Block truncation signature coding for hyperspectral analysis
NASA Astrophysics Data System (ADS)
Chakravarty, Sumit; Chang, Chein-I.
2008-08-01
This paper introduces a new signature coding which is designed based on the well-known Block Truncation Coding (BTC). It comprises of bit-maps of the signature blocks generated by different threshold criteria. Two new BTC-based algorithms are developed for signature coding, to be called Block Truncation Signature Coding (BTSC) and 2-level BTSC (2BTSC). In order to compare the developed BTC based algorithms with current binary signature coding schemes such as Spectral Program Analysis Manager (SPAM) developed by Mazer et al. and Spectral Feature-based Binary Coding (SFBC) by Qian et al., three different thresholding functions, local block mean, local block gradient, local block correlation are derived to improve the BTSC performance where the combined bit-maps generated by these thresholds can provide better spectral signature characterization. Experimental results reveal that the new BTC-based signature coding performs more effectively in characterizing spectral variations than currently available binary signature coding methods.
Adaptively truncated Hilbert spaces for Hamiltonian-based impurity solvers
NASA Astrophysics Data System (ADS)
Go, Ara; Millis, Andrew
We investigate truncations of the exponentially large Hilbert space in the exact diagonalization (ED) as an impurity solver for the dynamical mean-field theory (DMFT). A key issue is to maintain the high degree of numerical accuracy required in the construction of Greens functions. We test various truncation schemes with similar number of Slater determinants in both Hilbert spaces for the ground state and a particle- or a hole-excited state, and show that the excited states play an important role in accurate computation as well as the ground state. Appropriate truncation for both spaces enables us to compute the accurate self-energy of the impurity Hamiltonian with up to eight correlated orbitals hybridized with a sufficient number of bath orbitals to obtain converged solutions of the self-consistent equation in the DMFT, which is not solvable by the original ED. Application to spin-orbit coupled multi-orbital models and the one-dimensional Hubbard model and comparison to results from exact diagonalization and the configuration interaction based impurity solvers demonstrate the power of the method. This work was supported by the US Department of Energy under Grants No. DE-FG02-04ER46169 and DE-SC0006613.
Implementation of Multimode-Multilevel Block Truncation Coding for LCD Overdrive
NASA Astrophysics Data System (ADS)
Oh, Taegeun; Lee, Sanghoon
The Liquid-crystal display (LCD) overdrive technique has been utilized to reduce motion blur on a display via a reduction in the response time. However, to measure the variation of the pixel amplitudes, it is necessary to store the previous frame using a large frame memory. To downscale the frame memory, block truncation coding (BTC) is commonly employed due to the simplicity of its implementation, even if some visual artifacts may occur for image blocks with high frequency components. In this paper, we present a multimode-multilevel BTC (MBTC) technique that improves performance while maintaining simplicity. To improve the visual quality, we uniquely determine the quantization level and coding mode of each block according to the distribution of the luminance and chrominance amplitudes. For a compression ratio of 6: 1, the proposed method demonstrates higher coding efficiency and overdrive performance by up to 3.81dB in the PSNR compared to other methods.
Guo, Jing-Ming; Prasetyo, Heri
2015-03-01
This paper presents a technique for content-based image retrieval (CBIR) by exploiting the advantage of low-complexity ordered-dither block truncation coding (ODBTC) for the generation of image content descriptor. In the encoding step, ODBTC compresses an image block into corresponding quantizers and bitmap image. Two image features are proposed to index an image, namely, color co-occurrence feature (CCF) and bit pattern features (BPF), which are generated directly from the ODBTC encoded data streams without performing the decoding process. The CCF and BPF of an image are simply derived from the two ODBTC quantizers and bitmap, respectively, by involving the visual codebook. Experimental results show that the proposed method is superior to the block truncation coding image retrieval systems and the other earlier methods, and thus prove that the ODBTC scheme is not only suited for image compression, because of its simplicity, but also offers a simple and effective descriptor to index images in CBIR system. PMID:25420264
Deformable image registration of CT and truncated cone-beam CT for adaptive radiation therapy
NASA Astrophysics Data System (ADS)
Zhen, Xin; Yan, Hao; Zhou, Linghong; Jia, Xun; Jiang, Steve B.
2013-11-01
Truncation of a cone-beam computed tomography (CBCT) image, mainly caused by the limited field of view (FOV) of CBCT imaging, poses challenges to the problem of deformable image registration (DIR) between computed tomography (CT) and CBCT images in adaptive radiation therapy (ART). The missing information outside the CBCT FOV usually causes incorrect deformations when a conventional DIR algorithm is utilized, which may introduce significant errors in subsequent operations such as dose calculation. In this paper, based on the observation that the missing information in the CBCT image domain does exist in the projection image domain, we propose to solve this problem by developing a hybrid deformation/reconstruction algorithm. As opposed to deforming the CT image to match the truncated CBCT image, the CT image is deformed such that its projections match all the corresponding projection images for the CBCT image. An iterative forward-backward projection algorithm is developed. Six head-and-neck cancer patient cases are used to evaluate our algorithm, five with simulated truncation and one with real truncation. It is found that our method can accurately register the CT image to the truncated CBCT image and is robust against image truncation when the portion of the truncated image is less than 40% of the total image. Part of this work was presented at the 54th AAPM Annual Meeting (Charlotte, NC, USA, 29 July-2 August 2012).
Amicone, L; Spagnoli, F M; Späth, G; Giordano, S; Tommasini, C; Bernardini, S; De Luca, V; Della Rocca, C; Weiss, M C; Comoglio, P M; Tripodi, M
1997-01-01
Hepatocyte growth factor induces proliferation, motility and differentiation of epithelial cells through the tyrosine kinase receptor encoded by the MET protooncogene. The cytoplasmic portion of Met (referred to as cyto-Met) is activated but only weakly transforming. In order to determine the effect of activated Met on hepatocytes, we have targeted truncated Met expression to the liver by incorporating the cDNA into a vector carrying the entire human alpha-1-antitrypsin transcriptional unit. Transgenic expression in the liver of truncated human Met, containing the regulatory and the catalytic cytoplasmic domains, renders hepatocytes constitutively resistant to apoptosis and reproducibly permits immortalization. The emerging stable cell lines are not transformed and maintain a highly differentiated phenotype judged by the retention of epithelial cell polarity and the expression of hepatocyte-enriched transcription factors as well as hepatic products. PMID:9034332
NASA Astrophysics Data System (ADS)
Teal, Paul D.; Eccles, Craig
2015-04-01
The two most successful methods of estimating the distribution of nuclear magnetic resonance relaxation times from two dimensional data are data compression followed by application of the Butler-Reeds-Dawson algorithm, and a primal-dual interior point method using preconditioned conjugate gradient. Both of these methods have previously been presented using a truncated singular value decomposition of matrices representing the exponential kernel. In this paper it is shown that other matrix factorizations are applicable to each of these algorithms, and that these illustrate the different fundamental principles behind the operation of the algorithms. These are the rank-revealing QR (RRQR) factorization and the LDL factorization with diagonal pivoting, also known as the Bunch-Kaufman-Parlett factorization. It is shown that both algorithms can be improved by adaptation of the truncation as the optimization process progresses, improving the accuracy as the optimal value is approached. A variation on the interior method viz, the use of barrier function instead of the primal-dual approach, is found to offer considerable improvement in terms of speed and reliability. A third type of algorithm, related to the algorithm known as Fast iterative shrinkage-thresholding algorithm, is applied to the problem. This method can be efficiently formulated without the use of a matrix decomposition.
NASA Astrophysics Data System (ADS)
Hirthe, E. M.; Graf, T.
