive acoustic detector throughout thrombolytic treatment. Thrombolytic efficacy was measured by comparing clot mass before and after treatment. Average mass loss for clots exposed to rt-PA and Definity® without ultrasound (n = 7) was 34%, and with ultrasound (n = 6) was 83%, which constituted a significant difference (p < 0.0001). Without Definity® there was no thrombolytic enhancement by ultrasound exposure alone at this pressure amplitude (n = 5, p < 0.0001). In the low-oxygen environment of the ischemic artery, significant loss of endothelium occurred but no correlation was observed between arterial tissue damage and treatment type. Acoustic stable cavitation nucleated by an infusion of Definity® enhances rt-PA thrombolysis without apparent treatment-related damage in this ex vivo porcine carotid artery model. Copyright © 2011. Published by Elsevier Inc.

BCR-ABL1 expression, RT-qPCR and treatment decisions in chronic myeloid leukaemia.

PubMed

Latham, Susan; Bartley, Paul A; Budgen, Bradley; Ross, David M; Hughes, Elizabeth; Branford, Susan; White, Deborah; Hughes, Timothy P; Morley, Alexander A

2016-09-01

RT-qPCR is used to quantify minimal residual disease (MRD) in chronic myeloid leukaemia (CML) in order to make decisions on treatment, but its results depend on the level of BCR-ABL1 expression as well as leukaemic cell number. The aims of the study were to quantify inter-individual differences in expression level, to determine the relationship between expression level and response to treatment, and to investigate the effect of expression level on interpretation of the RT-qPCR result. BCR-ABL1 expression was studied in 248 samples from 65 patients with CML by determining the difference between MRD quantified by RT-qPCR and DNA-qPCR. The results were analysed statistically and by simple indicative modelling. Inter-individual levels of expression approximated a normal distribution with an SD of 0.36 log. Expression at diagnosis correlated with expression during treatment. Response to treatment, as measured by the number of leukaemic cells after 3, 6 or 12 months of treatment, was not related to the level of expression. Indicative modelling suggested that interpretation of RT-qPCR results in relation to treatment guidelines could be affected by variation in expression when MRD was around 10% at 3 months and by both expression variation and Poisson variation when MRD was around or below the limit of detection of RT-qPCR. Variation between individuals in expression of BCR-ABL1 can materially affect interpretation of the RT-qPCR when this test is used to make decisions on treatment. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Incidental Statin Use and the Risk of Stroke or Transient Ischemic Attack after Radiotherapy for Head and Neck Cancer

PubMed Central

Addison, Daniel; Lawler, Patrick R.; Emami, Hamed; Janjua, Sumbal A.; Staziaki, Pedro V.; Hallett, Travis R.; Hennessy, Orla; Lee, Hang; Szilveszter, Bálint; Lu, Michael; Mousavi, Negar; Nayor, Matthew G.; Delling, Francesca N.; Romero, Javier M.; Wirth, Lori J.; Chan, Annie W.; Hoffmann, Udo; Neilan, Tomas G.

2018-01-01

Background and Purpose Interventions to reduce the risk for cerebrovascular events (CVE; stroke and transient ischemic attack [TIA]) after radiotherapy (RT) for head and neck cancer (HNCA) are needed. Among broad populations, statins reduce CVEs; however, whether statins reduce CVEs after RT for HNCA is unclear. Therefore, we aimed to test whether incidental statin use at the time of RT is associated with a lower rate of CVEs after RT for HNCA. Methods From an institutional database we identified all consecutive subjects treated with neck RT from 2002 to 2012 for HNCA. Data collection and event adjudication was performed by blinded teams. The primary outcome was a composite of ischemic stroke and TIA. The secondary outcome was ischemic stroke. The association between statin use and events was determined using Cox proportional hazard models after adjustment for traditional and RT-specific risk factors. Results The final cohort consisted of 1,011 patients (59±13 years, 30% female, 44% hypertension) with 288 (28%) on statins. Over a median follow-up of 3.4 years (interquartile range, 0.1 to 14) there were 102 CVEs (89 ischemic strokes and 13 TIAs) with 17 in statin users versus 85 in nonstatins users. In a multivariable model containing known predictors of CVE, statins were associated with a reduction in the combination of stroke and TIA (hazard ratio [HR], 0.4; 95% confidence interval [CI], 0.2 to 0.8; P=0.01) and ischemic stroke alone (HR, 0.4; 95% CI, 0.2 to 0.8; P=0.01). Conclusions Incidental statin use at the time of RT for HNCA is associated with a lower risk of stroke or TIA. PMID:29402065

Reprogramming of single-cell derived mesenchymal stem cells into hair cell-like cells

PubMed Central

Lin, Zhaoyu; Perez, Philip; Sun, Zhenyu; Liu, Jan-Jan; Shin, June Ho; Hyrc, Krzysztof L.; Samways, Damien; Egan, Terry; Holley, Matthew C.; Bao, Jianxin

2012-01-01

Hypothesis Adult mesenchymal stem cells (MSCs) can be converted into hair cell-like cells by transdetermination. Background Given the fundamental role sensory hair cells play in sound detection and the irreversibility of their loss in mammals, much research has focused on developing methods to generate new hair cells as a means of treating permanent hearing loss. Although MSCs can differentiate into multiple cell lineages, no efficient means of reprogramming them into sensory hair cells exists. Earlier work has shown that the transcription factor Atoh1 is necessary for early development of hair cells, but it is not clear whether Atoh1 can be used to convert MSCs into hair cells. Methods Clonal MSC cell lines were established and reprogrammed into hair cell-like cells by a combination of protein transfer, adenoviral based gene transfer and co-culture with neurons. During transdetermination, inner ear molecular markers were analyzed by RT-PCR, and cell structures were examined by immunocytochemistry. Results Atoh1 overexpression in MSCs failed to convert MSCs into hair cell-like cells, suggesting that the ability of Atoh1 to induce hair cell differentiation is context dependent. Because Atoh1 overexpression successfully transforms VOT-E36 cells into hair cell-like cells, we modified the cell context of MSCs by performing a total protein transfer from VOT-E36 cells prior to overexpressing Atoh1. The modified MSCs were transformed into hair cell-like cells and attracted contacts from spiral ganglion neurons in a co-culture model. Conclusion We established a new procedure, consisting of VOT-E36 protein transfer, Atoh1 overexpression, and co-culture with spiral ganglion neurons, which can transform MSCs into hair cell-like cells. PMID:23111404

Enabling complex queries to drug information sources through functional composition.

PubMed

Peters, Lee; Mortensen, Jonathan; Nguyen, Thang; Bodenreider, Olivier

2013-01-01

Our objective was to enable an end-user to create complex queries to drug information sources through functional composition, by creating sequences of functions from application program interfaces (API) to drug terminologies. The development of a functional composition model seeks to link functions from two distinct APIs. An ontology was developed using Protégé to model the functions of the RxNorm and NDF-RT APIs by describing the semantics of their input and output. A set of rules were developed to define the interoperable conditions for functional composition. The operational definition of interoperability between function pairs is established by executing the rules on the ontology. We illustrate that the functional composition model supports common use cases, including checking interactions for RxNorm drugs and deploying allergy lists defined in reference to drug properties in NDF-RT. This model supports the RxMix application (http://mor.nlm.nih.gov/RxMix/), an application we developed for enabling complex queries to the RxNorm and NDF-RT APIs.

Three-Stage Production Cost Modeling Approach for Evaluating the Benefits of Intra-Hour Scheduling Between Balancing Authorities

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

Samaan, Nader; Milligan, Michael; Hunsaker, Matt

This paper introduces a production cost modeling approach for evaluating the benefits of intra-hour scheduling among Balancing Authorities (BAs). System operation is modeled in a three-stage sequential manner: day ahead (DA)-hour ahead (HA) real time (RT). In addition to contingency reserve, each BA will need to carry out 'up' and 'down' load following and regulation reserve capacity requirements in the DA and HA time frames. In the RT simulation, only contingency and regulation reserves are carried out as load following is deployed. To model current RT operation with hourly schedules, a new constraint was introduced to force each BA netmore » exchange schedule deviation from HA schedules to be within North American Electric Reliability Corporation (NERC) area control error (ACE) limits. Case studies that investigate the benefits of moving from hourly exchange schedules between Western Electricity Coordinating Council (WECC) BAs into 10-minute exchange schedules under two different levels of wind and solar penetration (11% and 33%) are presented.« less

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

Rong, Y; Walston, S

Purpose: To evaluate the use of 3D optical surface imaging as a new surrogate for respiratory motion gated deep-inspiration breath-hold (DIBH) technique for left breast cancer patients. Methods: Patients with left-sided breast cancer after lumpectomy or mastectomy were selected as candidates for DIBH technique for their external beam radiation therapy. Treatment plans were created on both free breathing (FB) and DIBH CTs to determine whether DIBH was beneficial in reducing heart doses. The Real-time Position Management (RPM) system was used to acquire patient's breathing trace during DIBH CT acquisition and treatment delivery. The reference 3D surface models from FB andmore » DIBH CTs were generated and transferred to the “AlignRT” system for patient positioning and real-time treatment monitoring. MV Cine images were acquired for each beam as quality assurance for intra-fractional position verification. The chest wall excursions measured on these images were used to define the actual target position during treatment, and to investigate the accuracy and reproducibility of RPM and AlignRT. Results: Reduction in heart dose can be achieved for left-sided breast patients using DIBH. Results showed that RPM has poor correlation with target position, as determined by the MV Cine imaging. This indicates that RPM may not be an adequate surrogate in defining the breath-hold level when used alone. Alternatively, the AlignRT surface imaging demonstrated a better correlation with the actual CW excursion during DIBH. Both the vertical and magnitude real-time deltas (RTDs) reported by AlignRT can be used as the gating parameter, with a recommend threshold of ±3 mm and 5 mm, respectively. Conclusion: 3D optical surface imaging serves as a superior target surrogate for the left breast treatment when compared to RPM. Working together with the realtime MV Cine imaging, they ensure accurate patient setup and dose delivery, while minimizing the imaging dose to patients.« less

Dietary trehalose enhances virulence of epidemic Clostridium difficile.

PubMed

Collins, J; Robinson, C; Danhof, H; Knetsch, C W; van Leeuwen, H C; Lawley, T D; Auchtung, J M; Britton, R A

2018-01-18

Clostridium difficile disease has recently increased to become a dominant nosocomial pathogen in North America and Europe, although little is known about what has driven this emergence. Here we show that two epidemic ribotypes (RT027 and RT078) have acquired unique mechanisms to metabolize low concentrations of the disaccharide trehalose. RT027 strains contain a single point mutation in the trehalose repressor that increases the sensitivity of this ribotype to trehalose by more than 500-fold. Furthermore, dietary trehalose increases the virulence of a RT027 strain in a mouse model of infection. RT078 strains acquired a cluster of four genes involved in trehalose metabolism, including a PTS permease that is both necessary and sufficient for growth on low concentrations of trehalose. We propose that the implementation of trehalose as a food additive into the human diet, shortly before the emergence of these two epidemic lineages, helped select for their emergence and contributed to hypervirulence.

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.

Optimal Location of Radiation Therapy Centers With Respect to Geographic Access

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

Santibáñez, Pablo; Gaudet, Marc; French, John

2014-07-15

Purpose: To develop a framework with which to evaluate locations of radiation therapy (RT) centers in a region based on geographic access. Methods and Materials: Patient records were obtained for all external beam radiation therapy started in 2011 for the province of British Columbia, Canada. Two metrics of geographic access were defined. The primary analysis was percentage of patients (coverage) within a 90-minute drive from an RT center (C90), and the secondary analysis was the average drive time (ADT) to an RT center. An integer programming model was developed to determine optimal center locations, catchment areas, and capacity required undermore » different scenarios. Results: Records consisted of 11,096 courses of radiation corresponding to 161,616 fractions. Baseline geographic access was estimated at 102.5 minutes ADT (each way, per fraction) and 75.9% C90. Adding 2 and 3 new centers increased C90 to 88% and 92%, respectively, and decreased ADT by between 43% and 61%, respectively. A scenario in which RT was provided in every potential location that could support at least 1 fully utilized linear accelerator resulted in 35.3 minutes' ADT and 93.6% C90. Conclusions: The proposed framework and model provide a data-driven means to quantitatively evaluate alternative configurations of a regional RT system. Results suggest that the choice of location for future centers can significantly improve geographic access to RT.« less

Is the progression free survival advantage of concurrent gemcitabine plus cisplatin and radiation followed by adjuvant gemcitabine and cisplatin in patients with advanced cervical cancer worth the additional cost? A cost-effectiveness analysis.

PubMed

Smith, B; Cohn, D E; Clements, A; Tierney, B J; Straughn, J M

2013-09-01

The objective of this study is to determine whether concurrent and adjuvant chemoradiation with gemcitabine/cisplatin is cost-effective in patients with stage IIB to IVA cervical cancer. A cost-effectiveness model compared two arms of the trial performed by Duenas-Gonzalez et al. [1]: concurrent and adjuvant chemoradiation with gemcitabine/cisplatin (RT/GC+GC) versus concurrent radiation with cisplatin (RT/C). Major adverse events (AEs) and progression free survival (PFS) rates of each arm were incorporated in the model. AEs were defined as any hospitalization including grade 4 anemia, grade 4 neutropenia, and death. Medicare data and literature review were used to estimate costs. Incremental cost-effectiveness ratios (ICERs) per progression-free life-year saved (PF-LYS) were calculated. Sensitivity analyses were performed for pertinent uncertainties. For 10,000 women with locally advanced cervical cancer, the cost of therapy and AEs was $173.9 million (M) for RT/C versus $259.8M for RT/GC+GC. There were 879 additional 3-year progression-free survivors in the RT/GC+GC arm. The ICER for RT/GC+GC was $97,799 per PF-LYS. When the rate of hospitalization was equalized to 4.3%, the ICER for RT/GC+GC exceeded $80,000. The resultant ICER when increasing PFS in the RT/GC+GC arm by 5% was $62,605 per PF-LYS. When the cost of chemotherapy was decreased by 50%, the ICER was below $50,000 at $41,774 per PF-LYS. Radiation and gemcitabine/cisplatin for patients with stage IIB to IVA cervical cancer are not cost-effective. The increased financial burden of radiation with gemcitabine/cisplatin and associated toxicities appears to outweigh the benefit of increased 3-year PFS and is primarily dependent on chemotherapy drug costs. Copyright © 2013 Elsevier Inc. All rights reserved.

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.

Development of Virtual Airspace Simulation Technology - Real-Time (VAST-RT) Capability 2 and Experimental Plans

NASA Technical Reports Server (NTRS)

Lehmer, R.; Ingram, C.; Jovic, S.; Alderete, J.; Brown, D.; Carpenter, D.; LaForce, S.; Panda, R.; Walker, J.; Chaplin, P.;

New Breast Cancer Radiotherapy Technology Confers Higher Complications and Costs Before Effectiveness Proven: A Medicare Data Analysis

PubMed Central

Walter, Dawn; Tousimis, Eleni; Hayes, Mary Katherine

2018-01-01

A new breast cancer treatment, brachytherapy-based accelerated partial breast radiotherapy (RT), was adopted before long-term effectiveness evidence, potentially increasing morbidity and costs compared with whole breast RT. The aim of this study was to estimate complication rates and RT-specific and 1-year costs for a cohort of female Medicare beneficiaries diagnosed with breast cancer (N = 47 969). We analyzed 2005-2007 Medicare claims using multivariable logistic regression for complications and generalized linear models (log link, gamma distribution) for costs. Overall, 11% (n = 5296) underwent brachytherapy-based RT; 9.4% had complications. Odds of any complication were higher (odds ratio [OR]: 1.62; 95% confidence interval [CI]: 1.49-1.76) for brachytherapy versus whole breast RT, similarly to seroma (OR: 2.85; 95% CI: 1.97-4.13), wound complication/infection (OR: 1.72; 95% CI: 1.52-1.95), cellulitis (OR: 1.48; 95% CI: 1.27-1.73), and necrosis (OR: 2.07; 95% CI: 1.55-2.75). Mean RT-specific and 1-year total costs for whole breast RT were $6375, and $19 917, $4886, and $4803 lower than brachytherapy (P < .0001). Multivariable analyses indicated brachytherapy yielded 76% higher RT costs (risk ratio: 1.76; 95% CI: 1.74-1.78, P < .0001) compared with whole breast RT. Brachytherapy had higher complications and costs before long-term evidence proved its effectiveness. Policies should require treatment registries with reimbursement incentives to capture surveillance data for new technologies. PMID:29502466

Radio-photothermal therapy mediated by a single compartment nanoplatform depletes tumor initiating cells and reduces lung metastasis in the orthotopic 4T1 breast tumor model

NASA Astrophysics Data System (ADS)

Zhou, Min; Zhao, Jun; Tian, Mei; Song, Shaoli; Zhang, Rui; Gupta, Sanjay; Tan, Dongfeng; Shen, Haifa; Ferrari, Mauro; Li, Chun

2015-11-01

Tumor Initiating Cells (TICs) are resistant to radiotherapy and chemotherapy, and are believed to be responsible for tumor recurrence and metastasis. Combination therapies can overcome the limitation of conventional cancer treatments, and have demonstrated promising application in the clinic. Here, we show that dual modality radiotherapy (RT) and photothermal therapy (PTT) mediated by a single compartment nanosystem copper-64-labeled copper sulfide nanoparticles ([64Cu]CuS NPs) could suppress breast tumor metastasis through eradication of TICs. Positron electron tomography (PET) imaging and biodistribution studies showed that more than 90% of [64Cu]CuS NPs was retained in subcutaneously grown BT474 breast tumor 24 h after intratumoral (i.t.) injection, indicating the NPs are suitable for the combination therapy. Combined RT/PTT therapy resulted in significant tumor growth delay in the subcutaneous BT474 breast cancer model. Moreover, RT/PTT treatment significantly prolonged the survival of mice bearing orthotopic 4T1 breast tumors compared to no treatment, RT alone, or PTT alone. The RT/PTT combination therapy significantly reduced the number of tumor nodules in the lung and the formation of tumor mammospheres from treated 4T1 tumors. No obvious side effects of the CuS NPs were noted in the treated mice in a pilot toxicity study. Taken together, our data support the feasibility of a therapeutic approach for the suppression of tumor metastasis through localized RT/PTT therapy.Tumor Initiating Cells (TICs) are resistant to radiotherapy and chemotherapy, and are believed to be responsible for tumor recurrence and metastasis. Combination therapies can overcome the limitation of conventional cancer treatments, and have demonstrated promising application in the clinic. Here, we show that dual modality radiotherapy (RT) and photothermal therapy (PTT) mediated by a single compartment nanosystem copper-64-labeled copper sulfide nanoparticles ([64Cu]CuS NPs) could suppress breast tumor metastasis through eradication of TICs. Positron electron tomography (PET) imaging and biodistribution studies showed that more than 90% of [64Cu]CuS NPs was retained in subcutaneously grown BT474 breast tumor 24 h after intratumoral (i.t.) injection, indicating the NPs are suitable for the combination therapy. Combined RT/PTT therapy resulted in significant tumor growth delay in the subcutaneous BT474 breast cancer model. Moreover, RT/PTT treatment significantly prolonged the survival of mice bearing orthotopic 4T1 breast tumors compared to no treatment, RT alone, or PTT alone. The RT/PTT combination therapy significantly reduced the number of tumor nodules in the lung and the formation of tumor mammospheres from treated 4T1 tumors. No obvious side effects of the CuS NPs were noted in the treated mice in a pilot toxicity study. Taken together, our data support the feasibility of a therapeutic approach for the suppression of tumor metastasis through localized RT/PTT therapy. Electronic supplementary information (ESI) available: Details of methods used for radiolabeling efficiency and stability of 64Cu-labeled CuS NPs. See DOI: 10.1039/c5nr04587h

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

Jeong, J; Deasy, J O

Purpose: Concurrent chemo-radiation therapy (CCRT) has become a more common cancer treatment option with a better tumor control rate for several tumor sites, including head and neck and lung cancer. In this work, possible optimal chemotherapy schedules were investigated by implementing chemotherapy cell-kill into a tumor response model of RT. Methods: The chemotherapy effect has been added into a published model (Jeong et al., PMB (2013) 58:4897), in which the tumor response to RT can be simulated with the effects of hypoxia and proliferation. Based on the two-compartment pharmacokinetic model, the temporal concentration of chemotherapy agent was estimated. Log cell-killmore » was assumed and the cell-kill constant was estimated from the observed increase in local control due to concurrent chemotherapy. For a simplified two cycle CCRT regime, several different starting times and intervals were simulated with conventional RT regime (2Gy/fx, 5fx/wk). The effectiveness of CCRT was evaluated in terms of reduction in radiation dose required for 50% of control to find the optimal chemotherapy schedule. Results: Assuming the typical slope of dose response curve (γ50=2), the observed 10% increase in local control rate was evaluated to be equivalent to an extra RT dose of about 4 Gy, from which the cell-kill rate of chemotherapy was derived to be about 0.35. Best response was obtained when chemotherapy was started at about 3 weeks after RT began. As the interval between two cycles decreases, the efficacy of chemotherapy increases with broader range of optimal starting times. Conclusion: The effect of chemotherapy has been implemented into the resource-conservation tumor response model to investigate CCRT. The results suggest that the concurrent chemotherapy might be more effective when delayed for about 3 weeks, due to lower tumor burden and a larger fraction of proliferating cells after reoxygenation.« less

Effective Tree Scattering at L-Band

NASA Technical Reports Server (NTRS)

Kurum, Mehmet; ONeill, Peggy E.; Lang, Roger H.; Joseph, Alicia T.; Cosh, Michael H.; Jackson, Thomas J.