2012-04-01
Fluid density variations occur due to changes in the solute concentration, temperature and pressure of groundwater. Examples are interaction between freshwater and seawater, radioactive waste disposal, groundwater contamination, and geothermal energy production. The physical coupling between flow and transport introduces non-linearity in the governing mathematical equations, such that solving variable-density flow problems typically requires very long computational time. Computational efficiency can be attained through the use of adaptive time-stepping schemes. The aim of this work is therefore to apply a non-iterative adaptive time-stepping scheme based on local truncation error in variable-density flow problems. That new scheme is implemented into the code of the HydroGeoSphere model (Therrien et al., 2011). The new time-stepping scheme is applied to the Elder (1967) and the Shikaze et al. (1998) problem of free convection in porous and fractured-porous media, respectively. Numerical simulations demonstrate that non-iterative time-stepping based on local truncation error control fully automates the time step size and efficiently limits the temporal discretization error to the user-defined tolerance. Results of the Elder problem show that the new time-stepping scheme presented here is significantly more efficient than uniform time-stepping when high accuracy is required. Results of the Shikaze problem reveal that the new scheme is considerably faster than conventional time-stepping where time step sizes are either constant or controlled by absolute head/concentration changes. Future research will focus on the application of the new time-stepping scheme to variable-density flow in complex real-world fractured-porous rock.
NASA Astrophysics Data System (ADS)
Gao, Shigen; Dong, Hairong; Lyu, Shihang; Ning, Bin
2016-07-01
This paper studies decentralised neural adaptive control of a class of interconnected nonlinear systems, each subsystem is in the presence of input saturation and external disturbance and has independent system order. Using a novel truncated adaptation design, dynamic surface control technique and minimal-learning-parameters algorithm, the proposed method circumvents the problems of 'explosion of complexity' and 'dimension curse' that exist in the traditional backstepping design. Comparing to the methodology that neural weights are online updated in the controllers, only one scalar needs to be updated in the controllers of each subsystem when dealing with unknown systematic dynamics. Radial basis function neural networks (NNs) are used in the online approximation of unknown systematic dynamics. It is proved using Lyapunov stability theory that all the signals in the closed-loop system are semi-globally uniformly ultimately bounded. The tracking errors of each subsystems, the amplitude of NN approximation residuals and external disturbances can be attenuated to arbitrarily small by tuning proper design parameters. Simulation results are given to demonstrate the effectiveness of the proposed method.
Shewell, Lucy K.; Ku, Shan C.; Schulz, Benjamin L.; Jen, Freda E.-C.; Mubaiwa, Tsitsi D.; Ketterer, Margaret R.; Apicella, Michael A.; Jennings, Michael P.
2015-01-01
AniA of the pathogenic Neisseria is glycosylated in its C-terminal repeat region by the pilin glycosylation (pgl) pathway. AniA appears to be unique among bacterial nitrite reductases as it contains an N-terminal extension that includes a lipid modification site as well as a C-terminal extension that is glycosylated. Immunising with various glycoforms of the AniA protein demonstrated a strong humoral immune response to the basal monosaccharide. In addition, when animals were immunised with a truncated form of AniA, completely lacking the glycosylated C-terminal region, the antibody response was directed against AniA regardless of the glycosylation state of the protein. Immuno-SEM confirmed that AniA is expressed on the cell surface in N. gonorrhoeae. Antisera generated against a truncated, non-glycosylated, recombinant form of the AniA protein are capable of blocking nitrite reductase function in a whole cell assay. We propose that recombinant modified AniA has potential as a vaccine antigen for N. gonorrhoeae. PMID:23313483
Global adaptive rank truncated product method for gene-set analysis in association studies.
Vilor-Tejedor, Natalia; Calle, M Luz
2014-08-01
Gene set analysis (GSA) aims to assess the overall association of a set of genetic variants with a phenotype and has the potential to detect subtle effects of variants in a gene or a pathway that might be missed when assessed individually. We present a new implementation of the Adaptive Rank Truncated Product method (ARTP) for analyzing the association of a set of Single Nucleotide Polymorphisms (SNPs) in a gene or pathway. The new implementation, referred to as globalARTP, improves the original one by allowing the different SNPs in the set to have different modes of inheritance. We perform a simulation study for exploring the power of the proposed methodology in a set of scenarios with different numbers of causal SNPs with different effect sizes. Moreover, we show the advantage of using the gene set approach in the context of an Alzheimer's disease case-control study where we explore the endocytosis pathway. The new method is implemented in the R function globalARTP of the globalGSA package available at http://cran.r-project.org. PMID:25082012
NASA Astrophysics Data System (ADS)
Hirthe, Eugenia M.; Graf, Thomas
2012-12-01
The automatic non-iterative second-order time-stepping scheme based on the temporal truncation error proposed by Kavetski et al. [Kavetski D, Binning P, Sloan SW. Non-iterative time-stepping schemes with adaptive truncation error control for the solution of Richards equation. Water Resour Res 2002;38(10):1211, http://dx.doi.org/10.1029/2001WR000720.] is implemented into the code of the HydroGeoSphere model. This time-stepping scheme is applied for the first time to the low-Rayleigh-number thermal Elder problem of free convection in porous media [van Reeuwijk M, Mathias SA, Simmons CT, Ward JD. Insights from a pseudospectral approach to the Elder problem. Water Resour Res 2009;45:W04416, http://dx.doi.org/10.1029/2008WR007421.], and to the solutal [Shikaze SG, Sudicky EA, Schwartz FW. Density-dependent solute transport in discretely-fractured geological media: is prediction possible? J Contam Hydrol 1998;34:273-91] problem of free convection in fractured-porous media. Numerical simulations demonstrate that the proposed scheme efficiently limits the temporal truncation error to a user-defined tolerance by controlling the time-step size. The non-iterative second-order time-stepping scheme can be applied to (i) thermal and solutal variable-density flow problems, (ii) linear and non-linear density functions, and (iii) problems including porous and fractured-porous media.
An adaptive algorithm for removing the blocking artifacts in block-transform coded images
NASA Astrophysics Data System (ADS)
Yang, Jingzhong; Ma, Zheng
2005-11-01
JPEG and MPEG compression standards adopt the macro block encoding approach, but this method can lead to annoying blocking effects-the artificial rectangular discontinuities in the decoded images. Many powerful postprocessing algorithms have been developed to remove the blocking effects. However, all but the simplest algorithms can be too complex for real-time applications, such as video decoding. We propose an adaptive and easy-to-implement algorithm that can removes the artificial discontinuities. This algorithm contains two steps, firstly, to perform a fast linear smoothing of the block edge's pixel by average value replacement strategy, the next one, by comparing the variance that is derived from the difference of the processed image with a reasonable threshold, to determine whether the first step should stop or not. Experiments have proved that this algorithm can quickly remove the artificial discontinuities without destroying the key information of the decoded images, it is robust to different images and transform strategy.