2011-01-01

For routine microwave Soil Moisture (SM) retrieval through vegetation, the tau-omega [1] model [zero-order Radiative Transfer (RT) solution] is attractive due to its simplicity and eases of inversion and implementation. It is the model used in baseline retrieval algorithms for several planned microwave space missions, such as ESA's Soil Moisture Ocean Salinity (SMOS) mission (launched November 2009) and NASA's Soil Moisture Active Passive (SMAP) mission (to be launched 2014/2015) [2 and 3]. These approaches are adapted for vegetated landscapes with effective vegetation parameters tau and omega by fitting experimental data or simulation outputs of a multiple scattering model [4-7]. The model has been validated over grasslands, agricultural crops, and generally light to moderate vegetation. As the density of vegetation increases, sensitivity to the underlying SM begins to degrade significantly and errors in the retrieved SM increase accordingly. The zero-order model also loses its validity when dense vegetation (i.e. forest, mature corn, etc.) includes scatterers, such as branches and trunks (or stalks in the case of corn), which are large with respect to the wavelength. The tau-omega model (when applied over moderately to densely vegetated landscapes) will need modification (in terms of form or effective parameterization) to enable accurate characterization of vegetation parameters with respect to specific tree types, anisotropic canopy structure, presence of leaves and/or understory. More scattering terms (at least up to first-order at L-band) should be included in the RT solutions for forest canopies [8]. Although not really suitable to forests, a zero-order tau-omega model might be applied to such vegetation canopies with large scatterers, but that equivalent or effective parameters would have to be used [4]. This requires that the effective values (vegetation opacity and single scattering albedo) need to be evaluated (compared) with theoretical definitions of these parameters. In a recent study [9], effective vegetation opacity of coniferous trees was compared with two independent estimates of the same parameter. First, a zero-order RT model was fitted to multiangular microwave emissivity data in a least-square sense to provide effective vegetation optical depth as done in spaceborne retrieval algorithms. Second, a ratio between radar backscatter measurements with a corner reflector under trees and in an open area was calculated to obtain measured tree propagation characteristics. Finally, the theoretical propagation constant was determined by forward scattering theorem using detailed measurements of size/angle distributions and dielectric constants of the tree constituents (trunk, branches, and needles). Results indicated that the effective attenuation values are smaller than but of similar magnitude to both the theoretical and measured values. This study will complement the previous work [9] and will focus on characterization of effective scattering albedo by assuming that effective vegetation opacity is same as theoretical opacity. The resultant effective albedo will not be the albedo of single forest canopy element anymore, but it becomes a global parameter, which depends on all the processes taking place within the canopy including multiple scattering as described.

TH-E-BRF-09: Gaussian Mixture Model Analysis of Radiation-Induced Parotid-Gland Injury: An Ultrasound Study of Acute and Late Xerostomia in Head-And-Neck Radiotherapy

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

Liu, T; Yu, D; Beitler, J

Purpose: Xerostomia (dry mouth), secondary to parotid-gland injury, is a distressing side-effect in head-and-neck radiotherapy (RT). This study's purpose is to develop a novel ultrasound technique to quantitatively evaluate post-RT parotid-gland injury. Methods: Recent ultrasound studies have shown that healthy parotid glands exhibit homogeneous echotexture, whereas post-RT parotid glands are often heterogeneous, with multiple hypoechoic (inflammation) or hyperechoic (fibrosis) regions. We propose to use a Gaussian mixture model to analyze the ultrasonic echo-histogram of the parotid glands. An IRB-approved clinical study was conducted: (1) control-group: 13 healthy-volunteers, served as the control; (2) acutetoxicity group − 20 patients (mean age: 62.5more » ± 8.9 years, follow-up: 2.0±0.8 months); and (3) late-toxicity group − 18 patients (mean age: 60.7 ± 7.3 years, follow-up: 20.1±10.4 months). All patients experienced RTOG grade 1 or 2 salivary-gland toxicity. Each participant underwent an ultrasound scan (10 MHz) of the bilateral parotid glands. An echo-intensity histogram was derived for each parotid and a Gaussian mixture model was used to fit the histogram using expectation maximization (EM) algorithm. The quality of the fitting was evaluated with the R-squared value. Results: (1) Controlgroup: all parotid glands fitted well with one Gaussian component, with a mean intensity of 79.8±4.9 (R-squared>0.96). (2) Acute-toxicity group: 37 of the 40 post-RT parotid glands fitted well with two Gaussian components, with a mean intensity of 42.9±7.4, 73.3±12.2 (R-squared>0.95). (3) Latetoxicity group: 32 of the 36 post-RT parotid fitted well with 3 Gaussian components, with mean intensities of 49.7±7.6, 77.2±8.7, and 118.6±11.8 (R-squared>0.98). Conclusion: RT-associated parotid-gland injury is common in head-and-neck RT, but challenging to assess. This work has demonstrated that the Gaussian mixture model of the echo-histogram could quantify acute and late toxicity of the parotid glands. This study provides meaningful preliminary data from future observational and interventional clinical research.« less

Estimation of mineral dust direct radiative forcing at the European Aerosol Research Lidar NETwork site of Lecce, Italy, during the ChArMEx/ADRIMED summer 2013 campaign: Impact of radiative transfer model spectral resolutions

NASA Astrophysics Data System (ADS)

Barragan, Ruben; Romano, Salvatore; Sicard, Michaël.; Burlizzi, Pasquale; Perrone, Maria Rita; Comeron, Adolfo

2016-09-01

A field campaign took place in the western and central Mediterranean basin on June-July 2013 in the framework of the ChArMEx (Chemistry-Aerosol Mediterranean Experiment, http://charmex.lsce.ipsl.fr/)/ADRIMED (Aerosol Direct Radiative Impact on the regional climate in the MEDiterranean region, http://adrimed.sedoo.fr/) project to characterize the aerosol direct radiative forcing (DRF) over the Mediterranean. This work focuses on the aerosol DRF estimations at Lecce (40.33°N; 18.11°E; 30 m above sea level) during the Saharan dust outbreak that affected southern Italy from 20 to 24 June 2013. The Global Atmospheric Model (GAME) and the Two-Stream (TS) model were used to calculate the instantaneous aerosol DRF in the short-wave (SW) and long-wave (LW) spectral ranges, at the surface and at the top of the atmosphere (TOA). The main differences between the two models were due to the different numerical methods to solve the radiative transfer (RT) equations and to the more detailed spectral resolution of GAME compared to that of TS. 167 and 115 subbands were used by GAME in the 0.3-4 and 4-37 µm spectral ranges, respectively. Conversely, the TS model used 8 and 11 subbands in the same spectral ranges, respectively. We found on 22 June that the SW-DRFs from the two models were in good agreement, both at the TOA and at the surface. The instantaneous SW-DRFs at the surface and at the TOA varied from -50 to -34 W m-2 and from -6 to +8 W m-2, respectively, while the surface and TOA LW-DRFs ranged between +3.5 and +8.0 W m-2 and between +1.7 and +6.9 W m-2, respectively. In particular, both models provided positive TOA SW-DRFs at solar zenith angles smaller than 25° because of the mixing of the desert dust with anthropogenic pollution during its transport to the study site. In contrast, the TS model overestimated the GAME LW-DRF up to about 5 and 7.5 times at the surface and at the TOA, respectively, when the dust particle contribution was largest. The low spectral resolution of the real (n) and imaginary (k) refractive index values was mainly responsible for the LW-DRF overestimates of the TS model. However, we found that the "optimization" of the n and k values at 8.75 and 11.5 µm was sufficient in this study to obtain a satisfactory agreement between the LW-DRFs from the two models, both at the TOA and at the surface. The impact of the spectral dependence of the water vapor absorption coefficients on the estimation of the flux without aerosol has also been addressed. Paper results did not reveal any significant impact due to the different numerical methods used by the two models to solve the RT equations.

Accelerating NLTE radiative transfer by means of the Forth-and-Back Implicit Lambda Iteration: A two-level atom line formation in 2D Cartesian coordinates

NASA Astrophysics Data System (ADS)

Milić, Ivan; Atanacković, Olga

2014-10-01

State-of-the-art methods in multidimensional NLTE radiative transfer are based on the use of local approximate lambda operator within either Jacobi or Gauss-Seidel iterative schemes. Here we propose another approach to the solution of 2D NLTE RT problems, Forth-and-Back Implicit Lambda Iteration (FBILI), developed earlier for 1D geometry. In order to present the method and examine its convergence properties we use the well-known instance of the two-level atom line formation with complete frequency redistribution. In the formal solution of the RT equation we employ short characteristics with two-point algorithm. Using an implicit representation of the source function in the computation of the specific intensities, we compute and store the coefficients of the linear relations J=a+bS between the mean intensity J and the corresponding source function S. The use of iteration factors in the ‘local’ coefficients of these implicit relations in two ‘inward’ sweeps of 2D grid, along with the update of the source function in other two ‘outward’ sweeps leads to four times faster solution than the Jacobi’s one. Moreover, the update made in all four consecutive sweeps of the grid leads to an acceleration by a factor of 6-7 compared to the Jacobi iterative scheme.

Phase III Trial of Chemoradiotherapy for Anaplastic Oligodendroglioma: Long-Term Results of RTOG 9402

PubMed Central

Cairncross, Gregory; Wang, Meihua; Shaw, Edward; Jenkins, Robert; Brachman, David; Buckner, Jan; Fink, Karen; Souhami, Luis; Laperriere, Normand; Curran, Walter; Mehta, Minesh

2013-01-01

Purpose Anaplastic oligodendrogliomas, pure (AO) and mixed (anaplastic oligoastrocytoma [AOA]), are chemosensitive, especially if codeleted for 1p/19q, but whether patients live longer after chemoradiotherapy is unknown. Patients and Methods Eligible patients with AO/AOA were randomly assigned to procarbazine, lomustine, and vincristine (PCV) plus radiotherapy (RT) versus RT alone. The primary end point was overall survival (OS). Results Two hundred ninety-one eligible patients were randomly assigned: 148 to PCV plus RT and 143 to RT. For the entire cohort, there was no difference in median survival by treatment (4.6 years for PCV plus RT v 4.7 years for RT; hazard ratio [HR] = 0.79; 95% CI, 0.60 to 1.04; P = .1). Patients with codeleted tumors lived longer than those with noncodeleted tumors (PCV plus RT: 14.7 v 2.6 years, HR = 0.36, 95% CI, 0.23 to 0.57, P < .001; RT: 7.3 v 2.7 years, HR = 0.40, 95% CI, 0.27 to 0.60, P < .001), and the median survival of those with codeleted tumors treated with PCV plus RT was twice that of patients receiving RT (14.7 v 7.3 years; HR = 0.59; 95% CI, 0.37 to 0.95; P = .03). For those with noncodeleted tumors, there was no difference in median survival by treatment arm (2.6 v 2.7 years; HR = 0.85; 95% CI, 0.58 to 1.23; P = .39). In Cox models that included codeletion status, the adjusted OS for all patients was prolonged by PCV plus RT (HR = 0.67; 95% CI, 0.50 to 0.91; P = .01). Conclusion For the subset of patients with 1p/19q codeleted AO/AOA, PCV plus RT may be an especially effective treatment, although this observation was derived from an unplanned analysis. PMID:23071247

Prediction of Liver Function by Using Magnetic Resonance-based Portal Venous Perfusion Imaging

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

Cao Yue, E-mail: yuecao@umich.edu; Department of Radiology, University of Michigan, Ann Arbor, Michigan; Wang Hesheng

2013-01-01

Purpose: To evaluate whether liver function can be assessed globally and spatially by using volumetric dynamic contrast-enhanced magnetic resonance imaging MRI (DCE-MRI) to potentially aid in adaptive treatment planning. Methods and Materials: Seventeen patients with intrahepatic cancer undergoing focal radiation therapy (RT) were enrolled in institution review board-approved prospective studies to obtain DCE-MRI (to measure regional perfusion) and indocyanine green (ICG) clearance rates (to measure overall liver function) prior to, during, and at 1 and 2 months after treatment. The volumetric distribution of portal venous perfusion in the whole liver was estimated for each scan. We assessed the correlation betweenmore » mean portal venous perfusion in the nontumor volume of the liver and overall liver function measured by ICG before, during, and after RT. The dose response for regional portal venous perfusion to RT was determined using a linear mixed effects model. Results: There was a significant correlation between the ICG clearance rate and mean portal venous perfusion in the functioning liver parenchyma, suggesting that portal venous perfusion could be used as a surrogate for function. Reduction in regional venous perfusion 1 month after RT was predicted by the locally accumulated biologically corrected dose at the end of RT (P<.0007). Regional portal venous perfusion measured during RT was a significant predictor for regional venous perfusion assessed 1 month after RT (P<.00001). Global hypovenous perfusion pre-RT was observed in 4 patients (3 patients with hepatocellular carcinoma and cirrhosis), 3 of whom had recovered from hypoperfusion, except in the highest dose regions, post-RT. In addition, 3 patients who had normal perfusion pre-RT had marked hypervenous perfusion or reperfusion in low-dose regions post-RT. Conclusions: This study suggests that MR-based volumetric hepatic perfusion imaging may be a biomarker for spatial distribution of liver function, which could aid in individualizing therapy, particularly for patients at risk for liver injury after RT.« less

Detection of Acute Myocardial Infarction in a Pig Model Using the SAN-Atrial-AVN-His (SAAH) Electrocardiogram (ECG), Model PHS-A10, an Automated and Integrated Signals Recognition System

PubMed Central

Zhao, Wenjiao; Lu, Guihua; Liu, Li; Sun, Zhishan; Wu, Mingxin; Yi, Wenyan; Chen, Haiyan; Li, Yanhui

2018-01-01

Background The aim of this study was to compare the use of the standard 12-lead electrocardiogram (ECG) with the SAN-Atrial-AVN-His (SAAH) ECG (Model PHS-A10), a new automated and integrated signals recognition system that detects micro-waveforms within the P, QRS, and T-wave, in a pig model of acute myocardial infarction (MI). Material/Methods Six medium-sized domestic Chinese pigs underwent general anesthesia, and an angioplasty balloon was placed and dilated for 120 minutes in the first diagonal coronary artery arising from the left anterior descending (LAD) coronary artery. A standard ECG and a SAAH ECG (Model PHS-A10) were used to evaluate: 1) the number of wavelets in ST-T segment in lead V5; 2) the duration of the repolarization initial (Ri), or duration of the wavelets starting from the J-point to the endpoint of the wavelets in the ST interval; 3) the duration of the repolarization terminal (Rt), of the wavelets, starting from the endpoint of the wavelets in the ST interval to the cross-point of the T-wave and baseline; 4) the ratio Ri: Rt. Results Following coronary artery occlusion, duration of Ri and Ri/Rt increased, and Rt decreased, which was detected by the SAAH ECG (Model PHS-A10) within 12 seconds, compared with standard ECG that detected ST segment depression at 24 seconds following coronary artery occlusion. Conclusions The findings from this preliminary study in a pig model of acute MI support the need for clinical studies to evaluate the SAAH ECG (Model PHS-A10) for the early detection of acute MI. PMID:29502127

Detection of Acute Myocardial Infarction in a Pig Model Using the SAN-Atrial-AVN-His (SAAH) Electrocardiogram (ECG), Model PHS-A10, an Automated and Integrated Signals Recognition System.

PubMed

Zhao, Wenjiao; Lu, Guihua; Liu, Li; Sun, Zhishan; Wu, Mingxin; Yi, Wenyan; Chen, Haiyan; Li, Yanhui; Tang, Lilong; Zeng, Jianping

2018-03-04

BACKGROUND The aim of this study was to compare the use of the standard 12-lead electrocardiogram (ECG) with the SAN-Atrial-AVN-His (SAAH) ECG (Model PHS-A10), a new automated and integrated signals recognition system that detects micro-waveforms within the P, QRS, and T-wave, in a pig model of acute myocardial infarction (MI). MATERIAL AND METHODS Six medium-sized domestic Chinese pigs underwent general anesthesia, and an angioplasty balloon was placed and dilated for 120 minutes in the first diagonal coronary artery arising from the left anterior descending (LAD) coronary artery. A standard ECG and a SAAH ECG (Model PHS-A10) were used to evaluate: 1) the number of wavelets in ST-T segment in lead V5; 2) the duration of the repolarization initial (Ri), or duration of the wavelets starting from the J-point to the endpoint of the wavelets in the ST interval; 3) the duration of the repolarization terminal (Rt), of the wavelets, starting from the endpoint of the wavelets in the ST interval to the cross-point of the T-wave and baseline; 4) the ratio Ri: Rt. RESULTS Following coronary artery occlusion, duration of Ri and Ri/Rt increased, and Rt decreased, which was detected by the SAAH ECG (Model PHS-A10) within 12 seconds, compared with standard ECG that detected ST segment depression at 24 seconds following coronary artery occlusion. CONCLUSIONS The findings from this preliminary study in a pig model of acute MI support the need for clinical studies to evaluate the SAAH ECG (Model PHS-A10) for the early detection of acute MI.

Effect of glare on simple reaction time.