Xu, Guanlong; Zhang, Xuxiao; Sun, Yipeng; Liu, Qinfang; Sun, Honglei; Xiong, Xin; Jiang, Ming; He, Qiming; Wang, Yu; Pu, Juan; Guo, Xin; Yang, Hanchun; Liu, Jinhua
2016-01-01
The PA-X protein is a fusion protein incorporating the N-terminal 191 amino acids of the PA protein with a short C-terminal sequence encoded by an overlapping ORF (X-ORF) in segment 3 that is accessed by + 1 ribosomal frameshifting, and this X-ORF exists in either full length or a truncated form (either 61-or 41-condons). Genetic evolution analysis indicates that all swine influenza viruses (SIVs) possessed full-length PA-X prior to 1985, but since then SIVs with truncated PA-X have gradually increased and become dominant, implying that truncation of this protein may contribute to the adaptation of influenza virus in pigs. To verify this hypothesis, we constructed PA-X extended viruses in the background of a "triple-reassortment" H1N2 SIV with truncated PA-X, and evaluated their biological characteristics in vitro and in vivo. Compared with full-length PA-X, SIV with truncated PA-X had increased viral replication in porcine cells and swine respiratory tissues, along with enhanced pathogenicity, replication and transmissibility in pigs. Furthermore, we found that truncation of PA-X improved the inhibition of IFN-I mRNA expression. Hereby, our results imply that truncation of PA-X may contribute to the adaptation of SIV in pigs. PMID:26912401
Xu, Guanlong; Zhang, Xuxiao; Sun, Yipeng; Liu, Qinfang; Sun, Honglei; Xiong, Xin; Jiang, Ming; He, Qiming; Wang, Yu; Pu, Juan; Guo, Xin; Yang, Hanchun; Liu, Jinhua
2016-01-01
The PA-X protein is a fusion protein incorporating the N-terminal 191 amino acids of the PA protein with a short C-terminal sequence encoded by an overlapping ORF (X-ORF) in segment 3 that is accessed by + 1 ribosomal frameshifting, and this X-ORF exists in either full length or a truncated form (either 61-or 41-condons). Genetic evolution analysis indicates that all swine influenza viruses (SIVs) possessed full-length PA-X prior to 1985, but since then SIVs with truncated PA-X have gradually increased and become dominant, implying that truncation of this protein may contribute to the adaptation of influenza virus in pigs. To verify this hypothesis, we constructed PA-X extended viruses in the background of a “triple-reassortment” H1N2 SIV with truncated PA-X, and evaluated their biological characteristics in vitro and in vivo. Compared with full-length PA-X, SIV with truncated PA-X had increased viral replication in porcine cells and swine respiratory tissues, along with enhanced pathogenicity, replication and transmissibility in pigs. Furthermore, we found that truncation of PA-X improved the inhibition of IFN-I mRNA expression. Hereby, our results imply that truncation of PA-X may contribute to the adaptation of SIV in pigs. PMID:26912401
Synthetic aperture radar signal data compression using block adaptive quantization
NASA Technical Reports Server (NTRS)
Kuduvalli, Gopinath; Dutkiewicz, Melanie; Cumming, Ian
1994-01-01
This paper describes the design and testing of an on-board SAR signal data compression algorithm for ESA's ENVISAT satellite. The Block Adaptive Quantization (BAQ) algorithm was selected, and optimized for the various operational modes of the ASAR instrument. A flexible BAQ scheme was developed which allows a selection of compression ratio/image quality trade-offs. Test results show the high quality of the SAR images processed from the reconstructed signal data, and the feasibility of on-board implementation using a single ASIC.
Parallel Block Structured Adaptive Mesh Refinement on Graphics Processing Units
Beckingsale, D. A.; Gaudin, W. P.; Hornung, R. D.; Gunney, B. T.; Gamblin, T.; Herdman, J. A.; Jarvis, S. A.
2014-11-17
Block-structured adaptive mesh refinement is a technique that can be used when solving partial differential equations to reduce the number of zones necessary to achieve the required accuracy in areas of interest. These areas (shock fronts, material interfaces, etc.) are recursively covered with finer mesh patches that are grouped into a hierarchy of refinement levels. Despite the potential for large savings in computational requirements and memory usage without a corresponding reduction in accuracy, AMR adds overhead in managing the mesh hierarchy, adding complex communication and data movement requirements to a simulation. In this paper, we describe the design and implementation of a native GPU-based AMR library, including: the classes used to manage data on a mesh patch, the routines used for transferring data between GPUs on different nodes, and the data-parallel operators developed to coarsen and refine mesh data. We validate the performance and accuracy of our implementation using three test problems and two architectures: an eight-node cluster, and over four thousand nodes of Oak Ridge National Laboratory’s Titan supercomputer. Our GPU-based AMR hydrodynamics code performs up to 4.87× faster than the CPU-based implementation, and has been scaled to over four thousand GPUs using a combination of MPI and CUDA.
MR Image Reconstruction Using Block Matching and Adaptive Kernel Methods
Schmidt, Johannes F. M.; Santelli, Claudio; Kozerke, Sebastian
2016-01-01
An approach to Magnetic Resonance (MR) image reconstruction from undersampled data is proposed. Undersampling artifacts are removed using an iterative thresholding algorithm applied to nonlinearly transformed image block arrays. Each block array is transformed using kernel principal component analysis where the contribution of each image block to the transform depends in a nonlinear fashion on the distance to other image blocks. Elimination of undersampling artifacts is achieved by conventional principal component analysis in the nonlinear transform domain, projection onto the main components and back-mapping into the image domain. Iterative image reconstruction is performed by interleaving the proposed undersampling artifact removal step and gradient updates enforcing consistency with acquired k-space data. The algorithm is evaluated using retrospectively undersampled MR cardiac cine data and compared to k-t SPARSE-SENSE, block matching with spatial Fourier filtering and k-t ℓ1-SPIRiT reconstruction. Evaluation of image quality and root-mean-squared-error (RMSE) reveal improved image reconstruction for up to 8-fold undersampled data with the proposed approach relative to k-t SPARSE-SENSE, block matching with spatial Fourier filtering and k-t ℓ1-SPIRiT. In conclusion, block matching and kernel methods can be used for effective removal of undersampling artifacts in MR image reconstruction and outperform methods using standard compressed sensing and ℓ1-regularized parallel imaging methods. PMID:27116675
MR Image Reconstruction Using Block Matching and Adaptive Kernel Methods.
Schmidt, Johannes F M; Santelli, Claudio; Kozerke, Sebastian
2016-01-01
An approach to Magnetic Resonance (MR) image reconstruction from undersampled data is proposed. Undersampling artifacts are removed using an iterative thresholding algorithm applied to nonlinearly transformed image block arrays. Each block array is transformed using kernel principal component analysis where the contribution of each image block to the transform depends in a nonlinear fashion on the distance to other image blocks. Elimination of undersampling artifacts is achieved by conventional principal component analysis in the nonlinear transform domain, projection onto the main components and back-mapping into the image domain. Iterative image reconstruction is performed by interleaving the proposed undersampling artifact removal step and gradient updates enforcing consistency with acquired k-space data. The algorithm is evaluated using retrospectively undersampled MR cardiac cine data and compared to k-t SPARSE-SENSE, block matching with spatial Fourier filtering and k-t ℓ1-SPIRiT reconstruction. Evaluation of image quality and root-mean-squared-error (RMSE) reveal improved image reconstruction for up to 8-fold undersampled data with the proposed approach relative to k-t SPARSE-SENSE, block matching with spatial Fourier filtering and k-t ℓ1-SPIRiT. In conclusion, block matching and kernel methods can be used for effective removal of undersampling artifacts in MR image reconstruction and outperform methods using standard compressed sensing and ℓ1-regularized parallel imaging methods. PMID:27116675
Bosson, Maël; Grudinin, Sergei; Redon, Stephane
2013-03-01
We present a novel Block-Adaptive Quantum Mechanics (BAQM) approach to interactive quantum chemistry. Although quantum chemistry models are known to be computationally demanding, we achieve interactive rates by focusing computational resources on the most active parts of the system. BAQM is based on a divide-and-conquer technique and constrains some nucleus positions and some electronic degrees of freedom on the fly to simplify the simulation. As a result, each time step may be performed significantly faster, which in turn may accelerate attraction to the neighboring local minima. By applying our approach to the nonself-consistent Atom Superposition and Electron Delocalization Molecular Orbital theory, we demonstrate interactive rates and efficient virtual prototyping for systems containing more than a thousand of atoms on a standard desktop computer. PMID:23108532
Block-adaptive filtering and its application to seismic-event detection
Clark, G.A.