PubMed

Aguirre, Rolando C; Colombo, Elisa M; Barraza, José F

2008-07-01

We systematized the study of the effect of glare on reaction time (RT), for visual conditions similar to the ones found during night driving: Mesopic range of adaptation (0.14 cd/m2), glare levels of the order of those produced by car headlights (E(G)=15, 60 lx), suprathreshold luminance contrasts, and a variety of spatial frequencies covering the selected range of visibility (1, 2, 4, and 8 c/deg). We found that for the no-glare situation, RT increases with decreasing contrast and increasing spatial frequency, which agrees with previous findings. When data are plotted as a function of the inverse of contrast, RT varies linearly, with k--the RT-contrast factor of Pieron's law--representing the slope of the lines. The effect of glare on RT is an increase in the slope of these lines. This effect is different for each spatial frequency, which cannot be accounted for in the classic approach considering that glare can be replaced by a single veiling luminance. We show that the effect of glare on RT must be modeled by an equivalent glare luminance that depends on spatial frequency.

Prevalence and correlates of resistance training skill competence in adolescents.

PubMed

Smith, Jordan J; DeMarco, Matthew; Kennedy, Sarah G; Kelson, Mark; Barnett, Lisa M; Faigenbaum, Avery D; Lubans, David R

2018-06-01

The aim of this study is to examine the prevalence and correlates of adolescents' resistance training (RT) skill competence. Participants were 548 adolescents (14.1 ± 0.5 years) from 16 schools in New South Wales, Australia. RT skills were assessed using the Resistance Training Skills Battery. Demographics, BMI, muscular fitness, perceived strength, RT self-efficacy, and motivation for RT were also assessed. The proportion demonstrating "competence" and "near competence" in each of the six RT skills were calculated and sex differences explored. Associations between the combined RT skill score and potential correlates were examined using multi-level linear mixed models. Overall, the prevalence of competence was low (range = 3.3% to 27.9%). Females outperformed males on the squat, lunge and overhead press, whereas males performed better on the push-up (p < .05). Significant associations were seen for a number of correlates, which largely differed by sex. Muscular fitness was moderately and positively associated with RT skills among both males (β = 0.34, 95%CIs = 0.23 to 0.46) and females (β = 0.36, 95%CIs = 0.23 to 0.48). Our findings support a link between RT skills and muscular fitness. Other associations were statistically significant but small in magnitude, and should therefore be interpreted cautiously.

Effects of aging temperature and time on the corrosion protection provided by trivalent chromium process coatings on AA2024-T3.

PubMed

Li, Liangliang; Swain, Greg M

2013-08-28

The effects of aging temperature and time on the physical structure of and corrosion protection provided by trivalent chromium process (TCP) coatings on AA2024-T3 are reported. The TCP coating forms a partially blocking barrier layer on the alloy surface that consists of hydrated channels and or defects. It is through these channels and defects that ions and dissolved O2 can be transported to small areas of the underlying alloy. Reactions initiate at these sites, which can ultimately lead to undercutting of the coating and localized corrosion. We tested the hypothesis that collapsing the channels and or reducing the number of defects in the coating might be possible through post-deposition heat treatment, and that this would enhance the corrosion protection provided by the coating. This was tested by aging the TCP-coated AA2024 alloys in air overnight at room temperature (RT), 55, 100, or 150 °C. The TCP coating became dehydrated and thinner at the high temperatures (55 and 100 °C). This improved the corrosion protection as evidenced by a 2× increase in the charge transfer resistance. Aging at 150 °C caused excessive coating dehydration and shrinkage. This led to severe cracking and detachment of the coating from the surface. The TCP-coated AA2024 samples were also aged in air at RT from 1 to 7 days. There was no thinning of the coating, but the corrosion protection was enhanced with a longer aging period as evidenced by a 4× increase in the charge transfer resistance. The coating became more hydrophobic after aging at elevated temperature (up to 100 °C) and with aging time at RT as evidenced by an increased water contact angle from 7 to 100 °C.

Repeated Positron Emission Tomography-Computed Tomography and Perfusion-Computed Tomography Imaging in Rectal Cancer: Fluorodeoxyglucose Uptake Corresponds With Tumor Perfusion

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

Janssen, Marco H.M., E-mail: marco.janssen@maastro.nl; Aerts, Hugo J.W.L.; Buijsen, Jeroen

2012-02-01

Purpose: The purpose of this study was to analyze both the intratumoral fluorodeoxyglucose (FDG) uptake and perfusion within rectal tumors before and after hypofractionated radiotherapy. Methods and Materials: Rectal cancer patients, referred for preoperative hypofractionated radiotherapy (RT), underwent FDG-positron emission tomography (PET)-computed tomography (CT) and perfusion-CT (pCT) imaging before the start of hypofractionated RT and at the day of the last RT fraction. The pCT-images were analyzed using the extended Kety model, quantifying tumor perfusion with the pharmacokinetic parameters K{sup trans}, v{sub e}, and v{sub p}. The mean and maximum FDG uptake based on the standardized uptake value (SUV) andmore » transfer constant (K{sup trans}) within the tumor were correlated. Also, the tumor was subdivided into eight subregions and for each subregion the mean and maximum SUVs and K{sup trans} values were assessed and correlated. Furthermore, the mean FDG uptake in voxels presenting with the lowest 25% of perfusion was compared with the FDG uptake in the voxels with the 25% highest perfusion. Results: The mean and maximum K{sup trans} values were positively correlated with the corresponding SUVs ({rho} = 0.596, p = 0.001 and {rho} = 0.779, p < 0.001). Also, positive correlations were found for K{sup trans} values and SUVs within the subregions (mean, {rho} = 0.413, p < 0.001; and max, {rho} = 0.540, p < 0.001). The mean FDG uptake in the 25% highest-perfused tumor regions was significantly higher compared with the 25% lowest-perfused regions (10.6% {+-} 5.1%, p = 0.017). During hypofractionated radiotherapy, stable mean (p = 0.379) and maximum (p = 0.280) FDG uptake levels were found, whereas the mean (p = 0.040) and maximum (p = 0.003) K{sup trans} values were found to significantly increase. Conclusion: Highly perfused rectal tumors presented with higher FDG-uptake levels compared with relatively low perfused tumors. Also, intratumor regions with a high FDG uptake demonstrated with higher levels of perfusion than regions with a relatively low FDG-uptake. Early after hypofractionated RT, stable FDG uptake levels were found, whereas tumor perfusion was found to significantly increase.« less

Identification of rhizome-specific genes by genome-wide differential expression Analysis in Oryza longistaminata

PubMed Central

2011-01-01

Background Rhizomatousness is a key component of perenniality of many grasses that contribute to competitiveness and invasiveness of many noxious grass weeds, but can potentially be used to develop perennial cereal crops for sustainable farmers in hilly areas of tropical Asia. Oryza longistaminata, a perennial wild rice with strong rhizomes, has been used as the model species for genetic and molecular dissection of rhizome development and in breeding efforts to transfer rhizome-related traits into annual rice species. In this study, an effort was taken to get insights into the genes and molecular mechanisms underlying the rhizomatous trait in O. longistaminata by comparative analysis of the genome-wide tissue-specific gene expression patterns of five different tissues of O. longistaminata using the Affymetrix GeneChip Rice Genome Array. Results A total of 2,566 tissue-specific genes were identified in five different tissues of O. longistaminata, including 58 and 61 unique genes that were specifically expressed in the rhizome tips (RT) and internodes (RI), respectively. In addition, 162 genes were up-regulated and 261 genes were down-regulated in RT compared to the shoot tips. Six distinct cis-regulatory elements (CGACG, GCCGCC, GAGAC, AACGG, CATGCA, and TAAAG) were found to be significantly more abundant in the promoter regions of genes differentially expressed in RT than in the promoter regions of genes uniformly expressed in all other tissues. Many of the RT and/or RI specifically or differentially expressed genes were located in the QTL regions associated with rhizome expression, rhizome abundance and rhizome growth-related traits in O. longistaminata and thus are good candidate genes for these QTLs. Conclusion The initiation and development of the rhizomatous trait in O. longistaminata are controlled by very complex gene networks involving several plant hormones and regulatory genes, different members of gene families showing tissue specificity and their regulated pathways. Auxin/IAA appears to act as a negative regulator in rhizome development, while GA acts as the activator in rhizome development. Co-localization of the genes specifically expressed in rhizome tips and rhizome internodes with the QTLs for rhizome traits identified a large set of candidate genes for rhizome initiation and development in rice for further confirmation. PMID:21261937

'Information on the fly': Challenges in professional communication in high technological nursing. A focus group study from a radiotherapy department in Sweden.

PubMed

Widmark, Catarina; Tishelman, Carol; Gustafsson, Helena; Sharp, Lena

2012-07-23

Radiotherapy (RT) units are high-tech nursing environments. In Sweden, RT registered nurses (RNs) provide and manage RT in close collaboration with other professional groups, as well as providing nursing care for patients with cancer. Communication demands on these RNs are thus particularly complex. In this study, we aimed to better understand problems, strengths and change needs related to professional communication with and within the RT department, as a basis for developing a situation-specific intervention. Focus groups discussions (FGDs) were conducted with different professional (RNs, assistant nurses, physicians, engineers and physicists) and user stakeholders. Transcripts of the FGDs were inductively analyzed by a team of researchers, to generate clinically relevant and useful data. These findings give insight into RT safety climate and are presented under three major headings: Conceptualization of professional domains; Organization and leadership issues; and Communication forms, strategies and processes. The impact of existing hierarchies, including how they are conceptualized and acted out in practice, was noted throughout these data. Despite other differences, participating professionals agreed about communication problems related to RT, i.e. a lack of systems and processes for information transfer, unclear role differentiation, a sense of mutual disrespect, and ad hoc communication taking place 'on the fly'. While all professional groups recognized extensive communication problems, none acknowledged the potential negative effects on patient safety or care described in the FGD with patient representatives. While RNs often initially denied the existence of a hierarchy, they placed themselves on a hierarchy in their descriptions, describing their own role as passive, with a sense of powerlessness. Potential safety hazards described in the FGDs include not reporting medical errors and silently ignoring or actively opposing new guidelines and regulations. There is a risk that RNs who view themselves as disenfranchised within an organization will act with passive resistance to change, rather than as change promoters. As interventions to strengthen teams cannot be stronger than the weakest link, RNs may need support in the transition "from silence to voice" in order to take a position of full professional responsibility in a multi-professional health care team.

SU-C-17A-05: Quantification of Intra-Fraction Motion of Breast Tumors Using Cine-MRI

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

Heijst, T van; Philippens, M; Bongard, D van den

2014-06-01

Purpose: Magnetic resonance imaging (MRI) enables direct characterization of intra-fraction motion ofbreast tumors, due to high softtissue contrast and geometric accuracy. The purpose is to analyzethis motion in early-stage breast-cancer patients using pre-operative supine cine-MRI. Methods: MRI was performed in 12 female early-stage breast-cancer patients on a 1.5-T Ingenia (Philips)wide-bore scanner in supine radiotherapy (RT) position, prior to breast-conserving surgery. Twotwodimensional (2D) T2-weighted balanced fast-field echo (cine-MRI) sequences were added tothe RT protocol, oriented through the tumor. They were alternately acquired in the transverse andsagittal planes, every 0.3 s during 1 min. A radiation oncologist delineated gross target volumes(GTVs) onmore » 3D contrast-enhanced MRI. Clinical target volumes (CTV = GTV + 15 mm isotropic)were generated and transferred onto the fifth time-slice of the time-series, to which subsequents lices were registered using a non-rigid Bspline algorithm; delineations were transformed accordingly. To evaluate intra-fraction CTV motion, deformation fields between the transformed delineations were derived to acquire the distance ensuring 95% surface coverage during scanning(P95%), for all in-plane directions: anteriorposterior (AP), left-right (LR), and caudal-cranial(CC). Information on LR was derived from transverse scans, CC from sagittal scans, AP fromboth sets. Results: Time-series with registration errors - induced by motion artifacts - were excluded by visual inspection. For our analysis, 11 transverse, and 8 sagittal time-series were taken into account. Themedian P95% calculated in AP (19 series), CC (8), and LR (11) was 1.8 mm (range: 0.9–4.8), 1.7mm (0.8–3.6), and 1.0 mm (0.6–3.5), respectively. Conclusion: Intra-fraction motion analysis of breast tumors was achieved using cine-MRI. These first results show that in supine RT position, motion amplitudes are limited. This information can be used for adaptive RT planning, and to develop preoperative partial-breast RT strategies, such asablative RT for early-stage breast-cancer patients.« less

Biomarker discovery for colon cancer using a 761 gene RT-PCR assay.

PubMed

Clark-Langone, Kim M; Wu, Jenny Y; Sangli, Chithra; Chen, Angela; Snable, James L; Nguyen, Anhthu; Hackett, James R; Baker, Joffre; Yothers, Greg; Kim, Chungyeul; Cronin, Maureen T

2007-08-15

Reverse transcription PCR (RT-PCR) is widely recognized to be the gold standard method for quantifying gene expression. Studies using RT-PCR technology as a discovery tool have historically been limited to relatively small gene sets compared to other gene expression platforms such as microarrays. We have recently shown that TaqMan RT-PCR can be scaled up to profile expression for 192 genes in fixed paraffin-embedded (FPE) clinical study tumor specimens. This technology has also been used to develop and commercialize a widely used clinical test for breast cancer prognosis and prediction, the Onco typeDX assay. A similar need exists in colon cancer for a test that provides information on the likelihood of disease recurrence in colon cancer (prognosis) and the likelihood of tumor response to standard chemotherapy regimens (prediction). We have now scaled our RT-PCR assay to efficiently screen 761 biomarkers across hundreds of patient samples and applied this process to biomarker discovery in colon cancer. This screening strategy remains attractive due to the inherent advantages of maintaining platform consistency from discovery through clinical application. RNA was extracted from formalin fixed paraffin embedded (FPE) tissue, as old as 28 years, from 354 patients enrolled in NSABP C-01 and C-02 colon cancer studies. Multiplexed reverse transcription reactions were performed using a gene specific primer pool containing 761 unique primers. PCR was performed as independent TaqMan reactions for each candidate gene. Hierarchal clustering demonstrates that genes expected to co-express form obvious, distinct and in certain cases very tightly correlated clusters, validating the reliability of this technical approach to biomarker discovery. We have developed a high throughput, quantitatively precise multi-analyte gene expression platform for biomarker discovery that approaches low density DNA arrays in numbers of genes analyzed while maintaining the high specificity, sensitivity and reproducibility that are characteristics of RT-PCR. Biomarkers discovered using this approach can be transferred to a clinical reference laboratory setting without having to re-validate the assay on a second technology platform.

WE-E-BRE-05: Ensemble of Graphical Models for Predicting Radiation Pneumontis Risk

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

Lee, S; Ybarra, N; Jeyaseelan, K

Purpose: We propose a prior knowledge-based approach to construct an interaction graph of biological and dosimetric radiation pneumontis (RP) covariates for the purpose of developing a RP risk classifier. Methods: We recruited 59 NSCLC patients who received curative radiotherapy with minimum 6 month follow-up. 16 RP events was observed (CTCAE grade ≥2). Blood serum was collected from every patient before (pre-RT) and during RT (mid-RT). From each sample the concentration of the following five candidate biomarkers were taken as covariates: alpha-2-macroglobulin (α2M), angiotensin converting enzyme (ACE), transforming growth factor β (TGF-β), interleukin-6 (IL-6), and osteopontin (OPN). Dose-volumetric parameters were alsomore » included as covariates. The number of biological and dosimetric covariates was reduced by a variable selection scheme implemented by L1-regularized logistic regression (LASSO). Posterior probability distribution of interaction graphs between the selected variables was estimated from the data under the literature-based prior knowledge to weight more heavily the graphs that contain the expected associations. A graph ensemble was formed by averaging the most probable graphs weighted by their posterior, creating a Bayesian Network (BN)-based RP risk classifier. Results: The LASSO selected the following 7 RP covariates: (1) pre-RT concentration level of α2M, (2) α2M level mid- RT/pre-RT, (3) pre-RT IL6 level, (4) IL6 level mid-RT/pre-RT, (5) ACE mid-RT/pre-RT, (6) PTV volume, and (7) mean lung dose (MLD). The ensemble BN model achieved the maximum sensitivity/specificity of 81%/84% and outperformed univariate dosimetric predictors as shown by larger AUC values (0.78∼0.81) compared with MLD (0.61), V20 (0.65) and V30 (0.70). The ensembles obtained by incorporating the prior knowledge improved classification performance for the ensemble size 5∼50. Conclusion: We demonstrated a probabilistic ensemble method to detect robust associations between RP covariates and its potential to improve RP prediction accuracy. Our Bayesian approach to incorporate prior knowledge can enhance efficiency in searching of such associations from data. The authors acknowledge partial support by: 1) CREATE Medical Physics Research Training Network grant of the Natural Sciences and Engineering Research Council (Grant number: 432290) and 2) The Terry Fox Foundation Strategic Training Initiative for Excellence in Radiation Research for the 21st Century (EIRR21)« less

NASA SPoRT GOES-R Proving Ground Activities

NASA Technical Reports Server (NTRS)

Stano, Geoffrey T.; Fuell, Kevin K.; Jedloec, Gary J.

2010-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) program is a partner with the GOES-R Proving Ground (PG) helping prepare forecasters understand the unique products to come from the GOES-R instrument suite. SPoRT is working collaboratively with other members of the GOES-R PG team and Algorithm Working Group (AWG) scientists to develop and disseminate a suite of proxy products that address specific forecast problems for the WFOs, Regional and National Support Centers, and other NOAA users. These products draw on SPoRT s expertise with the transition and evaluation of products into operations from the MODIS instrument and the North Alabama Lightning Mapping Array (NALMA). The MODIS instrument serves as an excellent proxy for the Advanced Baseline Imager (ABI) that will be aboard GOES-R. SPoRT has transitioned and evaluated several multi-channel MODIS products. The true and false color products are being used in natural hazard detection by several SPoRT partners to provide better observation of land features, such as fires, smoke plumes, and snow cover. Additionally, many of SPoRT s partners are coastal offices and already benefit from the MODIS sea surface temperature composite. This, along with other surface feature observations will be developed into ABI proxy products for diagnostic use in the forecast process as well as assimilation into forecast models. In addition to the MODIS instrument, the NALMA has proven very valuable to WFOs with access to these total lightning data. These data provide situational awareness and enhanced warning decision making to improve lead times for severe thunderstorm and tornado warnings. One effort by SPoRT scientists includes a lightning threat product to create short-term model forecasts of lightning activity. Additionally, SPoRT is working with the AWG to create GLM proxy data from several of the ground based total lightning networks, such as the NALMA. The evaluation will focus on the vastly improved spatial coverage of the GLM, but with the trade-off of lower resolution compared to the NALMA. In addition to the above tasks, SPoRT will make these data available in the NWS next generation display software, AWIPS II. This has already been successfully completed for the two basic GLM proxies. SPoRT will use these products to train forecasters on the capabilities of GOES-R and foster feedback to develop additional products, visualizations, and requirements beneficial to end users needs. These developments and feedback will be made available to the GOES-R Proving Ground for the upcoming 2010 Spring Program in Norman, Oklahoma.

Effective Albedo of Vegetated Terrain at L-Band

NASA Technical Reports Server (NTRS)

Kurum, Mehmet; O'Neill, Peggy E.; Lang, Roger H.

2011-01-01

This paper derives an explicit expression for an effective albedo of vegetated terrain from the zero- and multiple- order radiative transfer (RT) model comparison. The formulation establishes a direct physical link between the effective vegetation parameterization and the theoretical description of absorption and scattering within the canopy. The paper will present an evaluation of the derived albedo for corn canopies with data taken during an experiment at Alabama A&M Winfield A. Thomas Agricultural Research Station near Huntsville, Alabama in June, 1998. The test site consisted of two 50-m x 60-m plots - one with a bare surface and the other with grass cover - and four 30-m x 50-m plots of corn at different planting densities. One corn field was planted at a full density of 9.5 plants/sq m while the others were planted at 1/3, 1/2 and 2/3 of the full density. The fields were observed with a truck-mounted L-band radiometer at incident angle of 15 degree for the period of two weeks. Soil moisture (SM) changed daily due to irrigation and natural rainfall. Variations in gravimetric SM from 18 % to 34 % were seen during this period. Ground truth data, including careful characterization of the corn size and orientation statistics, and its dielectric, was also collected and used to simulate the effective albedo for the vegetation. The single-scattering albedo is defined as the fractional power scattered from individual vegetation constituents with respect to canopy extinction. It represents single-scattering properties of vegetation elements only, and is independent of ground properties. The values of the albedo get higher when there is dense vegetation (i.e. forest, mature corn, etc.) with scatterers, such as branches and trunks (or stalks in the case of corn), which are large with respect to the wavelength. This large albedo leads to a reduction in brightness temperature in the zero-order RT solution (known as tau-omega model). Higher-order multiple-scattering RT solutions are required for proper representation of scattering within vegetation. In this paper, an expression for an effective albedo for the whole canopy including the ground is derived for use in the zero-order RT model-based SM retrieval. This effective albedo takes into account of all the processes taking place within the canopy, including multiple-scattering. This new formulation will be presented and its importance for microwave SM retrieval will be evaluated for corn canopies in conjunction with the detailed ground truth data obtained during the experiment at Alabama in 1998. Emphasis will be placed on examining how the radiometer response to SM is modified by the corn canopy scattering under different field conditions. A semi-empirical parameterization of the effective albedo will be investigated through analysis of SM and vegetation water content effects on the effective albedo.

Treatment of Inherited Eye Defects by Systemic Hematopoietic Stem Cell Transplantation.

PubMed

Rocca, Celine J; Kreymerman, Alexander; Ur, Sarah N; Frizzi, Katie E; Naphade, Swati; Lau, Athena; Tran, Tammy; Calcutt, Nigel A; Goldberg, Jeffrey L; Cherqui, Stephanie

2015-11-01

Cystinosis is caused by a deficiency in the lysosomal cystine transporter, cystinosin (CTNS gene), resulting in cystine crystal accumulation in tissues. In eyes, crystals accumulate in the cornea causing photophobia and eventually blindness. Hematopoietic stem progenitor cells (HSPCs) rescue the kidney in a mouse model of cystinosis. We investigated the potential for HSPC transplantation to treat corneal defects in cystinosis. We isolated HSPCs from transgenic DsRed mice and systemically transplanted irradiated Ctns-/- mice. A year posttransplantation, we investigated the fate and function of HSPCs by in vivo confocal and fluorescence microscopy (IVCM), quantitative RT-PCR (RT-qPCR), mass spectrometry, histology, and by measuring the IOP. To determine the mechanism by which HSPCs may rescue disease cells, we transplanted Ctns-/- mice with Ctns-/- DsRed HSPCs virally transduced to express functional CTNS-eGFP fusion protein. We found that a single systemic transplantation of wild-type HSPCs prevented ocular pathology in the Ctns-/- mice. Engraftment-derived HSPCs were detected within the cornea, and also in the sclera, ciliary body, retina, choroid, and lens. Transplantation of HSPC led to substantial decreases in corneal cystine crystals, restoration of normal corneal thickness, and lowered IOP in mice with high levels of donor-derived cell engraftment. Finally, we found that HSPC-derived progeny differentiated into macrophages, which displayed tunneling nanotubes capable of transferring cystinosin-bearing lysosomes to diseased cells. To our knowledge, this is the first demonstration that HSPCs can rescue hereditary corneal defects, and supports a new potential therapeutic strategy for treating ocular pathologies.

Analysis on the electromagnetic scattering properties of crops at multi-band

NASA Astrophysics Data System (ADS)

Wu, Tao; Wu, Zhensen; Liu, Xiaoyi

2014-12-01

The vector radiative transfer (VRT) theory for active microwave remote sensing and Rayleigh-Gans approximation (GRG) are applied in the study, and an iterative algorithm is used to solve the RT equations, thus we obtain the zeroorder and first-order equation for numerical results. The Michigan Microwave Canopy Scattering (MIMICS) model is simplified to adapt to the crop model, by analyzing body-surface bistatic scattering and backscattering properties between a layer of soybean or wheat consisting of stems and leaves and different underlying soil surface at multi-band (i.e. P, L, S, X, Ku-band), we obtain microwave scattering mechanisms of crop components and the effect of underlying ground on total crop scattering. Stem and leaf are regard as a needle and a circular disk, respectively. The final results are compared with some literature data to verify our calculating method, numerical results show multi-band crop microwave scattering properties differ from scattering angle, azimuth angle and moisture of vegetation and soil, which offer the part needed information for the design of future bistatic radar systems for crop sensing applications.

Modeling Optical Spectra of Large Organic Systems Using Real-Time Propagation of Semiempirical Effective Hamiltonians.

PubMed

Ghosh, Soumen; Andersen, Amity; Gagliardi, Laura; Cramer, Christopher J; Govind, Niranjan

2017-09-12

We present an implementation of a time-dependent semiempirical method (INDO/S) in NWChem using real-time (RT) propagation to address, in principle, the entire spectrum of valence electronic excitations. Adopting this model, we study the UV/vis spectra of medium-sized systems such as P3B2 and f-coronene, and in addition much larger systems such as ubiquitin in the gas phase and the betanin chromophore in the presence of two explicit solvents (water and methanol). RT-INDO/S provides qualitatively and often quantitatively accurate results when compared with RT- TDDFT or experimental spectra. Even though we only consider the INDO/S Hamiltonian in this work, our implementation provides a framework for performing electron dynamics in large systems using semiempirical Hartree-Fock Hamiltonians in general.

Modeling Optical Spectra of Large Organic Systems Using Real-Time Propagation of Semiempirical Effective Hamiltonians

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

Ghosh, Soumen; Andersen, Amity; Gagliardi, Laura

2017-08-16

We present an implementation of a time-dependent semiempirical method (INDO/S) in NWChem using real-time (RT) propagation to address, in principle, the entire spectrum of valence electronic excitations. Adopting this model, we study the UV-visible spectra of medium-sized systems like P3B2, f-coronene, and in addition much larger systems like ubiquitin in the gas phase and the betanin chromophore in the presence of two explicit solvents (water and methanol). RT-INDO/S provides qualitatively and indeed often quantitatively accurate results when compared with RT- TDDFT or experimental spectra. While demonstrated here for INDO/S in particular, our implementation provides a framework for performing electron dynamicsmore » in large systems using semiempirical Hartree-Fock (HF) Hamiltonians in general.« less

Connections between physical, optical and biogeochemical processes in the Pacific Ocean

NASA Astrophysics Data System (ADS)

Xiu, Peng; Chai, Fei

2014-03-01

A new biogeochemical model has been developed and coupled to a three-dimensional physical model in the Pacific Ocean. With the explicitly represented dissolved organic pools, this new model is able to link key biogeochemical processes with optical processes. Model validation against satellite and in situ data indicates the model is robust in reproducing general biogeochemical and optical features. Colored dissolved organic matter (CDOM) has been suggested to play an important role in regulating underwater light field. With the coupled model, physical and biological regulations of CDOM in the euphotic zone are analyzed. Model results indicate seasonal variability of CDOM is mostly determined by biological processes, while the importance of physical regulation manifests in the annual mean terms. Without CDOM attenuating light, modeled depth-integrated primary production is about 10% higher than the control run when averaged over the entire basin, while this discrepancy is highly variable in space with magnitudes reaching higher than 100% in some locations. With CDOM dynamics integrated in physical-biological interactions, a new mechanism by which physical processes affect biological processes is suggested, namely, physical transport of CDOM changes water optical properties, which can further modify underwater light field and subsequently affect the distribution of phytoplankton chlorophyll. This mechanism tends to occur in the entire Pacific basin but with strong spatial variability, implying the importance of including optical processes in the coupled physical-biogeochemical model. If ammonium uptake is sufficient to permit utilization of DOM, that is, UB∗⩾-U{U}/{U}-{(1-r_b)}/{RB}, then bacteria uptake of DOM has the form of FB=(1-r_b){U}/{RB}, bacteria respiration, SB=r_b×U, remineralization by bacteria, EB=UC{UN}/{UC}-{(1-r_b)}/{RB}. If EB > 0, then UB = 0; otherwise, UB = -EB. If there is insufficient ammonium, that is, UB∗<-U{U}/{U}-{(1-r_b)}/{RB}, then bacteria uptake of ammonia is obtained by, UB=UB∗, bacteria uptake of DOM, FB=U+UB, bacteria respiration, SB=RBFB{r_b}/{1-r_b}, remineralization by bacteria, EB=-UB. CDOM photolysis (Bissett et al., 1999a): UVLDOC=a(410)×RtUVLDOC×{PAR(0)}/{410}×exp∫z0Kd(300)dz, UVSDOC=a(410)×RtUVSDOC×{PAR(0)}/{410}×exp∫z0Kd(300)dz, UVLDIC=a(410)×RtUVLDIC×{PAR(0)}/{410}×exp∫z0Kd(300)dz, UVSDIC=a(410)×RtUVSDIC×{PAR(0)}/{410}×exp∫z0Kd(300)dz, a(410)=acdoc∗×CLDOC, a(410)=acdoc∗×CSDOC, Kd(300)=[a(410)+a(410)]×exp[0.0145×(410-300)]+0.154. The dissolution rate for biogenic silica (Jiang et al., 2003): D=(0.19T/25+0.01)×exp(0.069(T-25)). The air-sea flux of CO2 is calculated using the transfer velocity-wind speed relationships from Wanninkhof (1992): air-sea CO flux=0.31U2(660S{()sea-()air}, where U is the wind speed at sea surface and Sc is the Schmidt number for CO2 that can be calculated as: Sc=2073.1-125.62T+3.6276T2-0.043219T3, S is the solubility of CO2 and (pCO2)air is the partial pressure of CO2 in the air. In the model, we set a spatially uniform distribution of (pCO2)air observed at the Mauna Loa Observatory (Keeling et al., 1976).Dissolved oxygen (DO) is modeled using constant oxygen-to-nitrate and oxygen-to-ammonium ratios. At the surface, air-sea exchange of O2 is calculated as: O flux=0.31U2(660(DOsat-DO), where DOsat is the saturation concentration of DO calculated from temperature and salinity. So2 is the Schmidt number for O2 that can be calculated as follows: So2=1638.0-81.83T+1.483T2-0.008004T3.

Groundwater age, life expectancy and transit time distributions in advective dispersive systems; 2. Reservoir theory for sub-drainage basins

NASA Astrophysics Data System (ADS)

Cornaton, F.; Perrochet, P.

2006-09-01

Groundwater age and life expectancy probability density functions (pdf) have been defined, and solved in a general three-dimensional context by means of forward and backward advection-dispersion equations [Cornaton F, Perrochet P. Groundwater age, life expectancy and transit time distributions in advective-dispersive systems; 1. Generalized reservoir theory. Adv Water Res (xxxx)]. The discharge and recharge zones transit time pdfs were then derived by applying the reservoir theory (RT) to the global system, thus considering as ensemble the union of all inlet boundaries on one hand, and the union of all outlet boundaries on the other hand. The main advantages in using the RT to calculate the transit time pdf is that the outlet boundary geometry does not represent a computational limiting factor (e.g. outlets of small sizes), since the methodology is based on the integration over the entire domain of each age, or life expectancy, occurrence. In the present paper, we extend the applicability of the RT to sub-drainage basins of groundwater reservoirs by treating the reservoir flow systems as compartments which transfer the water fluxes to a particular discharge zone, and inside which mixing and dispersion processes can take place. Drainage basins are defined by the field of probability of exit at outlet. In this way, we make the RT applicable to each sub-drainage system of an aquifer of arbitrary complexity and configuration. The case of the well-head protection problem is taken as illustrative example, and sensitivity analysis of the effect of pore velocity variations on the simulated ages is carried out.

Radio Tomography of Ionospheric Structures (probably) due to Underground-Surface-Atmosphere-Ionosphere Coupling

NASA Astrophysics Data System (ADS)

Kunitsyn, V.; Nesterov, I.; Andreeva, E.; Rekenthaler, D. A.

2012-12-01

Ionospheric radio-tomography (RT) utilizes radio signals transmitted from the global navigational satellite systems (GNSS), including low-orbiting (LO) navigational systems such as Transit, Tsikada, etc., and high-orbiting (HO) navigational systems such as GPS, GLONASS, Galileo, Beidou, etc. The signals that are transmitted from the LO navigational satellites and recorded by ground receiving chains can be inverted for almost instantaneous (5-8 min) 2D snapshots of electron density. The data from the networks of ground receivers that record the signals of the HO satellites are suitable for implementing high-orbital RT (HORT), i.e. reconstructing the 4D distributions of the ionospheric electron density (one 3D image every 20-30 min). In the regions densely covered by the GNSS receivers, it is currently possible to get a time step of 2-4 min. The LORT and HORT approaches have a common methodical basis: in both these techniques, the integrals of electron density along the ray between the satellite and the receiver are measured, and then the tomographic procedures are applied to reconstruct the distributions of electron density. We present several examples of the experiments on the ionospheric RT, which are related to the Underground-Surface-Atmosphere-Ionosphere (USAI) coupling. In particular, we demonstrate examples of RT images of the ionosphere after industrial explosions, rocket launches, and modification of the ionosphere by high-power radio waves. We also show RT cross sections reflecting ionospheric disturbances caused by the earthquakes (EQ) and tsunami waves. In these cases, there is an evident cause-and-effect relationship. The perturbations are transferred between the geospheres predominantly by acoustic gravity waves (AGW), whose amplitudes increase with increasing height. As far as EQ are concerned, the cause of the USAI coupling mechanism is not obvious. It is clear, however, that the regular RT studies can promote the solution of this challenging problem. The single-point measurements (by ionosondes or by isolated receivers) are not amenable to unambiguous interpretation; based on these data, it is impossible to distinguish the contribution of USAI coupling from the ionospheric effects induced by the "ordinary" impacts (the Sun, the solar wind, geomagnetic perturbations, galactic cosmic rays, etc.). In order to localize sources of the ionospheric disturbances, the geophysicist needs information on the spatial structure and dynamics of the ionospheric perturbations. This information (2D-4D RT images) is optimally provided by RT methods. We present examples of the ionospheric disturbances caused by EQs as well as the ionospheric precursors of these EQs in the form of specific ionospheric irregularities: AGW- and soliton-like wave disturbances, which we identified using RT methods. Based on the results of the RT studies in the Alaska and Taiwan regions, we have detected several dozen AGW-related precursors of EQs. These data allow us to attempt to locate the source of these perturbations. We discuss the possibilities and prospects of further research aimed at identifying and analyzing precursors of EQs and establishing the mechanisms of USAI coupling. We are grateful to Northwest Research Associates, Inc., and Dr. L.-C.Tsai for providing raw RT data for Alaska and Taiwan.

WE-H-207B-03: MRI Guidance in the Radiation Therapy Clinic: Site-Specific Discussions

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

Shang, C.

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

Temperature affects thrombolytic efficacy using rt-PA and eptifibatide, an in vitro study.

PubMed

Meunier, Jason M; Chang, Wan-Tsu W; Bluett, Brent; Wenker, Evan; Lindsell, Christopher J; Shaw, George J

2012-09-01

The potential for hypothermia as a neuroprotectant during stroke has led to its increase in clinical use. At the same time, combination pharmaceutical therapies for ischemic stroke using recombinant tissue plasminogen activator (rt-PA), and GP IIb-IIIa inhibitors, such as Eptifibatide (Epf ), are under study. However, there is little data on how the reactions triggered by these agents are impacted by temperature. Here, clot lysis during exposure to the combination of rt-PA and Epf is measured in an in vitro human clot model at hypothermic temperatures. The hypothesis is that lytic efficacy of rt-PA and Epf decreases with decreasing temperature. Whole blood clots from 31 volunteers were exposed to rt-PA (0.5 μg/mL) and Epf (0.63 μg/mL) in human fresh-frozen plasma (rt-PA+Epf ), rt-PA alone in plasma (rt-PA Alone), or to plasma alone (Control), at temperatures from 30°C to 37°C, for 30 minutes. Clot lysis was measured using a microscopic imaging technique; the mean fractional clot loss (FCL) at 30 minutes was used to determine lytic efficacy. Temperature had a significant impact on FCL in clots exposed to rt-PA+Epf, with the FCL being lower at 30°C to 36°C than at 37°C. The FCL remained significantly higher for rt-PA+Epf–treated clots than Controls regardless of temperature, with the exception of measurements made at 30°C when no significant differences in the FCL were observed between groups. The use of hypothermia as a neuroprotectant may negatively impact the therapeutic benefit of thrombolytic agents.

Temperature Affects Thrombolytic Efficacy Using rt-PA and Eptifibatide, an In Vitro Study

PubMed Central

Chang, Wan-Tsu W.; Bluett, Brent; Wenker, Evan; Lindsell, Christopher J.; Shaw, George J.

2012-01-01

The potential for hypothermia as a neuroprotectant during stroke has led to its increase in clinical use. At the same time, combination pharmaceutical therapies for ischemic stroke using recombinant tissue plasminogen activator (rt-PA), and GP IIb-IIIa inhibitors, such as Eptifibatide (Epf ), are under study. However, there is little data on how the reactions triggered by these agents are impacted by temperature. Here, clot lysis during exposure to the combination of rt-PA and Epf is measured in an in vitro human clot model at hypothermic temperatures. The hypothesis is that lytic efficacy of rt-PA and Epf decreases with decreasing temperature. Whole blood clots from 31 volunteers were exposed to rt-PA (0.5 μg/mL) and Epf (0.63 μg/mL) in human fresh-frozen plasma (rt-PA+Epf ), rt-PA alone in plasma (rt-PA Alone), or to plasma alone (Control), at temperatures from 30°C to 37°C, for 30 minutes. Clot lysis was measured using a microscopic imaging technique; the mean fractional clot loss (FCL) at 30 minutes was used to determine lytic efficacy. Temperature had a significant impact on FCL in clots exposed to rt-PA+Epf, with the FCL being lower at 30°C to 36°C than at 37°C. The FCL remained significantly higher for rt-PA+Epf–treated clots than Controls regardless of temperature, with the exception of measurements made at 30°C when no significant differences in the FCL were observed between groups. The use of hypothermia as a neuroprotectant may negatively impact the therapeutic benefit of thrombolytic agents. PMID:23667777

Characteristics and Impact Factors of Renal Threshold for Glucose Excretion in Patients with Type 2 Diabetes Mellitus.