1981-04-01
Block digital filtering involves the calculation of a block or finite set of filter output samples from a block of input samples. The motivation for block processing arises from computational advantages of the technique. Block filters take good advantage of parallel processing architectures, which are becoming more and more attractive with the advent of very large scale integrated (VLSI) circuits. This thesis extends the block technique to Wiener and adaptive filters, both of which are statistical filters. The key ingredient to this extension turns out to be the definition of a new performance index, block mean square error (BMSE), which combines the well known sum square error (SSE) and mean square error (MSE). A block adaptive filtering procedure is derived in which the filter coefficients are adjusted once per each output block in accordance with a generalized block least mean-square (BLMS) algorithm. Convergence properties of the BLMS algorithm are studied, including conditions for guaranteed convergence, convergence speed, and convergence accuracy. Simulation examples are given for clarity. Convergence properties of the BLMS and LMS algorithms are analyzed and compared. They are shown to be analogous, and under the proper circumstances, equivalent. The block adaptive filter was applied to the problem of detecting small seismic events in microseismic background noise. The predictor outperformed the world-wide standardized seismograph network (WWSSN) seismometers in improving signal-to-noise ratio (SNR).
A structured multi-block solution-adaptive mesh algorithm with mesh quality assessment
NASA Technical Reports Server (NTRS)
Ingram, Clint L.; Laflin, Kelly R.; Mcrae, D. Scott
1995-01-01
The dynamic solution adaptive grid algorithm, DSAGA3D, is extended to automatically adapt 2-D structured multi-block grids, including adaption of the block boundaries. The extension is general, requiring only input data concerning block structure, connectivity, and boundary conditions. Imbedded grid singular points are permitted, but must be prevented from moving in space. Solutions for workshop cases 1 and 2 are obtained on multi-block grids and illustrate both increased resolution of and alignment with the solution. A mesh quality assessment criteria is proposed to determine how well a given mesh resolves and aligns with the solution obtained upon it. The criteria is used to evaluate the grid quality for solutions of workshop case 6 obtained on both static and dynamically adapted grids. The results indicate that this criteria shows promise as a means of evaluating resolution.
Block-structured adaptive mesh refinement - theory, implementation and application
Deiterding, Ralf
2011-01-01
Structured adaptive mesh refinement (SAMR) techniques can enable cutting-edge simulations of problems governed by conservation laws. Focusing on the strictly hyperbolic case, these notes explain all algorithmic and mathematical details of a technically relevant implementation tailored for distributed memory computers. An overview of the background of commonly used finite volume discretizations for gas dynamics is included and typical benchmarks to quantify accuracy and performance of the dynamically adaptive code are discussed. Large-scale simulations of shock-induced realistic combustion in non-Cartesian geometry and shock-driven fluid-structure interaction with fully coupled dynamic boundary motion demonstrate the applicability of the discussed techniques for complex scenarios.
The successively temporal error concealment algorithm using error-adaptive block matching principle
NASA Astrophysics Data System (ADS)
Lee, Yu-Hsuan; Wu, Tsai-Hsing; Chen, Chao-Chyun
2014-09-01
Generally, the temporal error concealment (TEC) adopts the blocks around the corrupted block (CB) as the search pattern to find the best-match block in previous frame. Once the CB is recovered, it is referred to as the recovered block (RB). Although RB can be the search pattern to find the best-match block of another CB, RB is not the same as its original block (OB). The error between the RB and its OB limits the performance of TEC. The successively temporal error concealment (STEC) algorithm is proposed to alleviate this error. The STEC procedure consists of tier-1 and tier-2. The tier-1 divides a corrupted macroblock into four corrupted 8 × 8 blocks and generates a recovering order for them. The corrupted 8 × 8 block with the first place of recovering order is recovered in tier-1, and remaining 8 × 8 CBs are recovered in tier-2 along the recovering order. In tier-2, the error-adaptive block matching principle (EA-BMP) is proposed for the RB as the search pattern to recover remaining corrupted 8 × 8 blocks. The proposed STEC outperforms sophisticated TEC algorithms on average PSNR by 0.3 dB on the packet error rate of 20% at least.
Adaptive stereo medical image watermarking using non-corresponding blocks.
Mohaghegh, H; Karimi, N; Soroushmehr, S M R; Samavi, S; Najarian, K
2015-08-01
Today with the advent of technology in different medical imaging fields, the use of stereoscopic images has increased. Furthermore, with the rapid growth in telemedicine for remote diagnosis, treatment, and surgery, there is a need for watermarking. This is for copyright protection and tracking of digital media. Also, the efficient use of bandwidth for transmission of such data is another concern. In this paper an adaptive watermarking scheme is proposed that considers human visual system in depth perception. Our proposed scheme modifies maximum singular values of wavelet coefficients of stereo pair for embedding watermark bits. Experimental results show high 3D visual quality of watermarked video frames. Moreover, comparison with a compatible state of the art method shows that the proposed method is highly robust against attacks such as AWGN, salt and pepper noise, and JPEG compression. PMID:26737224
NASA Technical Reports Server (NTRS)
Linares, Irving; Mersereau, Russell M.; Smith, Mark J. T.
1994-01-01
Two representative sample images of Band 4 of the Landsat Thematic Mapper are compressed with the JPEG algorithm at 8:1, 16:1 and 24:1 Compression Ratios for experimental browsing purposes. We then apply the Optimal PSNR Estimated Spectra Adaptive Postfiltering (ESAP) algorithm to reduce the DCT blocking distortion. ESAP reduces the blocking distortion while preserving most of the image's edge information by adaptively postfiltering the decoded image using the block's spectral information already obtainable from each block's DCT coefficients. The algorithm iteratively applied a one dimensional log-sigmoid weighting function to the separable interpolated local block estimated spectra of the decoded image until it converges to the optimal PSNR with respect to the original using a 2-D steepest ascent search. Convergence is obtained in a few iterations for integer parameters. The optimal logsig parameters are transmitted to the decoder as a negligible byte of overhead data. A unique maxima is guaranteed due to the 2-D asymptotic exponential overshoot shape of the surface generated by the algorithm. ESAP is based on a DFT analysis of the DCT basis functions. It is implemented with pixel-by-pixel spatially adaptive separable FIR postfilters. PSNR objective improvements between 0.4 to 0.8 dB are shown together with their corresponding optimal PSNR adaptive postfiltered images.
Parallel architectures for iterative methods on adaptive, block structured grids
NASA Technical Reports Server (NTRS)
Gannon, D.; Vanrosendale, J.
1983-01-01
A parallel computer architecture well suited to the solution of partial differential equations in complicated geometries is proposed. Algorithms for partial differential equations contain a great deal of parallelism. But this parallelism can be difficult to exploit, particularly on complex problems. One approach to extraction of this parallelism is the use of special purpose architectures tuned to a given problem class. The architecture proposed here is tuned to boundary value problems on complex domains. An adaptive elliptic algorithm which maps effectively onto the proposed architecture is considered in detail. Two levels of parallelism are exploited by the proposed architecture. First, by making use of the freedom one has in grid generation, one can construct grids which are locally regular, permitting a one to one mapping of grids to systolic style processor arrays, at least over small regions. All local parallelism can be extracted by this approach. Second, though there may be a regular global structure to the grids constructed, there will be parallelism at this level. One approach to finding and exploiting this parallelism is to use an architecture having a number of processor clusters connected by a switching network. The use of such a network creates a highly flexible architecture which automatically configures to the problem being solved.
Europlanet IDIS: Adapting existing VO building blocks to Planetary Sciences
NASA Astrophysics Data System (ADS)
Cecconi, Baptiste; Jacquey, Christian; Erard, Stéphane; Le Sidaner, Pierre; Andre, Nicolas; Bourrel, Nataliya; Berthier, Jerome; Gangloff, Michel
2012-07-01
IDIS (Integrated and Distributed Information System) is part of the Europlanet project. Its purpose is to develop a prototype of a planetology Virtual Observatory (VO). In the frame of its participation to this project, and in collaboration with VO-Paris (Virtual Observatory Paris Data Centre), the CDPP (Data Centre for Plasma Physics, based in Toulouse) has developed a data model to describe the wide variety of data products that can be found in the planetology community, which includes a wide variety of science thematics such as plasma physics, planetary surfaces, interiors, atmospheres or small bodies. This data model is making extensive use of existing standards provided by various groups (IVOA, IPDA, SPASE...) and its scope is to describe the scientific content of datasets, in order to be able to locate and retrieve data files corresponding to a given request. Two generic protocols has been identified for data exchange: PDAP (Planetary Data Access Protocol), developed by IPDA and Obs-TAP (Observation Table Access Protocol), developed by IVOA. In this latter case, Obs-TAP has been adapted to better fit to the planetology community; this protocol is called IDIS-TAP. The data model and the protocols are now tested in collaboration with VO-Paris and other Europlanet IDIS partners. The EuroPlaNet-RI project is funded by the European Commission under the 7th Framework Program, grant 228319 "Capacities Specific Programme".