PubMed

Yue, Xiao Dan; Wang, Jing Yu; Zhang, Xin Rong; Yang, Ju Hong; Shan, Chun Yan; Zheng, Miao Yan; Ren, Hui Zhu; Zhang, Yi; Yang, Shao Hua; Guo, Zhen Hong; Chang, Bai; Chang, Bao Cheng

2017-04-01

Sodium glucose co-transporter 2 (SGLT-2) inhibitors are newly developed but promising medicine for type 2 diabetes. However, patients with a different renal threshold for glucose excretion (RT(G)) may have a different reaction to this medicine. Therefore, the objective of this study was to investigate the characteristics of RT(G) and its impact factors in patients with type 2 diabetes mellitus (T2DM). The clinical and laboratory data of 36 healthy individuals and 168 in-hospital patients with T2DM were collected and analyzed, RT(G) was calculated using blood glucose (BG) measured by dynamic BG monitoring, urinary glucose excretion (UGE) and estimated glomerular filtration rate (eGFR). The characteristics of RT(G) were investigated. The risk factors for high RT(G) were analyzed using non-conditional logistic regression analysis. Our results found that RT(G) of the T2DM group was higher than that of the healthy individuals (P < 0.05); and 22.22% from the healthy individuals group but 58.33% from the T2DM group had high RT(G). Age, duration of diabetes, body mass index (BMI), and homeostasis model assessment insulin resistance index (HOMA-IR) were independently associated with high RT(G) (P < 0.05). Further stratified analysis revealed that RT(G) in T2DM patients increased with age, duration of diabetes, and BMI. In conclusion, RT(G) is increased in patients with T2DM, especially in those with longer diabetic duration, higher BMI, and those who are older. Therefore, these patients may be more sensitive to SGLT-2 inhibitors. © 2017 The Korean Academy of Medical Sciences.

Disparities in the Use of Radiation Therapy in Patients With Local-Regionally Advanced Breast Cancer

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

Martinez, Steve R., E-mail: steve.martinez@ucdmc.ucdavis.ed; Beal, Shannon H.; Chen, Steven L.

2010-11-01

Background: Radiation therapy (RT) is indicated for the treatment of local-regionally advanced breast cancer (BCa). Hypothesis: We hypothesized that black and Hispanic patients with local-regionally advanced BCa would receive lower rates of RT than their white counterparts. Methods: The Surveillance Epidemiology and End Results database was used to identify white, black, Hispanic, and Asian patients with invasive BCa and {>=}10 metastatic lymph nodes diagnosed between 1988 and 2005. Univariate and multivariate logistic regression evaluated the relationship of race/ethnicity with use of RT. Multivariate models stratified for those undergoing mastectomy or lumpectomy. Results: Entry criteria were met by 12,653 patients. Approximatelymore » half of the patients did not receive RT. Most patients were white (72%); the remainder were Hispanic (10.4%), black (10.3%), and Asian (7.3%). On univariate analysis, Hispanics (odd ratio [OR] 0.89; 95% confidence interval [CI], 0.79-1.00) and blacks (OR 0.79; 95% CI, 0.70-0.89) were less likely to receive RT than whites. On multivariate analysis, blacks (OR 0.76; 95% CI, 0.67-0.86) and Hispanics (OR 0.80; 95% CI, 0.70-0.90) were less likely than whites to receive RT. Disparities persisted for blacks (OR 0.74; 95% CI, 0.64-0.85) and Hispanics (OR 0.77; 95% CI, 0.67-0.89) who received mastectomy, but not for those who received lumpectomy. Conclusions: Many patients with local-regionally advanced BCa do not receive RT. Blacks and Hispanics were less likely than whites to receive RT. This disparity was noted predominately in patients who received mastectomy. Future efforts at improving rates of RT are warranted. Efforts at eliminating racial/ethnic disparities should focus on black and Hispanic candidates for postmastectomy RT.« less

Is a reduction in radiation lung volume and dose necessary with paclitaxel chemotherapy for node-positive breast cancer?

PubMed

Taghian, Alphonse G; Assaad, Sherif I; Niemierko, Andrzej; Floyd, Scott R; Powell, Simon N

2005-06-01

To evaluate and quantify the effect of irradiated lung volume, radiation dose, and paclitaxel chemotherapy on the development of radiation pneumonitis (RP) in breast cancer patients with positive lymph nodes. We previously reported the incidence of RP among 41 patients with breast cancer treated with radiotherapy (RT) and adjuvant paclitaxel-containing chemotherapy. We recorded the central lung distance, a measure of the extent of lung included in the RT volume, in these patients. We used this measure and the historical and observed rates of RP in our series to model the lung tolerance to RT in patients receiving chemotherapy (CHT) both with and without paclitaxel. To evaluate the risk factors for the development of RP, we performed a case-control study comparing paclitaxel-treated patients who developed RP with those who did not, and a second case-control study comparing patients receiving paclitaxel in addition to standard CHT/RT (n = 41) and controls receiving standard CHT/RT alone (n = 192). The actuarial rate of RP in the paclitaxel-treated group was 15.4% compared with 0.9% among breast cancer patients treated with RT and non-paclitaxel-containing CHT. Our mathematical model found that the effective lung tolerance for patients treated with paclitaxel was reduced by approximately 24%. No statistically significant difference was found with regard to the dose delivered to specific radiation fields, dose per fraction, central lung distance, or percentage of lung irradiated in the case-control study of paclitaxel-treated patients who developed RP compared with those who did not. In the comparison of 41 patients receiving RT and CHT with paclitaxel and 192 matched controls receiving RT and CHT without paclitaxel, the only significant differences identified were the more frequent use of a supraclavicular radiation field and a decrease in the RT lung dose among the paclitaxel-treated patients. This finding indicates that the major factor associated with development of RP was paclitaxel treatment. The use of paclitaxel chemotherapy and RT in the primary treatment of node-positive breast cancer is likely to increase the incidence of RP. In patients treated with paclitaxel, reducing the percentage of lung irradiated by 24% should reduce the risk of RP to 1%, according to our calculations of lung tolerance. Future clinical trials using combination CHT that includes paclitaxel and RT should carefully evaluate the incidence and severity of RP and should also accurately monitor the extent of lung included within the RT volume to develop safe guidelines for the delivery of what is becoming standard therapy for node-positive breast cancer.

3-D Numerical Modelling of Oblique Continental Collisions with ASPECT

NASA Astrophysics Data System (ADS)

Karatun, L.; Pysklywec, R.

2017-12-01

Among the fundamental types of tectonic plate boundaries, continent-continent collision is least well understood. Deformation of the upper and middle crustal layers can be inferred from surface structures and geophysical imaging, but the fate of lower crustal rocks and mantle lithosphere is not well resolved. Previous research suggests that shortening of mantle lithosphere generally may be occurring by either: 1) a distributed thickening with a formation of a Raleigh-Tailor (RT) type instability (possibly accompanied with lithospheric folding); or 2) plate-like subduction, which can be one- or two-sided, with or without delamination and slab break-off; a combination of both could be taking place too. 3-D features of the orogens such as along-trench material transfer, bounding subduction zones can influence the evolution of the collision zone significantly. The current study was inspired by South Island of New Zealand - a young collision system where a block of continental crust is being shortened by the relative Australian-Pacific plate motion. The collision segment of the plate boundary is relatively small ( 800 km), and is bounded by oppositely verging subduction zones to the North and South. Here, we present results of 3-D forward numerical modelling of continental collision to investigate some of these processes. To conduct the simulations, we used ASPECT - a highly parallel community-developed code based on the Finite Element method. Model setup for three different sets of models featured 2-D vertical across strike, 3-D with periodic front and back walls, and 3-D with open front and back walls, with velocities prescribed on the left and right faces. We explored the importance of values of convergent velocity, strike-slip velocity and their ratio, which defines the resulting velocity direction relative to the plate boundary (obliquity). We found that higher strike-slip motion promotes strain localization, weakens the lithosphere close to the plate boundary and pushes the balance towards RT instability. Incorporation of the bounding subduction zones caused large amount of material to be pulled out through the sides of the model and into the subduction channel, with slab tear happening at high obliquity values.

76 FR 25534 - Airworthiness Directives; Hamilton Sundstrand Propellers Model 247F Propellers

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-05

... 5 p.m., Monday through Friday, except Federal holidays. The AD docket contains this AD, the... through FR2279 inclusive, FR 2398, FR2449 to FR2958 inclusive, FR20010710 to FR20010722 inclusive, and FR20010723RT to FR20020127RT inclusive, installed. Propeller blades reworked to Hamilton Sundstrand Service...

The Development from Effortful to Automatic Processing in Mathematical Cognition.

ERIC Educational Resources Information Center

Kaye, Daniel B.; And Others

This investigation capitalizes upon the information processing models that depend upon measurement of latency of response to a mathematical problem and the decomposition of reaction time (RT). Simple two term addition problems were presented with possible solutions for true-false verification, and accuracy and RT to response were recorded. Total…

The NASA Short-term Prediction Research and Transition (SPoRT) Center: A Collaborative Model for Accelerating Research into Operations

NASA Technical Reports Server (NTRS)

Goodman, S. J.; Lapenta, W.; Jedlovec, G.; Dodge, J.; Bradshaw, T.

2003-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center in Huntsville, Alabama was created to accelerate the infusion of NASA earth science observations, data assimilation and modeling research into NWS forecast operations and decision-making. The principal focus of experimental products is on the regional scale with an emphasis on forecast improvements on a time scale of 0-24 hours. The SPoRT Center research is aligned with the regional prediction objectives of the US Weather Research Program dealing with 0-1 day forecast issues ranging from convective initiation to 24-hr quantitative precipitation forecasting. The SPoRT Center, together with its other interagency partners, universities, and the NASA/NOAA Joint Center for Satellite Data Assimilation, provides a means and a process to effectively transition NASA Earth Science Enterprise observations and technology to National Weather Service operations and decision makers at both the global/national and regional scales. This paper describes the process for the transition of experimental products into forecast operations, current products undergoing assessment by forecasters, and plans for the future.

A Genuine TEAM Player

NASA Technical Reports Server (NTRS)

2001-01-01

Qualtech Systems, Inc. developed a complete software system with capabilities of multisignal modeling, diagnostic analysis, run-time diagnostic operations, and intelligent interactive reasoners. Commercially available as the TEAMS (Testability Engineering and Maintenance System) tool set, the software can be used to reveal unanticipated system failures. The TEAMS software package is broken down into four companion tools: TEAMS-RT, TEAMATE, TEAMS-KB, and TEAMS-RDS. TEAMS-RT identifies good, bad, and suspect components in the system in real-time. It reports system health results from onboard tests, and detects and isolates failures within the system, allowing for rapid fault isolation. TEAMATE takes over from where TEAMS-RT left off by intelligently guiding the maintenance technician through the troubleshooting procedure, repair actions, and operational checkout. TEAMS-KB serves as a model management and collection tool. TEAMS-RDS (TEAMS-Remote Diagnostic Server) has the ability to continuously assess a system and isolate any failure in that system or its components, in real time. RDS incorporates TEAMS-RT, TEAMATE, and TEAMS-KB in a large-scale server architecture capable of providing advanced diagnostic and maintenance functions over a network, such as the Internet, with a web browser user interface.

Population Accessibility to Radiotherapy Services in New South Wales Region of Australia: a methodological contribution

NASA Astrophysics Data System (ADS)

Shukla, Nagesh; Wickramasuriya, Rohan; Miller, Andrew; Perez, Pascal

2015-05-01

This paper proposes an integrated modelling process to assess the population accessibility to radiotherapy treatment services in future based on future cancer incidence and road network-based accessibility. Previous research efforts assessed travel distance/time barriers affecting access to cancer treatment services, as well as epidemiological studies that showed that cancer incidence rates vary with population demography. It is established that travel distances to treatment centres and demographic profiles of the accessible regions greatly influence the demand for cancer radiotherapy (RT) services. However, an integrated service planning approach that combines spatially-explicit cancer incidence projections, and the RT services accessibility based on patient road network have never been attempted. This research work presents this novel methodology for the accessibility assessment of RT services and demonstrates its viability by modelling New South Wales (NSW) cancer incidence rates for different age-sex groups based on observed cancer incidence trends; estimating the road network-based access to current NSW treatment centres; and, projecting the demand for RT services in New South Wales, Australia from year 2011 to 2026.

Stroop performance in multiple sclerosis: information processing, selective attention, or executive functioning?

PubMed

Macniven, J A B; Davis, C; Ho, M-Y; Bradshaw, C M; Szabadi, E; Constantinescu, C S

2008-09-01

Cognitive impairments in information processing speed, attention and executive functioning are widely reported in patients with multiple sclerosis (MS). Several studies have identified impaired performance on the Stroop test in people with MS, yet uncertainty remains over the cause of this phenomenon. In this study, 25 patients with MS were assessed with a neuropsychological test battery including a computerized Stroop test and a computerized test of information processing speed, the Graded Conditional Discrimination Tasks (GCDT). The patient group was compared with an individually age, sex and estimated premorbid IQ-matched healthy control group. The patients' reaction times (RTs) were significantly longer than those of the controls on all Stroop test trials and there was a significantly enhanced absolute (RT(incongruent)-RT(neutral)) and relative (100 x [RT(incongruent)-RT(neutral)]/RT(neutral)) Stroop interference effect for the MS group. The linear function relating RT to stimulus complexity in the GCDT was significantly steeper in the patient group, indicating slowed information processing. The results are discussed with reference to the difference engine model, a theory of diversity in speeded cognition. It is concluded that, in the assessment of people with MS, great caution must be used in the interpretation of performance on neuropsychological tests which rely on RT as the primary measure.

Estimation of internal organ motion-induced variance in radiation dose in non-gated radiotherapy

NASA Astrophysics Data System (ADS)

Zhou, Sumin; Zhu, Xiaofeng; Zhang, Mutian; Zheng, Dandan; Lei, Yu; Li, Sicong; Bennion, Nathan; Verma, Vivek; Zhen, Weining; Enke, Charles

2016-12-01

In the delivery of non-gated radiotherapy (RT), owing to intra-fraction organ motion, a certain degree of RT dose uncertainty is present. Herein, we propose a novel mathematical algorithm to estimate the mean and variance of RT dose that is delivered without gating. These parameters are specific to individual internal organ motion, dependent on individual treatment plans, and relevant to the RT delivery process. This algorithm uses images from a patient’s 4D simulation study to model the actual patient internal organ motion during RT delivery. All necessary dose rate calculations are performed in fixed patient internal organ motion states. The analytical and deterministic formulae of mean and variance in dose from non-gated RT were derived directly via statistical averaging of the calculated dose rate over possible random internal organ motion initial phases, and did not require constructing relevant histograms. All results are expressed in dose rate Fourier transform coefficients for computational efficiency. Exact solutions are provided to simplified, yet still clinically relevant, cases. Results from a volumetric-modulated arc therapy (VMAT) patient case are also presented. The results obtained from our mathematical algorithm can aid clinical decisions by providing information regarding both mean and variance of radiation dose to non-gated patients prior to RT delivery.

ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization.

PubMed

Sang, Jian; Wang, Zhennan; Li, Man; Cao, Jiabao; Niu, Guangyi; Xia, Lin; Zou, Dong; Wang, Fan; Xu, Xingjian; Han, Xiaojiao; Fan, Jinqi; Yang, Ye; Zuo, Wanzhu; Zhang, Yang; Zhao, Wenming; Bao, Yiming; Xiao, Jingfa; Hu, Songnian; Hao, Lili; Zhang, Zhang

2018-01-04

Real-time quantitative PCR (RT-qPCR) has become a widely used method for accurate expression profiling of targeted mRNA and ncRNA. Selection of appropriate internal control genes for RT-qPCR normalization is an elementary prerequisite for reliable expression measurement. Here, we present ICG (http://icg.big.ac.cn), a wiki-driven knowledgebase for community curation of experimentally validated internal control genes as well as their associated experimental conditions. Unlike extant related databases that focus on qPCR primers in model organisms (mainly human and mouse), ICG features harnessing collective intelligence in community integration of internal control genes for a variety of species. Specifically, it integrates a comprehensive collection of more than 750 internal control genes for 73 animals, 115 plants, 12 fungi and 9 bacteria, and incorporates detailed information on recommended application scenarios corresponding to specific experimental conditions, which, collectively, are of great help for researchers to adopt appropriate internal control genes for their own experiments. Taken together, ICG serves as a publicly editable and open-content encyclopaedia of internal control genes and accordingly bears broad utility for reliable RT-qPCR normalization and gene expression characterization in both model and non-model organisms. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Display size effects in visual search: analyses of reaction time distributions as mixtures.

PubMed

Reynolds, Ann; Miller, Jeff

2009-05-01

In a reanalysis of data from Cousineau and Shiffrin (2004) and two new visual search experiments, we used a likelihood ratio test to examine the full distributions of reaction time (RT) for evidence that the display size effect is a mixture-type effect that occurs on only a proportion of trials, leaving RT in the remaining trials unaffected, as is predicted by serial self-terminating search models. Experiment 1 was a reanalysis of Cousineau and Shiffrin's data, for which a mixture effect had previously been established by a bimodal distribution of RTs, and the results confirmed that the likelihood ratio test could also detect this mixture. Experiment 2 applied the likelihood ratio test within a more standard visual search task with a relatively easy target/distractor discrimination, and Experiment 3 applied it within a target identification search task within the same types of stimuli. Neither of these experiments provided any evidence for the mixture-type display size effect predicted by serial self-terminating search models. Overall, these results suggest that serial self-terminating search models may generally be applicable only with relatively difficult target/distractor discriminations, and then only for some participants. In addition, they further illustrate the utility of analysing full RT distributions in addition to mean RT.

Patterns of Practice in Palliative Radiotherapy for Painful Bone Metastases: Impact of a Regional Rapid Access Clinic on Access to Care

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

Wu, Jackson S.Y., E-mail: jackson.wu@cancerboard.ab.c; Kerba, Marc; Wong, Rebecca K.S.

2010-10-01

Purpose: External beam radiotherapy (RT) is commonly indicated for the palliation of symptomatic bone metastases, but there is evidence of underutilization of this treatment modality in palliative care for cancer populations. This study was conducted to investigate factors that influenced the use of palliative RT services at a regional comprehensive cancer center. Methods and Materials: A cohort of patients with radiographically confirmed bone metastases and first-time users of palliative RT between 2003 and 2005 was retrospectively reviewed from the time of initial diagnosis of bone metastases to death or last follow-up. Type of radiation treatment service provider used (rapid accessmore » or routine access) and patient-, tumor-, and treatment-related factors were analyzed for their influences on the number of treatment courses given over the duration of disease. Results: A total of 887 patients received 1,354 courses of palliative RT for bone metastases at a median interval of 4.0 months between courses. Thirty-three percent of patients required more than one RT course. Increased age and travel distance reduced the likelihood and number of treatment courses, while service through a rapid access clinic was independently associated with an increase in subsequent use of palliative RT. Conclusions: A rapid access service model for palliative RT facilitated access to RT. Travel distance and other factors remained substantial barriers to use of palliative RT services. The pattern of practice suggests an unmet need for symptom control in patients with bone metastases.« less

Factors Affecting Detection of Hepatitis E Virus on Canadian Retail Pork Chops and Pork Livers Assayed Using Real-Time RT-PCR.

PubMed

Wilhelm, B J; Leblanc, D; Avery, B; Pearl, D L; Houde, A; Rajić, A; McEwen, S A

2016-03-01

We collected 599 Canadian retail pork chops and 283 pork livers routinely (usually weekly) from April 2011 to March 2012 using the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) retail sampling platform. Samples were assayed using validated real-time (q) reverse transcriptase polymerase chain reaction (RT-PCR) and nested classical RT-PCR for the detection of hepatitis E virus (HEV), porcine enteric calicivirus (PEC) and rotavirus (RV). The presence of Escherichia coli, Salmonella spp. and Campylobacter spp. was measured on a subset of our samples. Exact logistic regression models were fitted for predictors for HEV detection, for each assay. For both assays, sample type (pork chop versus liver) was a significant predictor for HEV RNA detection. For nested classical RT-PCR but not qRT-PCR, region of sample collection was a significant predictor (P = 0.008) of HEV detection. Odds of HEV detection were greatest in spring relative to other seasons. E. coli was a significant predictor for HEV RNA detection using the qRT-PCR (P = 0.03). Overall, the prevalence of E. coli, Salmonella spp. and Campylobacter spp. was significantly greater than HEV, PEC or RV on our retail pork samples. Our sparse data set for the detection of PEC and RV precluded modelling of risk factors for the detection of these viruses. © 2015 Zoonoses and Public Health © 2015 Her Majesty the Queen in Right of Canada Reproduced with the permission of the Minister of the Public Health Agency of Canada.

Quantification of intra-fraction motion in breast radiotherapy using supine magnetic resonance imaging

NASA Astrophysics Data System (ADS)

van Heijst, Tristan C. F.; Philippens, Mariëlle E. P.; Charaghvandi, Ramona K.; den Hartogh, Mariska D.; Lagendijk, Jan J. W.; Desirée van den Bongard, H. J. G.; van Asselen, Bram

2016-02-01

In early-stage breast-cancer patients, accelerated partial-breast irradiation techniques (APBI) and hypofractionation are increasingly implemented after breast-conserving surgery (BCS). For a safe and effective radiation therapy (RT), the influence of intra-fraction motion during dose delivery becomes more important as associated fraction durations increase and targets become smaller. Current image-guidance techniques are insufficient to characterize local target movement in high temporal and spatial resolution for extended durations. Magnetic resonance imaging (MRI) can provide high soft-tissue contrast, allow fast imaging, and acquire images during longer periods. The goal of this study was to quantify intra-fraction motion using MRI scans from 21 breast-cancer patients, before and after BCS, in supine RT position, on two time scales. High-temporal 2-dimensional (2D) MRI scans (cine-MRI), acquired every 0.3 s during 2 min, and three 3D MRI scans, acquired over 20 min, were performed. The tumor (bed) and whole breast were delineated on 3D scans and delineations were transferred to the cine-MRI series. Consecutive scans were rigidly registered and delineations were transformed accordingly. Motion in sub-second time-scale (derived from cine-MRI) was generally regular and limited to a median of 2 mm. Infrequently, large deviations were observed, induced by deep inspiration, but these were temporary. Movement on multi-minute scale (derived from 3D MRI) varied more, although medians were restricted to 2.2 mm or lower. Large whole-body displacements (up to 14 mm over 19 min) were sparsely observed. The impact of motion on standard RT techniques is likely small. However, in novel hypofractionated APBI techniques, whole-body shifts may affect adequate RT delivery, given the increasing fraction durations and smaller targets. Motion management may thus be required. For this, on-line MRI guidance could be provided by a hybrid MRI/RT modality, such as the University Medical Center Utrecht MRI linear accelerator.

Magnetic nanoparticle hyperthermia enhances radiation therapy: A study in mouse models of human prostate cancer

PubMed Central

Attaluri, Anilchandra; Kandala, Sri Kamal; Wabler, Michele; Zhou, Haoming; Cornejo, Christine; Armour, Michael; Hedayati, Mohammad; Zhang, Yonggang; DeWeese, Theodore L.; Herman, Cila; Ivkov, Robert

2015-01-01

Purpose We aimed to characterise magnetic nanoparticle hyperthermia (mNPH) with radiation therapy (RT) for prostate cancer. Methods Human prostate cancer subcutaneous tumours, PC3 and LAPC-4, were grown in nude male mice. When tumours measured 150 mm3 magnetic iron oxide nanoparticles (MIONPs) were injected into tumours to a target dose of 5.5 mg Fe/cm3 tumour, and treated 24 h later by exposure to alternating magnetic field (AMF). Mice were randomly assigned to one of four cohorts to characterise (1) intratumour MIONP distribution, (2) effects of variable thermal dose mNPH (fixed AMF peak amplitude 24 kA/m at 160±5 kHz) with/without RT (5 Gy), (3) effects of RT (RT5: 5 Gy; RT8: 8 Gy), and (4) fixed thermal dose mNPH (43 °C for 20min) with/without RT (5 Gy). MIONP concentration and distribution were assessed following sacrifice and tissue harvest using inductively coupled plasma mass spectrometry (ICP-MS) and Prussian blue staining, respectively. Tumour growth was monitored and compared among treated groups. Results LAPC-4 tumours retained higher MIONP concentration and more uniform distribution than did PC3 tumours. AMF power modulation provided similar thermal dose for mNPH and combination therapy groups (CEM43: LAPC-4: 33.6 ± 3.4 versus 25.9 ± 0.8, and PC3: 27.19 ± 0.7 versus 27.50 ± 0.6), thereby overcoming limitations of MIONP distribution and yielding statistically significant tumour growth delay. Conclusion PC3 and LAPC-4 tumours represent two biological models that demonstrate different patterns of nanoparticle retention and distribution, offering a model to make comparisons of these effects for mNPH. Modulating power for mNPH offers potential to overcome limitations of MIONP distribution to enhance mNPH. PMID:25811736

Magnetic nanoparticle hyperthermia enhances radiation therapy: A study in mouse models of human prostate cancer.

PubMed

Attaluri, Anilchandra; Kandala, Sri Kamal; Wabler, Michele; Zhou, Haoming; Cornejo, Christine; Armour, Michael; Hedayati, Mohammad; Zhang, Yonggang; DeWeese, Theodore L; Herman, Cila; Ivkov, Robert

2015-06-01

We aimed to characterise magnetic nanoparticle hyperthermia (mNPH) with radiation therapy (RT) for prostate cancer. Human prostate cancer subcutaneous tumours, PC3 and LAPC-4, were grown in nude male mice. When tumours measured 150 mm3 magnetic iron oxide nanoparticles (MIONPs) were injected into tumours to a target dose of 5.5 mg Fe/cm3 tumour, and treated 24 h later by exposure to alternating magnetic field (AMF). Mice were randomly assigned to one of four cohorts to characterise (1) intratumour MIONP distribution, (2) effects of variable thermal dose mNPH (fixed AMF peak amplitude 24 kA/m at 160 ± 5 kHz) with/without RT (5 Gy), (3) effects of RT (RT5: 5 Gy; RT8: 8 Gy), and (4) fixed thermal dose mNPH (43 °C for 20 min) with/without RT (5 Gy). MIONP concentration and distribution were assessed following sacrifice and tissue harvest using inductively coupled plasma mass spectrometry (ICP-MS) and Prussian blue staining, respectively. Tumour growth was monitored and compared among treated groups. LAPC-4 tumours retained higher MIONP concentration and more uniform distribution than did PC3 tumours. AMF power modulation provided similar thermal dose for mNPH and combination therapy groups (CEM43: LAPC-4: 33.6 ± 3.4 versus 25.9 ± 0.8, and PC3: 27.19 ± 0.7 versus 27.50 ± 0.6), thereby overcoming limitations of MIONP distribution and yielding statistically significant tumour growth delay. PC3 and LAPC-4 tumours represent two biological models that demonstrate different patterns of nanoparticle retention and distribution, offering a model to make comparisons of these effects for mNPH. Modulating power for mNPH offers potential to overcome limitations of MIONP distribution to enhance mNPH.

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

Inflammatory biomarker C-reactive protein and radiotherapy-induced early adverse skin reactions in patients with breast cancer.

PubMed

Rodriguez-Gil, Jorge L; Takita, Cristiane; Wright, Jean; Reis, Isildinha M; Zhao, Wei; Lally, Brian E; Hu, Jennifer J

2014-09-01

Breast cancer is the most frequently diagnosed cancer and the second leading cause of cancer death in American women. Postsurgery adjuvant radiotherapy (RT) significantly reduced the local recurrence rate. However, many patients develop early adverse skin reactions (EASR) that impact quality of life and treatment outcomes. We evaluated an inflammatory biomarker, C-reactive protein (CRP), in predicting RT-induced EASRs in 159 patients with breast cancer undergoing RT. In each patient, we measured pre- and post-RT plasma CRP levels using a highly sensitive ELISA CRP assay. RT-induced EASRs were assessed at weeks 3 and 6 using the National Cancer Institute Common Toxicity Criteria (v3.0). Associations between EASRs and CRP levels were assessed using logistic regression models after adjusting for potential confounders. RT-induced grade 2+ EASRs were observed in 8 (5%) and 80 (50%) patients at weeks 3 and 6 (end of RT), respectively. At the end of RT, a significantly higher proportion of African Americans developed grade 3 EASRs (13.8% vs. 2.3% in others); grade 2+ EASRs were significantly associated with: change of CRP > 1 mg/L [odds ratio (OR), 2.51; 95% confidence interval (CI), 1.06-5.95; P = 0.04], obesity (OR, 2.08; 95% CI, 1.03-4.21; P = 0.04), or combined both factors (OR, 5.21; 95% CI, 1.77-15.38; P = 0.003). This is the first study to demonstrate that an inflammatory biomarker CRP is associated with RT-induced EASRs, particularly combined with obesity. Future larger studies are warranted to validate our findings and facilitate the discovery and development of anti-inflammatory agents to protect normal tissue from RT-induced adverse effects and improve quality of life in patients with breast cancer undergoing RT. ©2014 American Association for Cancer Research.

Whole-body hybrid imaging concept for the integration of PET/MR into radiation therapy treatment planning.

PubMed

Paulus, Daniel H; Oehmigen, Mark; Grüneisen, Johannes; Umutlu, Lale; Quick, Harald H

2016-05-07

Modern radiation therapy (RT) treatment planning is based on multimodality imaging. With the recent availability of whole-body PET/MR hybrid imaging new opportunities arise to improve target volume delineation in RT treatment planning. This, however, requires dedicated RT equipment for reproducible patient positioning on the PET/MR system, which has to be compatible with MR and PET imaging. A prototype flat RT table overlay, radiofrequency (RF) coil holders for head imaging, and RF body bridges for body imaging were developed and tested towards PET/MR system integration. Attenuation correction (AC) of all individual RT components was performed by generating 3D CT-based template models. A custom-built program for μ-map generation assembles all AC templates depending on the presence and position of each RT component. All RT devices were evaluated in phantom experiments with regards to MR and PET imaging compatibility, attenuation correction, PET quantification, and position accuracy. The entire RT setup was then evaluated in a first PET/MR patient study on five patients at different body regions. All tested devices are PET/MR compatible and do not produce visible artifacts or disturb image quality. The RT components showed a repositioning accuracy of better than 2 mm. Photon attenuation of  -11.8% in the top part of the phantom was observable, which was reduced to  -1.7% with AC using the μ-map generator. Active lesions of 3 subjects were evaluated in terms of SUVmean and an underestimation of  -10.0% and  -2.4% was calculated without and with AC of the RF body bridges, respectively. The new dedicated RT equipment for hybrid PET/MR imaging enables acquisitions in all body regions. It is compatible with PET/MR imaging and all hardware components can be corrected in hardware AC by using the suggested μ-map generator. These developments provide the technical and methodological basis for integration of PET/MR hybrid imaging into RT planning.

Xerostomia and its predictors following parotid-sparing irradiation of head-and-neck cancer.

PubMed

Eisbruch, A; Kim, H M; Terrell, J E; Marsh, L H; Dawson, L A; Ship, J A

2001-07-01

To assess long-term xerostomia in patients receiving parotid-sparing radiation therapy (RT) for head-and-neck cancer, and to find the patient and therapy-related factors that affect its severity. From March 1994 through January 2000, 84 patients received comprehensive bilateral neck RT using conformal and multisegmental intensity-modulated RT (IMRT) aiming to spare the major salivary glands. Before RT and periodically through 2 years after the completion of RT, salivary flow rates from each of the major salivary glands were selectively measured. At the same time intervals, each patient completed an 8-item self-reported xerostomia-specific questionnaire (XQ). To gain a relative measure of the effect of RT on the minor salivary glands, whose output could not be measured, the surfaces of the oral cavity (extending to include the surface of the base of tongue) were outlined in the planning CT scans. The mean doses to the new organ ("oral cavity") were recorded. Forty-eight patients receiving unilateral neck RT were similarly studied and served as a benchmark for comparison. Factors predicting the XQ scores were analyzed using a random-effects model. The XQ was found to be reliable and valid in measuring patient-reported xerostomia. The spared salivary glands which had received moderate doses in the bilateral RT group recovered to their baseline salivary flow rates during the second year after RT, and the spared glands in the unilateral RT group, which had received very low doses, demonstrated increased salivary production beyond their pre-RT levels. The increase in the salivary flow rates during the second year after RT paralleled an improvement in xerostomia in both patient groups. The improvement in xerostomia was faster in the unilateral compared with the bilateral RT group, but the difference narrowed at 2 years. The major salivary gland flow rates had only a weak correlation with the xerostomia scores. Factors found to be independently associated with the xerostomia scores were the pre-RT baseline scores, the time since RT, and the mean doses to the major salivary glands (notably to the submandibular glands) and to the oral cavity. An improvement over time in xerostomia, occurring in tandem with rising salivary production from the spared major salivary glands, suggests a long-term clinical benefit from their sparing. The oral cavity mean dose, representing RT effect on the minor salivary glands, was found to be a significant, independent predictor of xerostomia. Thus, in addition to the major salivary glands, sparing the uninvolved oral cavity should be considered as a planning objective to further reduce xerostomia.

Yellow fever in a traveller returning from Suriname to the Netherlands, March 2017

PubMed Central

Wouthuyzen-Bakker, Marjan; Knoester, Marjolein; van den Berg, Aad P; GeurtsvanKessel, Corine H; Koopmans, Marion PG; Van Leer-Buter, Coretta; Oude Velthuis, Bob; Pas, Suzan D; Ruijs, Wilhelmina LM; Schmidt-Chanasit, Jonas; Vreden, Stephen GS; van der Werf, Tjip S; Reusken, Chantal BEM; Bierman, Wouter FW

2017-01-01

A Dutch traveller returning from Suriname in early March 2017, presented with fever and severe acute liver injury. Yellow fever was diagnosed by (q)RT-PCR and sequencing. During hospital stay, the patient’s condition deteriorated and she developed hepatic encephalopathy requiring transfer to the intensive care. Although yellow fever has not been reported in the last four decades in Suriname, vaccination is recommended by the World Health Organization for visitors to this country. PMID:28333617

Yellow fever in a traveller returning from Suriname to the Netherlands, March 2017.

PubMed

Wouthuyzen-Bakker, Marjan; Knoester, Marjolein; van den Berg, Aad P; GeurtsvanKessel, Corine H; Koopmans, Marion Pg; Van Leer-Buter, Coretta; Oude Velthuis, Bob; Pas, Suzan D; Ruijs, Wilhelmina Lm; Schmidt-Chanasit, Jonas; Vreden, Stephen Gs; van der Werf, Tjip S; Reusken, Chantal Bem; Bierman, Wouter Fw

2017-03-16

A Dutch traveller returning from Suriname in early March 2017, presented with fever and severe acute liver injury. Yellow fever was diagnosed by (q)RT-PCR and sequencing. During hospital stay, the patient's condition deteriorated and she developed hepatic encephalopathy requiring transfer to the intensive care. Although yellow fever has not been reported in the last four decades in Suriname, vaccination is recommended by the World Health Organization for visitors to this country. This article is copyright of The Authors, 2017.

Airborne laser scanning for forest health status assessment and radiative transfer modelling

NASA Astrophysics Data System (ADS)

Novotny, Jan; Zemek, Frantisek; Pikl, Miroslav; Janoutova, Ruzena

2013-04-01

Structural parameters of forest stands/ecosystems are an important complementary source of information to spectral signatures obtained from airborne imaging spectroscopy when quantitative assessment of forest stands are in the focus, such as estimation of forest biomass, biochemical properties (e.g. chlorophyll /water content), etc. The parameterization of radiative transfer (RT) models used in latter case requires three-dimensional spatial distribution of green foliage and woody biomass. Airborne LiDAR data acquired over forest sites bears these kinds of 3D information. The main objective of the study was to compare the results from several approaches to interpolation of digital elevation model (DEM) and digital surface model (DSM). We worked with airborne LiDAR data with different density (TopEye Mk II 1,064nm instrument, 1-5 points/m2) acquired over the Norway spruce forests situated in the Beskydy Mountains, the Czech Republic. Three different interpolation algorithms with increasing complexity were tested: i/Nearest neighbour approach implemented in the BCAL software package (Idaho Univ.); ii/Averaging and linear interpolation techniques used in the OPALS software (Vienna Univ. of Technology); iii/Active contour technique implemented in the TreeVis software (Univ. of Freiburg). We defined two spatial resolutions for the resulting coupled raster DEMs and DSMs outputs: 0.4 m and 1 m, calculated by each algorithm. The grids correspond to the same spatial resolutions of hyperspectral imagery data for which the DEMs were used in a/geometrical correction and b/building a complex tree models for radiative transfer modelling. We applied two types of analyses when comparing between results from the different interpolations/raster resolution: 1/calculated DEM or DSM between themselves; 2/comparison with field data: DEM with measurements from referential GPS, DSM - field tree alometric measurements, where tree height was calculated as DSM-DEM. The results of the analyses show that: 1/averaging techniques tend to underestimate the tree height and the generated surface does not follow the first LiDAR echoes both for 1 m and 0.4 m pixel size; 2/we did not find any significant difference between tree heights calculated by nearest neighbour algorithm and the active contour technique for 1 m pixel output but the difference increased with finer resolution (0.4 m); 3/the accuracy of the DEMs calculated by tested algorithms is similar.

Heat stress effects on Holstein dairy cows' rumination.

PubMed

Moretti, R; Biffani, S; Chessa, S; Bozzi, R

2017-12-01

The objective of this study was to investigate the relationship between temperature-humidity index (THI) and rumination time (RT) in order to possibly exploit it as a useful tool for animal welfare improvement. During summer 2015 (1 June to 31 August), data from an Italian Holstein dairy farm located in the North of Italy were collected along with environmental data (i.e. ambient temperature and relative humidity) recorded with a weather station installed inside the barn. Rumination data were collected through the Heatime® HR system (SCR Engineers Ltd., Hadarim, Netanya, Israel), an automatic system composed of a neck collar with a Tag that records the RT and activity of each cow. A significant negative correlation was observed between RT and THI. Mixed linear models were fitted, including animal and test day as random effects, and parity, milk production level and date of last calving as fixed effects. A statistically significant effect of THI on RT was identified, with RT decreasing as THI increased.

Pretreatment to avoid positive RT-PCR results with inactivated viruses.

PubMed

Nuanualsuwan, Suphachai; Cliver, Dean O

2002-07-01

Enteric viruses that are important causes of human disease must often be detected by reverse transcription-polymerase chain reaction (RT-PCR), a method that commonly yields positive results with samples that contain only inactivated virus. This study was intended to develop a pretreatment for samples, so that inactivated viruses would not be detected by the RT-PCR procedure. Model viruses were human hepatitis A virus, vaccine poliovirus 1 and feline calicivirus as a surrogate for the Norwalk-like viruses. Each virus was inactivated (from an initial titer of approximately 10(3) PFU/ml) by ultraviolet light, hypochlorite or heating at 72 degrees C. Inactivated viruses, that were treated with proteinase K and ribonuclease for 30 min at 37 degrees C before RT-PCR, gave a negative result, which is to say that no amplicon was detected after the reaction was completed. This antecedent to the RT-PCR method may be applicable to other types of viruses, to viruses inactivated in other ways and to other molecular methods of virus detection.

Development of a One-Step Duplex RT-PCR Method for the Simultaneous Detection of VP3/VP1 and VP1/P2B Regions of the Hepatitis A Virus.