An object-oriented approach for parallel self adaptive mesh refinement on block structured grids
NASA Technical Reports Server (NTRS)
Lemke, Max; Witsch, Kristian; Quinlan, Daniel
1993-01-01
Self-adaptive mesh refinement dynamically matches the computational demands of a solver for partial differential equations to the activity in the application's domain. In this paper we present two C++ class libraries, P++ and AMR++, which significantly simplify the development of sophisticated adaptive mesh refinement codes on (massively) parallel distributed memory architectures. The development is based on our previous research in this area. The C++ class libraries provide abstractions to separate the issues of developing parallel adaptive mesh refinement applications into those of parallelism, abstracted by P++, and adaptive mesh refinement, abstracted by AMR++. P++ is a parallel array class library to permit efficient development of architecture independent codes for structured grid applications, and AMR++ provides support for self-adaptive mesh refinement on block-structured grids of rectangular non-overlapping blocks. Using these libraries, the application programmers' work is greatly simplified to primarily specifying the serial single grid application and obtaining the parallel and self-adaptive mesh refinement code with minimal effort. Initial results for simple singular perturbation problems solved by self-adaptive multilevel techniques (FAC, AFAC), being implemented on the basis of prototypes of the P++/AMR++ environment, are presented. Singular perturbation problems frequently arise in large applications, e.g. in the area of computational fluid dynamics. They usually have solutions with layers which require adaptive mesh refinement and fast basic solvers in order to be resolved efficiently.
NASA Astrophysics Data System (ADS)
Brüggemann, Matthias; Kays, Rüdiger; Springer, Paul; Erdler, Oliver
2015-03-01
In this paper we present a combination of block-matching and differential motion field estimation. We initialize the motion field using a predictive hierarchical block-matching approach. This vector field is refined by a pixel-recursive differential motion estimation method. We integrate image warping and adaptive filter kernels into the Horn and Schunck differential optical flow estimation approach to break the block structure of the initial correspondence vector fields and compute motion field updates to fulfill the smoothness constraint inside motion boundaries. The influence of occlusion areas is reduced by integrating an in-the-loop occlusion detection and adjusting the adaptive filter weights in the iteration process. We integrate the combined estimation into a hierarchical multi-scale framework. The refined motion on the current scale is upscaled and used as prediction for block-matching motion estimation on the next scale. With the proposed system we are able to combine the advantages of block-matching and differential motion estimation and achieve a dense vector field with floating point precision even for large motion.
Adenine nucleoside diphosphates block adaptation of mechanoelectrical transduction in hair cells.
Gillespie, P G; Hudspeth, A J
1993-04-01
By adapting to sustained stimuli, hair cells in the internal ear retain their sensitivity to minute transient displacements. Because one model for adaptation asserts that this process is mediated by a myosin isozyme, we reasoned that we should be able to arrest adaptation by interfering with myosin's ATPase cycle though introduction of ADP into hair cells. During tight-seal, whole-cell recordings of transduction currents in cells isolated from bullfrog (Rana catesbeiana) sacculus, dialysis with 5-25 mM ADP gave variable results. In half of the cells examined, the rate of adaptation remained unchanged or even increased; adaptation was blocked in the remaining cells. Because we suspected that the variable effect of ADP resulted from the conversion of ADP to ATP by adenylate kinase, we employed the ADP analog adenosine 5'-[beta-thio]diphosphate (ADP[beta S]), which is not a substrate for adenylate kinase. Adaptation consistently disappeared in the presence of 1-10 mM ADP[beta S]; in addition, the transduction channels' open probability at rest grew from approximately 0.1 to 0.8 or more. Both effects could be reversed by 2 mM ATP. When used in conjunction with the adenylate kinase inhibitor P1,P5-bis(5'-adenosyl) pentaphosphate (Ap5A), ADP had effects similar to those of ADP[beta S]. These results suggest that adaptation by hair cells involves adenine nucleotides, and they lend support to the hypothesis that the adaptation process is powered by a myosin motor. PMID:8464880
Low bit rates image compression via adaptive block downsampling and super resolution
NASA Astrophysics Data System (ADS)
Chen, Honggang; He, Xiaohai; Ma, Minglang; Qing, Linbo; Teng, Qizhi
2016-01-01
A low bit rates image compression framework based on adaptive block downsampling and super resolution (SR) was presented. At the encoder side, the downsampling mode and quantization mode of each 16×16 macroblock are determined adaptively using the ratio distortion optimization method, then the downsampled macroblocks are compressed by the standard JPEG. At the decoder side, the sparse representation-based SR algorithm is applied to recover full resolution macroblocks from decoded blocks. The experimental results show that the proposed framework outperforms the standard JPEG and the state-of-the-art downsampling-based compression methods in terms of both subjective and objective comparisons. Specifically, the peak signal-to-noise ratio gain of the proposed framework over JPEG reaches up to 2 to 4 dB at low bit rates, and the critical bit rate to JPEG is raised to about 2.3 bits per pixel. Moreover, the proposed framework can be extended to other block-based compression schemes.
CRASH: A BLOCK-ADAPTIVE-MESH CODE FOR RADIATIVE SHOCK HYDRODYNAMICS-IMPLEMENTATION AND VERIFICATION
Van der Holst, B.; Toth, G.; Sokolov, I. V.; Myra, E. S.; Fryxell, B.; Drake, R. P.; Powell, K. G.; Holloway, J. P.; Stout, Q.; Adams, M. L.; Morel, J. E.; Karni, S.
2011-06-01
We describe the Center for Radiative Shock Hydrodynamics (CRASH) code, a block-adaptive-mesh code for multi-material radiation hydrodynamics. The implementation solves the radiation diffusion model with a gray or multi-group method and uses a flux-limited diffusion approximation to recover the free-streaming limit. Electrons and ions are allowed to have different temperatures and we include flux-limited electron heat conduction. The radiation hydrodynamic equations are solved in the Eulerian frame by means of a conservative finite-volume discretization in either one-, two-, or three-dimensional slab geometry or in two-dimensional cylindrical symmetry. An operator-split method is used to solve these equations in three substeps: (1) an explicit step of a shock-capturing hydrodynamic solver; (2) a linear advection of the radiation in frequency-logarithm space; and (3) an implicit solution of the stiff radiation diffusion, heat conduction, and energy exchange. We present a suite of verification test problems to demonstrate the accuracy and performance of the algorithms. The applications are for astrophysics and laboratory astrophysics. The CRASH code is an extension of the Block-Adaptive Tree Solarwind Roe Upwind Scheme (BATS-R-US) code with a new radiation transfer and heat conduction library and equation-of-state and multi-group opacity solvers. Both CRASH and BATS-R-US are part of the publicly available Space Weather Modeling Framework.
CRASH: A Block-adaptive-mesh Code for Radiative Shock Hydrodynamics—Implementation and Verification
NASA Astrophysics Data System (ADS)
van der Holst, B.; Tóth, G.; Sokolov, I. V.; Powell, K. G.; Holloway, J. P.; Myra, E. S.; Stout, Q.; Adams, M. L.; Morel, J. E.; Karni, S.; Fryxell, B.; Drake, R. P.