PubMed

Kim, Mi-Ju; Lee, Shin-Young; Kim, Hyun-Joong; Lee, Jeong Su; Joo, In Sun; Kwak, Hyo Sun; Kim, Hae-Yeong

2016-08-28

The simultaneous detection and accurate identification of hepatitis A virus (HAV) is critical in food safety and epidemiological studies to prevent the spread of HAV outbreaks. Towards this goal, a one-step duplex reverse-transcription (RT)-PCR method was developed targeting the VP1/P2B and VP3/VP1 regions of the HAV genome for the qualitative detection of HAV. An HAV RT-qPCR standard curve was produced for the quantification of HAV RNA. The detection limit of the duplex RT-PCR method was 2.8 × 10(1) copies of HAV. The PCR products enabled HAV genotyping analysis through DNA sequencing, which can be applied for epidemiological investigations. The ability of this duplex RT-PCR method to detect HAV was evaluated with HAV-spiked samples of fresh lettuce, frozen strawberries, and oysters. The limit of detection of the one-step duplex RT-PCR for each food model was 9.4 × 10(2) copies/20 g fresh lettuce, 9.7 × 10(3) copies/20 g frozen strawberries, and 4.1 × 10(3) copies/1.5 g oysters. Use of a one-step duplex RT-PCR method has advantages such as shorter time, decreased cost, and decreased labor owing to the single amplification reaction instead of four amplifications necessary for nested RT-PCR.

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

Retrieval of cloud microphysical parameters from INSAT-3D: a feasibility study using radiative transfer simulations

NASA Astrophysics Data System (ADS)

Jinya, John; Bipasha, Paul S.

2016-05-01

Clouds strongly modulate the Earths energy balance and its atmosphere through their interaction with the solar and terrestrial radiation. They interact with radiation in various ways like scattering, emission and absorption. By observing these changes in radiation at different wavelength, cloud properties can be estimated. Cloud properties are of utmost importance in studying different weather and climate phenomena. At present, no satellite provides cloud microphysical parameters over the Indian region with high temporal resolution. INSAT-3D imager observations in 6 spectral channels from geostationary platform offer opportunity to study continuous cloud properties over Indian region. Visible (0.65 μm) and shortwave-infrared (1.67 μm) channel radiances can be used to retrieve cloud microphysical parameters such as cloud optical thickness (COT) and cloud effective radius (CER). In this paper, we have carried out a feasibility study with the objective of cloud microphysics retrieval. For this, an inter-comparison of 15 globally available radiative transfer models (RTM) were carried out with the aim of generating a Look-up- Table (LUT). SBDART model was chosen for the simulations. The sensitivity of each spectral channel to different cloud properties was investigated. The inputs to the RT model were configured over our study region (50°S - 50°N and 20°E - 130°E) and a large number of simulations were carried out using random input vectors to generate the LUT. The determination of cloud optical thickness and cloud effective radius from spectral reflectance measurements constitutes the inverse problem and is typically solved by comparing the measured reflectances with entries in LUT and searching for the combination of COT and CER that gives the best fit. The products are available on the website www.mosdac.gov.in

Evaluation of reference genes for quantitative RT-PCR in Lolium temulentum under abiotic stress

USDA-ARS?s Scientific Manuscript database

Lolium temulentum is a valuable model grass species for the study of stress in forage and turf grasses. Gene expression analysis by quantitative real time RT-PCR relies on the use of proper internal standards. The aim of this study was to identify and evaluate reference genes for use in real-time q...

76 FR 7101 - Airworthiness Directives; Hamilton Sundstrand Propellers Model 247F Propellers

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-09

..., except Federal holidays. The AD docket contains this AD, the regulatory evaluation, any comments received... blades part number (P/N) 817370-1, S/Ns FR2449 to FR2958 inclusive, FR20010710 to FR20010722 inclusive, and FR20010723RT to FR20020127RT inclusive, before December 31, 2010. We determined that those S/N...

75 FR 62333 - Airworthiness Directives; Hamilton Sundstrand Propellers Model 247F Propellers

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-08

...., Monday through Friday, except Federal holidays. The AD docket contains this proposed AD, the regulatory... that the 247F propeller blades, P/N 817370-1, S/Ns FR2449 to FR2958 inclusive, FR20010710 to FR20010722 inclusive, and FR20010723RT to FR20020127RT inclusive, manufactured since January 1999, might also have...

Remediating Reading Difficulties in a Response to Intervention Model with Secondary Students

ERIC Educational Resources Information Center

Pyle, Nicole; Vaughn, Sharon

2012-01-01

The research on Response to Intervention (RtI) with secondary students is scant; however, a recently conducted, multiyear, large-scale implementation of RtI with middle-school students provides findings that inform practices and future directions for research. This article provides an overview of the findings from each of the 3 years of an…

Molecular Docking and Molecular Dynamics to Identify a Novel Human Immunodeficiency Virus Inhibitor from Alkaloids of Toddalia asiatica.

PubMed

Priya, R; Sumitha, Rajendrarao; Doss, C George Priya; Rajasekaran, C; Babu, S; Seenivasan, R; Siva, R

2015-10-01

Acquired immunodeficiency syndrome caused by human immunodeficiency virus (HIV) is an immunosuppressive disease. Over the past decades, it has plagued human health due to the grave consequences in its harness. For this reason, anti-HIV agents are imperative, and the search for the same from natural resources would assure the safety. In this investigation we have performed molecular docking, molecular property prediction, drug-likeness score, and molecular dynamics (MD) simulation to develop a novel anti-HIV drug. We have screened 12 alkaloids from a medicinal plant Toddalia asiatica for its probabilistic binding with the active site of the HIV-1-reverse transcriptase (HIV-1-RT) domain (the major contributor to the onset of the disease). The docking results were evaluated based on free energies of binding (ΔG), and the results suggested toddanol, toddanone, and toddalenone to be potent inhibitors of HIV-1-RT. In addition, the alkaloids were subjected to molecular property prediction analysis. Toddanol and toddanone with more rotatable bonds were found to have a drug-likeness score of 0.23 and 0.11, respectively. These scores were comparable with the standard anti-HIV drug zidovudine with a model score 0.28. Finally, two characteristic protein-ligand complexes were exposed to MD simulation to determine the stability of the predicted conformations. The toddanol-RT complex showed higher stability and stronger H-bonds than toddanone-RT complex. Based on these observations, we firmly believe that the alkaloid toddanol could aid in efficient HIV-1 drug discovery. In the present study, the molecular docking and MD simulations are performed to explore the possible binding mode of HIV 1 RT with 12 alkaloids of T. asiatica. Molecular docking by AutoDock4 revealed three alkaloids toddanol, toddanone, and toddalenone with highest binding affinity towards HIV 1 RT. The drug likeness model score revealed a positive score for toddanol and toddanone which is comparable to the drug likeness score of the standard anti HIV drug zidovudine. Results from simulation analysis revealed that toddanol RT complex is more stable than toddanone RT complex inferring toddanol as a potential anti HIV drug molecule. Abbreviations used: HIV: Human immunodeficiency virus, HIV 1 RT: HIV 1 reverse transcriptase, RNase H: Ribonuclease H, MD: Molecular dynamics, PDB: Protein databank, RMSD: Root mean square deviation, RMSF: Root mean square fluctuation.

Utilization of Radiation Therapy in Norway After the Implementation of The National Cancer Plan—A National, Population-Based Study

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

Åsli, Linn M., E-mail: linn.merete.asli@kreftregisteret.no; Kvaløy, Stein O.; Jetne, Vidar

2014-11-01

Purpose: To estimate actual utilization rates of radiation therapy (RT) in Norway, describe time trends (1997-2010), and compare these estimates with corresponding optimal RT rates. Methods and Materials: Data from the population-based Cancer Registry of Norway was used to identify all patients diagnosed with cancer and/or treated by RT for cancer in 1997-2010. Radiation therapy utilization rates (RURs) were calculated as (1) the proportion of incident cancer cases who received RT at least once within 1 year of diagnosis (RUR{sub 1Y}); and (2) the proportion who received RT within 5 years of diagnosis (RUR{sub 5Y}). The number of RT treatment courses per incidentmore » cancer case (TCI) was also calculated for all cancer sites combined. The actual RURs were compared with corresponding Australian and Canadian epidemiologic- and evidence-based model estimates and criterion-based benchmark estimates of optimal RURs. The TCIs were compared with TCI estimates from the 1997 Norwegian/National Cancer Plan (NCP). Joinpoint regression was used to identify changes in trends and to estimate annual percentage change (APC) in actual RUR{sub 1Y} and actual TCI. Results: The actual RUR{sub 5Y} (all sites) increased significantly to 29% in 2005 but still differed markedly from the Australian epidemiologic- and evidence-based model estimate of 48%. With the exception of RUR{sub 5Y} for breast cancer and RUR{sub 1Y} for lung cancers, all actual RURs were markedly lower than optimal RUR estimates. The actual TCI increased significantly during the study period, reaching 42.5% in 2010, but was still lower than the 54% recommended in the NCP. The trend for RUR{sub 1Y} (all sites) and TCI changed significantly, with the annual percentage change being largest during the first part of the study period. Conclusions: Utilization rates of RT in Norway increased after the NCP was implemented and RT capacity was increased, but they still seem to be lower than optimal levels.« less

ADHD performance reflects inefficient but not impulsive information processing: a diffusion model analysis.

PubMed

Metin, Baris; Roeyers, Herbert; Wiersema, Jan R; van der Meere, Jaap J; Thompson, Margaret; Sonuga-Barke, Edmund

2013-03-01

Attention-deficit/hyperactivity disorder (ADHD) is associated with performance deficits across a broad range of tasks. Although individual tasks are designed to tap specific cognitive functions (e.g., memory, inhibition, planning, etc.), these deficits could also reflect general effects related to either inefficient or impulsive information processing or both. These two components cannot be isolated from each other on the basis of classical analysis in which mean reaction time (RT) and mean accuracy are handled separately. Seventy children with a diagnosis of combined type ADHD and 50 healthy controls (between 6 and 17 years) performed two tasks: a simple two-choice RT (2-CRT) task and a conflict control task (CCT) that required higher levels of executive control. RT and errors were analyzed using the Ratcliff diffusion model, which divides decisional time into separate estimates of information processing efficiency (called "drift rate") and speed-accuracy tradeoff (SATO, called "boundary"). The model also provides an estimate of general nondecisional time. Results were the same for both tasks independent of executive load. ADHD was associated with lower drift rate and less nondecisional time. The groups did not differ in terms of boundary parameter estimates. RT and accuracy performance in ADHD appears to reflect inefficient rather than impulsive information processing, an effect independent of executive function load. The results are consistent with models in which basic information processing deficits make an important contribution to the ADHD cognitive phenotype. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Application of Suomi-NPP Green Vegetation Fraction and NUCAPS for Improving Regional Numerical Weather Prediction

NASA Technical Reports Server (NTRS)

Case, Jonathan L.; Berndt, Emily B.; Srikishen, Jayanthi; Zavodsky, Bradley T.

2014-01-01

The NASA SPoRT Center is working to incorporate Suomi-NPP products into its research and transition activities to improve regional numerical weather prediction (NWP). Specifically, SPoRT seeks to utilize two data products from NOAA/NESDIS: (1) daily global VIIRS green vegetation fraction (GVF), and (2) NOAA Unique CrIS and ATMS Processing System (NUCAPS) temperature and moisture retrieved profiles. The goal of (1) is to improve the representation of vegetation in the Noah land surface model (LSM) over existing climatological GVF datasets in order to improve the land-atmosphere energy exchanges in NWP models and produce better temperature, moisture, and precipitation forecasts. The goal of (2) is to assimilate NUCAPS retrieved profiles into the Gridpoint Statistical Interpolation (GSI) data assimilation system to assess the impact on a summer pre-frontal convection case. Most regional NWP applications make use of a monthly GVF climatology for use in the Noah LSM within the Weather Research and Forecasting (WRF) model. The GVF partitions incoming energy into direct surface heating/evaporation over bare soil versus evapotranspiration processes over vegetated surfaces. Misrepresentations of the fractional coverage of vegetation during anomalous weather/climate regimes (e.g., early/late bloom or freeze; drought) can lead to poor NWP model results when land-atmosphere feedback is important. SPoRT has been producing a daily MODIS GVF product based on the University of Wisconsin Direct Broadcast swaths of Normalized Difference Vegetation Index (NDVI). While positive impacts have been demonstrated in the WRF model for some cases, the reflectances composing these NDVI do not correct for atmospheric aerosols nor satellite view angle, resulting in temporal noisiness at certain locations (especially heavy vegetation). The method behind the NESDIS VIIRS GVF is expected to alleviate the issues seen in the MODIS GVF real-time product, thereby offering a higher-quality dataset for modeling applications. SPoRT is evaluating the VIIRS GVF data against the MODIS real-time and climatology GVF in both WRF and the NASA Land Information System. SPoRT has a history of assimilating hyperspectral infrared retrieved profiles

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.

EL_PSSM-RT: DNA-binding residue prediction by integrating ensemble learning with PSSM Relation Transformation.

PubMed

Zhou, Jiyun; Lu, Qin; Xu, Ruifeng; He, Yulan; Wang, Hongpeng

2017-08-29

Prediction of DNA-binding residue is important for understanding the protein-DNA recognition mechanism. Many computational methods have been proposed for the prediction, but most of them do not consider the relationships of evolutionary information between residues. In this paper, we first propose a novel residue encoding method, referred to as the Position Specific Score Matrix (PSSM) Relation Transformation (PSSM-RT), to encode residues by utilizing the relationships of evolutionary information between residues. PDNA-62 and PDNA-224 are used to evaluate PSSM-RT and two existing PSSM encoding methods by five-fold cross-validation. Performance evaluations indicate that PSSM-RT is more effective than previous methods. This validates the point that the relationship of evolutionary information between residues is indeed useful in DNA-binding residue prediction. An ensemble learning classifier (EL_PSSM-RT) is also proposed by combining ensemble learning model and PSSM-RT to better handle the imbalance between binding and non-binding residues in datasets. EL_PSSM-RT is evaluated by five-fold cross-validation using PDNA-62 and PDNA-224 as well as two independent datasets TS-72 and TS-61. Performance comparisons with existing predictors on the four datasets demonstrate that EL_PSSM-RT is the best-performing method among all the predicting methods with improvement between 0.02-0.07 for MCC, 4.18-21.47% for ST and 0.013-0.131 for AUC. Furthermore, we analyze the importance of the pair-relationships extracted by PSSM-RT and the results validates the usefulness of PSSM-RT for encoding DNA-binding residues. We propose a novel prediction method for the prediction of DNA-binding residue with the inclusion of relationship of evolutionary information and ensemble learning. Performance evaluation shows that the relationship of evolutionary information between residues is indeed useful in DNA-binding residue prediction and ensemble learning can be used to address the data imbalance issue between binding and non-binding residues. A web service of EL_PSSM-RT ( http://hlt.hitsz.edu.cn:8080/PSSM-RT_SVM/ ) is provided for free access to the biological research community.

Dual-Energy CT Imaging of Tumor Liposome Delivery After Gold Nanoparticle-Augmented Radiation Therapy

PubMed Central

Ashton, Jeffrey R.; Castle, Katherine D.; Qi, Yi; Kirsch, David G.; West, Jennifer L.; Badea, Cristian T.

2018-01-01

Gold nanoparticles (AuNPs) are emerging as promising agents for both cancer therapy and computed tomography (CT) imaging. AuNPs absorb x-rays and subsequently release low-energy, short-range photoelectrons during external beam radiation therapy (RT), increasing the local radiation dose. When AuNPs are near tumor vasculature, the additional radiation dose can lead to increased vascular permeability. This work focuses on understanding how tumor vascular permeability is influenced by AuNP-augmented RT, and how this effect can be used to improve the delivery of nanoparticle chemotherapeutics. Methods: Dual-energy CT was used to quantify the accumulation of both liposomal iodine and AuNPs in tumors following AuNP-augmented RT in a mouse model of primary soft tissue sarcoma. Mice were injected with non-targeted AuNPs, RGD-functionalized AuNPs (vascular targeting), or no AuNPs, after which they were treated with varying doses of RT. The mice were injected with either liposomal iodine (for the imaging study) or liposomal doxorubicin (for the treatment study) 24 hours after RT. Increased tumor liposome accumulation was assessed by dual-energy CT (iodine) or by tracking tumor treatment response (doxorubicin). Results: A significant increase in vascular permeability was observed for all groups after 20 Gy RT, for the targeted and non-targeted AuNP groups after 10 Gy RT, and for the vascular-targeted AuNP group after 5 Gy RT. Combining targeted AuNPs with 5 Gy RT and liposomal doxorubicin led to a significant tumor growth delay (tumor doubling time ~ 8 days) compared to AuNP-augmented RT or chemotherapy alone (tumor doubling time ~3-4 days). Conclusions: The addition of vascular-targeted AuNPs significantly improved the treatment effect of liposomal doxorubicin after RT, consistent with the increased liposome accumulation observed in tumors in the imaging study. Using this approach with a liposomal drug delivery system can increase specific tumor delivery of chemotherapeutics, which has the potential to significantly improve tumor response and reduce the side effects of both RT and chemotherapy. PMID:29556356

Single-Fraction Versus 5-Fraction Radiation Therapy for Metastatic Epidural Spinal Cord Compression in Patients With Limited Survival Prognoses: Results of a Matched-Pair Analysis

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

Rades, Dirk, E-mail: Rades.Dirk@gmx.net; Huttenlocher, Stefan; Šegedin, Barbara

Purpose: This study compared single-fraction to multi-fraction short-course radiation therapy (RT) for symptomatic metastatic epidural spinal cord compression (MESCC) in patients with limited survival prognosis. Methods and Materials: A total of 121 patients who received 8 Gy × 1 fraction were matched (1:1) to 121 patients treated with 4 Gy × 5 fractions for 10 factors including age, sex, performance status, primary tumor type, number of involved vertebrae, other bone metastases, visceral metastases, interval between tumor diagnosis and MESCC, pre-RT ambulatory status, and time developing motor deficits prior to RT. Endpoints included in-field repeated RT (reRT) for MESCC, overall survival (OS), and impact of RT onmore » motor function. Univariate analyses were performed with the Kaplan-Meier method and log-rank test for in-field reRT for MESCC and OS and with the ordered-logit model for effect of RT on motor function. Results: Doses of 8 Gy × 1 fraction and 4 Gy × 5 fractions were not significantly different with respect to the need for in-field reRT for MESCC (P=.11) at 6 months (18% vs 9%, respectively) and 12 months (30% vs 22%, respectively). The RT regimen also had no significant impact on OS (P=.65) and post-RT motor function (P=.21). OS rates at 6 and 12 months were 24% and 9%, respectively, after 8 Gy × 1 fraction versus 25% and 13%, respectively, after 4 Gy × 5 fractions. Improvement of motor function was observed in 17% of patients after 8 Gy × 1 fraction and 23% after 4 Gy × 5 fractions, respectively. Conclusions: There were no significant differences with respect to need for in-field reRT for MESCC, OS, and motor function by dose fractionation regimen. Thus, 8 Gy × 1 fraction may be a reasonable option for patients with survival prognosis of a few months.« less

Interval Between Hysterectomy and Start of Radiation Treatment Is Predictive of Recurrence in Patients With Endometrial Carcinoma

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

Cattaneo, Richard; Hanna, Rabbie K.; Jacobsen, Gordon

Purpose: Adjuvant radiation therapy (RT) has been shown to improve local control in patients with endometrial carcinoma. We analyzed the impact of the time interval between hysterectomy and RT initiation in patients with endometrial carcinoma. Methods and Materials: In this institutional review board-approved study, we identified 308 patients with endometrial carcinoma who received adjuvant RT after hysterectomy. All patients had undergone hysterectomy, oophorectomy, and pelvic and para-aortic lymph node evaluation from 1988 to 2010. Patients' demographics, pathologic features, and treatments were compared. The time interval between hysterectomy and the start of RT was calculated. The effects of time interval onmore » recurrence-free (RFS), disease-specific (DSS), and overall survival (OS) were calculated. Following univariate analysis, multivariate modeling was performed. Results: The median age and follow-up for the study cohort was 65 years and 72 months, respectively. Eighty-five percent of the patients had endometrioid carcinoma. RT was delivered with high-dose-rate brachytherapy alone (29%), pelvic RT alone (20%), or both (51%). Median time interval to start RT was 42 days (range, 21-130 days). A total of 269 patients (74%) started their RT <9 weeks after undergoing hysterectomy (group 1) and 26% started ≥9 weeks after surgery (group 2). There were a total of 43 recurrences. Tumor recurrence was significantly associated with treatment delay of ≥9 weeks, with 5-year RFS of 90% for group 1 compared to only 39% for group 2 (P<.001). On multivariate analysis, RT delay of ≥9 weeks (P<.001), presence of lymphovascular space involvement (P=.001), and higher International Federation of Gynecology and Obstetrics grade (P=.012) were independent predictors of recurrence. In addition, RT delay of ≥9 weeks was an independent significant predictor for worse DSS and OS (P=.001 and P=.01, respectively). Conclusions: Delay in administering adjuvant RT after hysterectomy was associated with worse survival endpoints. Our data suggest that shorter time interval between hysterectomy and start of RT may be beneficial.« less

Validation of a Radiosensitivity Molecular Signature in Breast Cancer

PubMed Central

Eschrich, Steven A.; Fulp, William J.; Pawitan, Yudi; Foekens, John A.; Smid, Marcel; Martens, John W. M.; Echevarria, Michelle; Kamath, Vidya; Lee, Ji-Hyun; Harris, Eleanor E.; Bergh, Jonas; Torres-Roca, Javier F.

2014-01-01

Purpose Previously, we developed a radiosensitivity molecular signature (RSI) that was clinically-validated in three independent datasets (rectal, esophageal, head and neck) in 118 patients. Here, we test RSI in radiotherapy (RT) treated breast cancer patients. Experimental Design RSI was tested in two previously published breast cancer datasets. Patients were treated at the Karolinska University Hospital (n=159) and Erasmus Medical Center (n=344). RSI was applied as previously described. Results We tested RSI in RT-treated patients (Karolinska). Patients predicted to be radiosensitive (RS) had an improved 5 yr relapse-free survival when compared with radioresistant (RR) patients (95% vs. 75%, p=0.0212) but there was no difference between RS/RR patients treated without RT (71% vs. 77%, p=0.6744), consistent with RSI being RT-specific (interaction term RSIxRT, p=0.05). Similarly, in the Erasmus dataset RT-treated RS patients had an improved 5-year distant-metastasis-free survival over RR patients (77% vs. 64%, p=0.0409) but no difference was observed in patients treated without RT (RS vs. RR, 80% vs. 81%, p=0.9425). Multivariable analysis showed RSI is the strongest variable in RT-treated patients (Karolinska, HR=5.53, p=0.0987, Erasmus, HR=1.64, p=0.0758) and in backward selection (removal alpha of 0.10) RSI was the only variable remaining in the final model. Finally, RSI is an independent predictor of outcome in RT-treated ER+ patients (Erasmus, multivariable analysis, HR=2.64, p=0.0085). Conclusions RSI is validated in two independent breast cancer datasets totaling 503 patients. Including prior data, RSI is validated in five independent cohorts (621 patients) and represents, to our knowledge, the most extensively validated molecular signature in radiation oncology. PMID:22832933

Omitting radiation therapy after lumpectomy for pure DCIS does not reduce the risk of salvage mastectomy.

PubMed

Rakovitch, Eileen; Nofech-Mozes, Sharon; Hanna, Wedad; Sutradhar, Rinku; Gu, Sumei; Fong, Cindy; Tuck, Alan; Youngson, Bruce; Miller, Naomi; Done, Susan J; Chang, Martin C; Sengupta, Sandip; Elavathil, Leela; Jani, Prashant A; Bonin, Michel; Lalani, Nafisha; Paszat, Lawrence

2018-02-01

Radiation therapy (RT) after breast-conserving surgery (BCS) for Ductal Carcinoma in Situ (DCIS) halves the risk of local recurrence (LR). The omission of RT is often supported by the paradigm that patients who develop LR can be salvaged with further breast-conserving therapy leading to higher rates of breast preservation and improved quality of life. However, population-based, long-term rates of breast preservation in women treated by upfront BCS ± RT are unknown. Women diagnosed with pure DCIS from 1994 to 2003 treated with BCS ± RT in Ontario were identified. Median follow-up is 12 years. The development and treatment of LR and contralateral breast cancers were determined by administrative databases with validation. The 10-year mastectomy-free survival was calculated using the Kaplan-Meier method. The impact of RT on breast preservation was determined by propensity-adjusted cox proportional hazards model. The cohort includes 3303 women with DCIS; 1649 (50%) underwent BCS alone, 1654 (50%) underwent BCS + RT. Women treated by BCS alone were more likely to develop a LR compared to those treated by upfront BCS + RT (20.8% versus 15.5%, p < 0.001). Mastectomy was used to treat LR in 57.4% (197/343) of women who recurred after BCS alone and 67.6% (174/257) of those who recurred after BCS + RT. Women treated with upfront BCS + RT had higher rates of bilateral breast preservation at 10 years compared to those treated by BCS alone (87.3% vs.82.7%, p = 0.0096). Local Recurrence after BCS alone does not favor breast preservation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Real-time magnetic resonance imaging-guided radiofrequency atrial ablation and visualization of lesion formation at 3 Tesla.

PubMed

Vergara, Gaston R; Vijayakumar, Sathya; Kholmovski, Eugene G; Blauer, Joshua J E; Guttman, Mike A; Gloschat, Christopher; Payne, Gene; Vij, Kamal; Akoum, Nazem W; Daccarett, Marcos; McGann, Christopher J; Macleod, Rob S; Marrouche, Nassir F

2011-02-01

Magnetic resonance imaging (MRI) allows visualization of location and extent of radiofrequency (RF) ablation lesion, myocardial scar formation, and real-time (RT) assessment of lesion formation. In this study, we report a novel 3-Tesla RT -RI based porcine RF ablation model and visualization of lesion formation in the atrium during RF energy delivery. The purpose of this study was to develop a 3-Tesla RT MRI-based catheter ablation and lesion visualization system. RF energy was delivered to six pigs under RT MRI guidance. A novel MRI-compatible mapping and ablation catheter was used. Under RT MRI, this catheter was safely guided and positioned within either the left or right atrium. Unipolar and bipolar electrograms were recorded. The catheter tip-tissue interface was visualized with a T1-weighted gradient echo sequence. RF energy was then delivered in a power-controlled fashion. Myocardial changes and lesion formation were visualized with a T2-weighted (T2W) half Fourier acquisition with single-shot turbo spin echo (HASTE) sequence during ablation. RT visualization of lesion formation was achieved in 30% of the ablations performed. In the other cases, either the lesion was formed outside the imaged region (25%) or the lesion was not created (45%) presumably due to poor tissue-catheter tip contact. The presence of lesions was confirmed by late gadolinium enhancement MRI and macroscopic tissue examination. MRI-compatible catheters can be navigated and RF energy safely delivered under 3-Tesla RT MRI guidance. Recording electrograms during RT imaging also is feasible. RT visualization of lesion as it forms during RF energy delivery is possible and was demonstrated using T2W HASTE imaging. Copyright © 2011 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

Statistical learning and adaptive decision-making underlie human response time variability in inhibitory control.

PubMed

Ma, Ning; Yu, Angela J

2015-01-01

Response time (RT) is an oft-reported behavioral measure in psychological and neurocognitive experiments, but the high level of observed trial-to-trial variability in this measure has often limited its usefulness. Here, we combine computational modeling and psychophysics to examine the hypothesis that fluctuations in this noisy measure reflect dynamic computations in human statistical learning and corresponding cognitive adjustments. We present data from the stop-signal task (SST), in which subjects respond to a go stimulus on each trial, unless instructed not to by a subsequent, infrequently presented stop signal. We model across-trial learning of stop signal frequency, P(stop), and stop-signal onset time, SSD (stop-signal delay), with a Bayesian hidden Markov model, and within-trial decision-making with an optimal stochastic control model. The combined model predicts that RT should increase with both expected P(stop) and SSD. The human behavioral data (n = 20) bear out this prediction, showing P(stop) and SSD both to be significant, independent predictors of RT, with P(stop) being a more prominent predictor in 75% of the subjects, and SSD being more prominent in the remaining 25%. The results demonstrate that humans indeed readily internalize environmental statistics and adjust their cognitive/behavioral strategy accordingly, and that subtle patterns in RT variability can serve as a valuable tool for validating models of statistical learning and decision-making. More broadly, the modeling tools presented in this work can be generalized to a large body of behavioral paradigms, in order to extract insights about cognitive and neural processing from apparently quite noisy behavioral measures. We also discuss how this behaviorally validated model can then be used to conduct model-based analysis of neural data, in order to help identify specific brain areas for representing and encoding key computational quantities in learning and decision-making.

Evaluation and hydrological application of satellite-based precipitation datasets in driving hydrological models over the Huifa river basin in Northeast China

NASA Astrophysics Data System (ADS)

Zhu, Honglei; Li, Ying; Huang, Yanwei; Li, Yingchen; Hou, Cuicui; Shi, Xiaoliang

2018-07-01

Satellite-based precipitation estimates with high spatial and temporal resolution and large areal coverage have provided hydrologists a potential alternative source for hydrological applications since the last few years, especially for ungauged regions. This study evaluates five satellite-based precipitation datasets, namely, Fengyun, TRMM 3B42, TRMM 3B42RT, CMORPH_BLD and CMORPH_RAW, against gauge observations for streamflow simulation with a distributed hydrological model (SWAT) over the Huifa river basin, Northeast China. Results show that, by comparing the statistical indices (MA, M5P, STDE, ME, BIAS and CC) and inter-annual precipitation, it is demonstrated that Fengyun TRMM 3B42 and CMORPH_BLD show better agreement with gauge precipitation data than CMORPH_RAW and TRMM 3B42RT. When the SWAT model for each dataset calibrated and validated individually, satisfactory model performances (defined as: NS > 0.5) are achieved at daily scale for Fengyun, TRMM 3B42 and gauge-driven model, and very good performances (defined as: NS > 0.75) are achieved at monthly scale for Fengyun and gauge-driven model, respectively. The CMORPH_BLD forced daily simulations also yield higher values of NS and R2 than CMORPH_RAW and TRMM 3B42RT at daily and monthly step. From the uncertainty results, variations of P-factor values and frequency distribution curves of NS suggest that the simulation uncertainty increase when operating the Fengyun, 3B42RT, CMORPH_BLD and CMORPH_RAW-driven model with best fitted parameters for rain gauge SWAT model. The results also indicate that the influence of parameter uncertainty on model simulation results may be greater than the effect of input data accuracy. It is noted that uncertainty analysis is necessary to evaluate the hydrological applications of satellite-based precipitation datasets.

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 New, More Physically Based Algorithm, for Retrieving Aerosol Properties over Land from MODIS

NASA Technical Reports Server (NTRS)

Levy, Robert C.; Kaufman, Yoram J.; Remer, Lorraine A.; Mattoo, Shana

2004-01-01

The MOD Imaging Spectrometer (MODIS) has been successfully retrieving aerosol properties, beginning in early 2000 from Terra and from mid 2002 from Aqua. Over land, the retrieval algorithm makes use of three MODIS channels, in the blue, red and infrared wavelengths. As part of the validation exercises, retrieved spectral aerosol optical thickness (AOT) has been compared via scatterplots against spectral AOT measured by the global Aerosol Robotic NETwork (AERONET). On one hand, global and long term validation looks promising, with two-thirds (average plus and minus one standard deviation) of all points falling between published expected error bars. On the other hand, regression of these points shows a positive y-offset and a slope less than 1.0. For individual regions, such as along the U.S. East Coast, the offset and slope are even worse. Here, we introduce an overhaul of the algorithm for retrieving aerosol properties over land. Some well-known weaknesses in the current aerosol retrieval from MODIS include: a) rigid assumptions about the underlying surface reflectance, b) limited aerosol models to choose from, c) simplified (scalar) radiative transfer (RT) calculations used to simulate satellite observations, and d) assumption that aerosol is transparent in the infrared channel. The new algorithm attempts to address all four problems: a) The new algorithm will include surface type information, instead of fixed ratios of the reflectance in the visible channels to the mid-IR reflectance. b) It will include updated aerosol optical properties to reflect the growing aerosol retrieved from eight-plus years of AERONE". operation. c) The effects of polarization will be including using vector RT calculations. d) Most importantly, the new algorithm does not assume that aerosol is transparent in the infrared channel. It will be an inversion of reflectance observed in the three channels (blue, red, and infrared), rather than iterative single channel retrievals. Thus, this new formulation of the MODIS aerosol retrieval over land includes more physically based surface, aerosol and radiative transfer with fewer potentially erroneous assumptions.

A doxycycline-dependent human immunodeficiency virus type 1 replicates in vivo without inducing CD4+ T-cell depletion

PubMed Central

Legrand, Nicolas; van der Velden, Gisela J.; Fang, Raphaël Ho Tsong; Douaisi, Marc; Weijer, Kees; Das, Atze T.; Blom, Bianca; Uittenbogaart, Christel H.; Berkhout, Ben

2012-01-01

A novel genetic approach for the control of virus replication was used for the design of a conditionally replicating human immunodeficiency virus (HIV) variant, HIV-rtTA. HIV-rtTA gene expression and virus replication are strictly dependent on the presence of a non-toxic effector molecule, doxycycline (dox), and thus can be turned on and off at will in a graded and reversible manner. The in vivo replication capacity, pathogenicity and genetic stability of this HIV-rtTA variant were evaluated in a humanized mouse model of haematopoiesis that harbours lymphoid and myeloid components of the human immune system (HIS). Infection of dox-fed BALB Rag/γc HIS (BRG-HIS) mice with HIV-rtTA led to the establishment of a productive infection without CD4+ T-cell depletion. The virus did not show any sign of escape from dox control for up to 10 weeks after the onset of infection. No reversion towards a functional Tat–transactivating responsive (TAR) RNA element axis was observed, confirming the genetic stability of the HIV-rtTA variant in vivo. These results demonstrate the proof of concept that HIV-rtTA replicates efficiently in vivo. HIV-rtTA is a promising tool for fundamental research to study virus–host interactions in vivo in a controlled fashion. PMID:22647372

Endovascular Therapy Demonstrates Benefit over Intravenous Recombinant Tissue Plasminogen Activator Based on Repeatedly Measured National Institutes of Health Stroke Scale.

PubMed

Fan, Liqiong; Yeatts, Sharon D; Foster, Lydia D; Khatri, Pooja; Tomsick, Thomas; Broderick, Joseph P; Palesch, Yuko Y

2017-03-01

The Interventional Management of Stroke (IMS) III trial was a randomized controlled trial designed to compare the effect of endovascular therapy after intravenous recombinant tissue plasminogen activator (i.v. rt-PA) as compared to i.v. rt-PA alone. The primary outcome was modified Rankin Scale at 90 days. Secondary outcomes included National Institutes of Health Stroke Scale (NIHSS), which was assessed repeatedly through 90 days. The objective of this analysis is to evaluate the treatment effect of endovascular therapy over time on NIHSS. 656 subjects were enrolled in the IMS III trial, including 434 subjects randomized to endovascular therapy and 222 to i.v. rt-PA only. NIHSS scores evaluated at 40 min, 24 h, Day 5, and Day 90 were included in the analysis. A covariance structure model was used to investigate the treatment effect on NIHSS over time, adjusting for relevant covariates including baseline stroke severity. Model assumptions were valid. Based on the covariance structure model, after adjusting for relevant baseline covariates, a significant time-by-treatment interaction effect ( p = 0.0137) was observed. Only NIHSS at Day 90 showed a significant treatment effect ( p = 0.0473), with subjects in the endovascular arm having a lower NIHSS (less neurologic deficit) compared to the i.v. rt-PA arm. The IMS III trial demonstrated an endovascular treatment effect based on the secondary outcome of NIHSS. However, the magnitude of this treatment effect varied by the time of assessment. It was only at Day 90 that the endovascular arm had a significantly lower NIHSS compared to that in the i.v. rt-PA arm.

Salicornia europaea L. Na⁺/H⁺ antiporter gene improves salt tolerance in transgenic alfalfa (Medicago sativa L.).

PubMed

Zhang, L Q; Niu, Y D; Huridu, H; Hao, J F; Qi, Z; Hasi, A

2014-07-24

In order to obtain a salt-tolerant perennial alfalfa (Medicago sativa L.), we transferred the halophyte Salicornia europaea L. Na(+)/H(+) antiporter gene, SeNHX1, to alfalfa by using the Agrobacterium-mediated transformation method. The transformants were confirmed by both PCR and RT-PCR analyses. Of 197 plants that were obtained after transformation, 36 were positive by PCR analysis using 2 primer pairs for the CaMV35S-SeNHX1 and SeNHX1-Nos fragments; 6 plants survived in a greenhouse. RT-PCR analysis revealed that SeNHX1 was expressed in 5 plants. The resultant transgenic alfalfa had better salt tolerance. After stress treatment for 21 days with 0.6% NaCl, the chlorophyll and MDA contents in transgenic plants were lower, but proline content and SOD, POD, and CAT activities were higher than those in wild-type plants. These results suggest that the salt tolerance of transgenic alfalfa was improved by the overexpression of the SeNHX1 gene.

Dual HIV-1 reverse transcriptase and integrase inhibitors from Limonium morisianum Arrigoni, an endemic species of Sardinia (Italy).

PubMed

Sanna, Cinzia; Rigano, Daniela; Corona, Angela; Piano, Dario; Formisano, Carmen; Farci, Domenica; Franzini, Genni; Ballero, Mauro; Chianese, Giuseppina; Tramontano, Enzo; Taglialatela-Scafati, Orazio; Esposito, Francesca

2018-02-04

During our search for potential templates of HIV-1 reverse transcriptase (RT) and integrase (IN) dual inhibitors, the methanolic extract obtained from aerial parts of Limonium morisianum was investigated. Repeated bioassay-guided chromatographic purifications led to the isolation of the following secondary metabolites: myricetin, myricetin 3-O-rutinoside, myricetin-3-O-(6″-O-galloyl)-β-d-galactopyranoside, (-)-epigallocatechin 3-O-gallate, tryptamine, ferulic and phloretic acids. The isolated compounds were tested on both HIV-1 RT-associated RNase H and IN activities. Interestingly, (-)-epigallocatechin-3-O-gallate and myricetin-3-O-(6″-O-galloyl)-β-d-galactopyranoside potently inhibited both enzyme activities with IC 50 values ranging from 0.21 to 10.9 μM. Differently, tryptamine and ferulic acid exhibited a significant inhibition only on the IN strand transfer reaction, showing a selectivity for this viral enzyme. Taken together these results strongly support the potential of this plant as a valuable anti HIV-1 drugs source worthy of further investigations.