2011-06-01
We describe the Center for Radiative Shock Hydrodynamics (CRASH) code, a block-adaptive-mesh code for multi-material radiation hydrodynamics. The implementation solves the radiation diffusion model with a gray or multi-group method and uses a flux-limited diffusion approximation to recover the free-streaming limit. Electrons and ions are allowed to have different temperatures and we include flux-limited electron heat conduction. The radiation hydrodynamic equations are solved in the Eulerian frame by means of a conservative finite-volume discretization in either one-, two-, or three-dimensional slab geometry or in two-dimensional cylindrical symmetry. An operator-split method is used to solve these equations in three substeps: (1) an explicit step of a shock-capturing hydrodynamic solver; (2) a linear advection of the radiation in frequency-logarithm space; and (3) an implicit solution of the stiff radiation diffusion, heat conduction, and energy exchange. We present a suite of verification test problems to demonstrate the accuracy and performance of the algorithms. The applications are for astrophysics and laboratory astrophysics. The CRASH code is an extension of the Block-Adaptive Tree Solarwind Roe Upwind Scheme (BATS-R-US) code with a new radiation transfer and heat conduction library and equation-of-state and multi-group opacity solvers. Both CRASH and BATS-R-US are part of the publicly available Space Weather Modeling Framework.
CRASH: A Block-Adaptive-Mesh Code for Radiative Shock Hydrodynamics
NASA Astrophysics Data System (ADS)
van der Holst, B.; Toth, G.; Sokolov, I. V.; Powell, K. G.; Holloway, J. P.; Myra, E. S.; Stout, Q.; Adams, M. L.; Morel, J. E.; Drake, R. P.
2011-01-01
We describe the CRASH (Center for Radiative Shock Hydrodynamics) code, a block adaptive mesh code for multi-material radiation hydrodynamics. The implementation solves the radiation diffusion model with the gray or multigroup method and uses a flux limited diffusion approximation to recover the free-streaming limit. The electrons and ions are allowed to have different temperatures and we include a flux limited electron heat conduction. The radiation hydrodynamic equations are solved in the Eulerian frame by means of a conservative finite volume discretization in either one, two, or three-dimensional slab geometry or in two-dimensional cylindrical symmetry. An operator split method is used to solve these equations in three substeps: (1) solve the hydrodynamic equations with shock-capturing schemes, (2) a linear advection of the radiation in frequency-logarithm space, and (3) an implicit solve of the stiff radiation diffusion, heat conduction, and energy exchange. We present a suite of verification test problems to demonstrate the accuracy and performance of the algorithms. The CRASH code is an extension of the Block-Adaptive Tree Solarwind Roe Upwind Scheme (BATS-R-US) code with this new radiation transfer and heat conduction library and equation-of-state and multigroup opacity solvers. Both CRASH and BATS-R-US are part of the publicly available Space Weather Modeling Framework (SWMF).
NASA Technical Reports Server (NTRS)
Rost, Martin C.; Sayood, Khalid
1991-01-01
A method for efficiently coding natural images using a vector-quantized variable-blocksized transform source coder is presented. The method, mixture block coding (MBC), incorporates variable-rate coding by using a mixture of discrete cosine transform (DCT) source coders. Which coders are selected to code any given image region is made through a threshold driven distortion criterion. In this paper, MBC is used in two different applications. The base method is concerned with single-pass low-rate image data compression. The second is a natural extension of the base method which allows for low-rate progressive transmission (PT). Since the base method adapts easily to progressive coding, it offers the aesthetic advantage of progressive coding without incorporating extensive channel overhead. Image compression rates of approximately 0.5 bit/pel are demonstrated for both monochrome and color images.
Block structured adaptive mesh and time refinement for hybrid, hyperbolic + N-body systems
NASA Astrophysics Data System (ADS)
Miniati, Francesco; Colella, Phillip
2007-11-01
We present a new numerical algorithm for the solution of coupled collisional and collisionless systems, based on the block structured adaptive mesh and time refinement strategy (AMR). We describe the issues associated with the discretization of the system equations and the synchronization of the numerical solution on the hierarchy of grid levels. We implement a code based on a higher order, conservative and directionally unsplit Godunov’s method for hydrodynamics; a symmetric, time centered modified symplectic scheme for collisionless component; and a multilevel, multigrid relaxation algorithm for the elliptic equation coupling the two components. Numerical results that illustrate the accuracy of the code and the relative merit of various implemented schemes are also presented.
Watanabe, Yurina; Yoshizaki, Kazuhito
2014-10-01
This study aimed to investigate the generality of conflict adaptation associated with block-wise conflict frequency between two types of stimulus scripts (Kanji and Hiragana). To this end, we examined whether the modulation of the compatibility effect with one type of script depending on block-wise conflict frequency (75% versus 25% generalized to the other type of script whose block-wise conflict frequency was kept constant (50%), using the Spatial Stroop task. In Experiment 1, 16 participants were required to identify the target orientation (up or down) presented in the upper or lower visual-field. The results showed that block-wise conflict adaptation with one type of stimulus script generalized to the other. The procedure in Experiment 2 was the same as that in Experiment 1, except that the presentation location differed between the two types of stimulus scripts. We did not find a generalization from one script to the other. These results suggest that presentation location is a critical factor contributing to the generality of block-wise conflict adaptation. PMID:25486848
Watanabe, Yurina; Yoshizaki, Kazuhito
2014-10-01
This study aimed to investigate the generality of conflict adaptation associated with block-wise conflict frequency between two types of stimulus scripts (Kanji and Hiragana). To this end, we examined whether the modulation of the compatibility effect with one type of script depending on block-wise conflict frequency (75% versus 25% generalized to the other type of script whose block-wise conflict frequency was kept constant (50%), using the Spatial Stroop task. In Experiment 1, 16 participants were required to identify the target orientation (up or down) presented in the upper or lower visual-field. The results showed that block-wise conflict adaptation with one type of stimulus script generalized to the other. The procedure in Experiment 2 was the same as that in Experiment 1, except that the presentation location differed between the two types of stimulus scripts. We did not find a generalization from one script to the other. These results suggest that presentation location is a critical factor contributing to the generality of block-wise conflict adaptation. PMID:25508979
NASA Astrophysics Data System (ADS)
Schneider, Martin; Kellermann, Walter
2016-01-01
Acoustic echo cancellation (AEC) is a well-known application of adaptive filters in communication acoustics. To implement AEC for multichannel reproduction systems, powerful adaptation algorithms like the generalized frequency-domain adaptive filtering (GFDAF) algorithm are required for satisfactory convergence behavior. In this paper, the GFDAF algorithm is rigorously derived as an approximation of the block recursive least-squares (RLS) algorithm. Thereby, the original formulation of the GFDAF algorithm is generalized while avoiding an error that has been in the original derivation. The presented algorithm formulation is applied to pruned transform-domain loudspeaker-enclosure-microphone models in a mathematically consistent manner. Such pruned models have recently been proposed to cope with the tremendous computational demands of massive multichannel AEC. Beyond its generalization, a regularization of the GFDAF is shown to have a close relation to the well-known block least-mean-squares algorithm.
Ray, Jaideep; Lefantzi, Sophia; Najm, Habib N.; Kennedy, Christopher A.
2006-01-01
Block-structured adaptively refined meshes (SAMR) strive for efficient resolution of partial differential equations (PDEs) solved on large computational domains by clustering mesh points only where required by large gradients. Previous work has indicated that fourth-order convergence can be achieved on such meshes by using a suitable combination of high-order discretizations, interpolations, and filters and can deliver significant computational savings over conventional second-order methods at engineering error tolerances. In this paper, we explore the interactions between the errors introduced by discretizations, interpolations and filters. We develop general expressions for high-order discretizations, interpolations, and filters, in multiple dimensions, using a Fourier approach, facilitating the high-order SAMR implementation. We derive a formulation for the necessary interpolation order for given discretization and derivative orders. We also illustrate this order relationship empirically using one and two-dimensional model problems on refined meshes. We study the observed increase in accuracy with increasing interpolation order. We also examine the empirically observed order of convergence, as the effective resolution of the mesh is increased by successively adding levels of refinement, with different orders of discretization, interpolation, or filtering.
Despeckling algorithm on ultrasonic image using adaptive block-based singular value decomposition
NASA Astrophysics Data System (ADS)
Sae-Bae, Napa; Udomhunsakul, Somkait
2008-03-01
Speckle noise reduction is an important technique to enhance the quality of ultrasonic image. In this paper, a despeckling algorithm based on an adaptive block-based singular value decomposition filtering (BSVD) applied on ultrasonic images is presented. Instead of applying BSVD directly to ultrasonic image, we propose to apply BSVD on the noisy edge image version obtained from the difference between the logarithmic transformations of the original image and blur image version of its. The recovered image is performed by combining the speckle noise-free edge image with blur image version of its. Finally, exponential transformation is applied in order to get the reconstructed image. To evaluate our algorithm compared with well-know algorithms such as Lee filter, Kuan filter, Homomorphic Wiener filter, median filter and wavelet soft thresholding, four image quality measurements, which are Mean Square Error (MSE), Signal to MSE (S/MSE), Edge preservation (β), and Correlation measurement (ρ), are used. From the results, it clearly shows that the proposed algorithm outperforms other methods in terms of quantitative and subjective assessments.
NASA Astrophysics Data System (ADS)
Ravindran, Prashaanth
The unstable nature of detonation waves is a result of the critical relationship between the hydrodynamic shock and the chemical reactions sustaining the shock. A perturbative analysis of the critical point is quite challenging due to the multiple spatio-temporal scales involved along with the non-linear nature of the shock-reaction mechanism. The author's research attempts to provide detailed resolution of the instabilities at the shock front. Another key aspect of the present research is to develop an understanding of the causality between the non-linear dynamics of the front and the eventual breakdown of the sub-structures. An accurate numerical simulation of detonation waves requires a very efficient solution of the Euler equations in conservation form with detailed, non-equilibrium chemistry. The difference in the flow and reaction length scales results in very stiff source terms, requiring the problem to be solved with adaptive mesh refinement. For this purpose, Berger-Colella's block-structured adaptive mesh refinement (AMR) strategy has been developed and applied to time-explicit finite volume methods. The block-structured technique uses a hierarchy of parent-child sub-grids, integrated recursively over time. One novel approach to partition the problem within a large supercomputer was the use of modified Peano-Hilbert space filling curves. The AMR framework was merged with CLAWPACK, a package providing finite volume numerical methods tailored for wave-propagation problems. The stiffness problem is bypassed by using a 1st order Godunov or a 2nd order Strang splitting technique, where the flow variables and source terms are integrated independently. A linearly explicit fourth-order Runge-Kutta integrator is used for the flow, and an ODE solver was used to overcome the numerical stiffness. Second-order spatial resolution is obtained by using a second-order Roe-HLL scheme with the inclusion of numerical viscosity to stabilize the solution near the discontinuity
NASA Astrophysics Data System (ADS)
Masmoudi, Atef; Zouari, Sonia; Ghribi, Abdelaziz
2015-11-01
We propose a new adaptive block-wise lossless image compression algorithm, which is based on the so-called alphabet reduction scheme combined with an adaptive arithmetic coding (AC). This new encoding algorithm is particularly efficient for lossless compression of images with sparse and locally sparse histograms. AC is a very efficient technique for lossless data compression and produces a rate that is close to the entropy; however, a compression performance loss occurs when encoding images or blocks with a limited number of active symbols by comparison with the number of symbols in the nominal alphabet, which consists in the amplification of the zero frequency problem. Generally, most methods add one to the frequency count of each symbol from the nominal alphabet, which leads to a statistical model distortion, and therefore reduces the efficiency of the AC. The aim of this work is to overcome this drawback by assigning to each image block the smallest possible set including all the existing symbols called active symbols. This is an alternative of using the nominal alphabet when applying the conventional arithmetic encoders. We show experimentally that the proposed method outperforms several lossless image compression encoders and standards including the conventional arithmetic encoders, JPEG2000, and JPEG-LS.
Adaption of the Cytokinesis-Block Micronucleus Cytome Assay for Improved Triage Biodosimetry.
Beinke, C; Port, M; Riecke, A; Ruf, C G; Abend, M
2016-05-01
The purpose of this work was to adapt a more advanced form of the cytokinesis-block micronucleus (CBMN) cytome assay for triage biodosimetry in the event of a mass casualty radiation incident. We modified scoring procedures for the CBMN cytome assay to optimize field deployability, dose range, accuracy, speed, economy, simplicity and stability. Peripheral blood of 20 donors was irradiated in vitro (0-6 Gy X ray, maximum photon energy 240 keV) and processed for CBMN. Initially, we assessed two manual scoring strategies for accuracy: 1. Conventional scoring, comprised of micronucleus (MN) frequency per 1,000 binucleated (BN) cells (MN/1,000 BN cells); and 2. Evaluation of 1,000, 2,000 and 3,000 cells in total and different cellular subsets based on MN formation and proliferation (e.g., BN cells with and without MN, mononucleated cells). We used linear and logistic regression models to identify the cellular subsets related closest to dose with the best discrimination ability among different doses/dose categories. We validated the most promising subsets and their combinations with 16 blind samples covering a dose range of 0-8.3 Gy. Linear dose-response relationships comparable to the conventional CBMN assay (r(2) = 0.86) were found for BN cells with MN (r(2) = 0.84) and BN cells without MN (r(2) = 0.84). Models of combined cell counts (CCC) of BN cells with and without MN (BN(+MN) and BN(-MN)) with mononucleated cells (Mono) improved this relationship (r(2) = 0.92). Conventional CBMN discriminated dose categories up to 3 Gy with a concordance between 0.96-1.0 upon scoring 1,000 total cells. In 1,000 BN cells, concordances were observed for conventional CBMN up to 4 Gy as well as BN(+MN) or BN(-MN) (about 0.85). At doses of 4-6 Gy, the concordance of conventional CBMN, BN(+MN) and BN(-MN) declined (about 0.55). We found about 20% higher concordance and more precise dose estimates of irradiated and blinded samples for CCC (Mono + BN(+MN)) after scoring 1,000 total cells
Investigation of Truncated Waveguides
NASA Technical Reports Server (NTRS)
Lourie, Nathan P.; Chuss, David T.; Henry, Ross M.; Wollack, Edward J.
2013-01-01
The design, fabrication, and performance of truncated circular and square waveguide cross-sections are presented. An emphasis is placed upon numerical and experimental validation of simple analytical formulae that describe the propagation properties of these structures. A test component, a 90-degree phase shifter, was fabricated and tested at 30 GHz. The concepts explored can be directly applied in the design, synthesis and optimization of components in the microwave to sub-millimeter wavebands.
Bite-Block Perturbation in People Who Stutter: Immediate Compensatory and Delayed Adaptive Processes
ERIC Educational Resources Information Center
Namasivayam, Aravind Kumar; van Lieshout, Pascal; De Nil, Luc
2008-01-01
This exploratory study investigated sensory-motor mechanisms in five people who stutter (PWS) and five people who do not (PNS). Lip kinematic and coordination data were recorded as they produced bi-syllabic nonwords at two rates (normal and fast) in three conditions (jaw-free, immediately after insertion of a bite-block, and after a 10-min…
NASA Astrophysics Data System (ADS)
Gutzwiller, David; Gontier, Mathieu; Demeulenaere, Alain
2014-11-01
Multi-Block structured solvers hold many advantages over their unstructured counterparts, such as a smaller memory footprint and efficient serial performance. Historically, multi-block structured solvers have not been easily adapted for use in a High Performance Computing (HPC) environment, and the recent trend towards hybrid GPU/CPU architectures has further complicated the situation. This paper will elaborate on developments and innovations applied to the NUMECA FINE/Turbo solver that have allowed near-linear scalability with real-world problems on over 250 hybrid GPU/GPU cluster nodes. Discussion will focus on the implementation of virtual partitioning and load balancing algorithms using a novel meta-block concept. This implementation is transparent to the user, allowing all pre- and post-processing steps to be performed using a simple, unpartitioned grid topology. Additional discussion will elaborate on developments that have improved parallel performance, including fully parallel I/O with the ADIOS API and the GPU porting of the computationally heavy CPUBooster convergence acceleration module. Head of HPC and Release Management, Numeca International.
Li, Chunyan; Meng, Gang; Su, Lei; Chen, Aiping; Xia, Mao; Xu, Chun; Yu, Decai; Jiang, Aiqin; Wei, Jiwu
2015-01-30
Targeting reprogrammed energy metabolism such as aerobic glycolysis is a potential strategy for cancer treatment. However, tumors exhibiting low-rate glycolysis or metabolic heterogeneity might be resistant to such treatment. We hypothesized that a therapeutic modality that drove cancer cells to high-rate glycolysis might sensitize cancer cells to interference directed against metabolic flux. In this study, we found that attenuated oncolytic measles virus Edmonston strain (MV-Edm) caused glioblastoma cells to shift to high-rate aerobic glycolysis; this adaptation was blocked by dichloroacetate (DCA), an inhibitor of glycolysis, leading to profound cell death of cancer cells but not of normal cells. DCA enhanced viral replication by mitigating mitochondrial antiviral signaling protein (MAVS)-mediated innate immune responses. In a subcutaneous glioblastoma (GBM) xenograft mouse model, low-dose MV-Edm and DCA significantly inhibited tumor growth in vivo. We found that DCA impaired glycolysis (blocking bioenergetic generation) and enhanced viral replication (increasing bioenergetic consumption), which, in combination, accelerated bioenergetic exhaustion leading to necrotic cell death. Taken together, oncolytic MV-Edm sensitized cancer cells to DCA, and in parallel, DCA promoted viral replication, thus, improving oncolysis. This novel therapeutic approach should be readily incorporated into clinical trials. PMID:25575816
An efficient second-order accurate and continuous interpolation for block-adaptive grids
NASA Astrophysics Data System (ADS)
Borovikov, Dmitry; Sokolov, Igor V.; Tóth, Gábor
2015-09-01
In this paper we present a second-order and continuous interpolation algorithm for cell-centered adaptive-mesh-refinement (AMR) grids. Continuity requirement poses a non-trivial problem at resolution changes. We develop a classification of the resolution changes, which allows us to employ efficient and simple linear interpolation in the majority of the computational domain. The algorithm is well suited for massively parallel computations. Our interpolation algorithm allows extracting jump-free interpolated data distribution along lines and surfaces within the computational domain. This capability is important for various applications, including kinetic particles tracking in three dimensional vector fields, visualization (i.e. surface extraction) and extracting variables along one-dimensional curves such as field lines, streamlines and satellite trajectories, etc. Particular examples are models for acceleration of solar energetic particles (SEPs) along magnetic field-lines. As such models are sensitive to sharp gradients and discontinuities the capability to interpolate the data from the AMR grid to be passed to the SEP model without producing false gradients numerically becomes crucial. We provide a complete description of the algorithm and make the code publicly available as a Fortran 90 library.
Ngunjiri, John M.; Ali, Ahmed; Boyaka, Prosper; Lee, Chang-Won
2015-01-01
Mutants of influenza virus that encode C-terminally truncated NS1 proteins (NS1-truncated mutants) characteristically induce high interferon responses. The dual activity of interferon in blocking virus replication and enhancing the development of adaptive immune responses makes these mutants promising as self-adjuvanting live-attenuated influenza vaccine (LAIV) candidates. Yet, among the NS1-truncated mutants, the length of NS1 is not directly correlated with the interferon-inducing efficiency, the level of attenuation, or effectiveness as LAIV. Using quantitative in vitro biologically active particle subpopulation analysis as a tool to identify potential LAIV candidates from a pool of NS1-truncated mutants, we previously predicted that a NS1-truncated mutant pc2, which was less effective as a LAIV in chickens, would be sufficiently effective as a LAIV in mammalian hosts. In this study, we confirmed that pc2 protected mice and pigs against heterologous virus challenge in terms of preventing clinical signs and reducing virus shedding. pc2 expresses a unique SLSYSINWRH motif at the C-terminus of its truncated NS1. Deletion of the SLSYSINWRH motif led to ~821-fold reduction in the peak yield of type I interferon induced in murine cells. Furthermore, replacement of the SLSYSINWRH motif with the wildtype MVKMDQAIMD sequence did not restore the interferon-inducing efficiency. The diminished interferon induction capacity in the absence of the SLSYSINWRH motif was similar to that observed in other mutants which are less effective LAIV candidates. Remarkably, pc2 induced 16-fold or more interferon in human lung and monkey kidney cells compared to the temperature-sensitive, cold-adapted Ann Arbor virus that is currently used as a master backbone for LAIVs such as FluMist. Although the mechanism by which the SLSYSINWRH motif regulates the vaccine properties of pc2 has not been elucidated, this motif has potential use in engineering self-adjuvanting NS1-truncated-based LAIVs
Ngunjiri, John M; Ali, Ahmed; Boyaka, Prosper; Marcus, Philip I; Lee, Chang-Won
2015-01-01
Mutants of influenza virus that encode C-terminally truncated NS1 proteins (NS1-truncated mutants) characteristically induce high interferon responses. The dual activity of interferon in blocking virus replication and enhancing the development of adaptive immune responses makes these mutants promising as self-adjuvanting live-attenuated influenza vaccine (LAIV) candidates. Yet, among the NS1-truncated mutants, the length of NS1 is not directly correlated with the interferon-inducing efficiency, the level of attenuation, or effectiveness as LAIV. Using quantitative in vitro biologically active particle subpopulation analysis as a tool to identify potential LAIV candidates from a pool of NS1-truncated mutants, we previously predicted that a NS1-truncated mutant pc2, which was less effective as a LAIV in chickens, would be sufficiently effective as a LAIV in mammalian hosts. In this study, we confirmed that pc2 protected mice and pigs against heterologous virus challenge in terms of preventing clinical signs and reducing virus shedding. pc2 expresses a unique SLSYSINWRH motif at the C-terminus of its truncated NS1. Deletion of the SLSYSINWRH motif led to ~821-fold reduction in the peak yield of type I interferon induced in murine cells. Furthermore, replacement of the SLSYSINWRH motif with the wildtype MVKMDQAIMD sequence did not restore the interferon-inducing efficiency. The diminished interferon induction capacity in the absence of the SLSYSINWRH motif was similar to that observed in other mutants which are less effective LAIV candidates. Remarkably, pc2 induced 16-fold or more interferon in human lung and monkey kidney cells compared to the temperature-sensitive, cold-adapted Ann Arbor virus that is currently used as a master backbone for LAIVs such as FluMist. Although the mechanism by which the SLSYSINWRH motif regulates the vaccine properties of pc2 has not been elucidated, this motif has potential use in engineering self-adjuvanting NS1-truncated-based LAIVs
Achary, V Mohan M; Parinandi, Narasimham L; Panda, Brahma B
2013-03-18
Calcium is an important second messenger in signal transduction pathways. The role of Ca(2+) signalling in Al-induced DNA damage, cell death, and adaptive response to genotoxic stress caused by ethyl methanesulfonate (EMS) or methylmercuric chloride (MMCl) in the root cells of Allium cepa was investigated in the current study. Root cells in planta were treated with Al(3+) (800μM of AlCl(3)) for 3h without or with 2h pre-treatment with the Ca(2+) chelator (EGTA) or Ca(2+) channel blockers (lanthanum chloride, verapamil) or CaM/CDPK antagonist (W7). In addition, root cells in planta were conditioned by treatment with Al(3+) (5 or 10μM of AlCl(3)) for 2h followed by the genotoxic challenge with MMCl (1.25μM) or EMS (2.5 or 5mM) for 3h without or with the pre-treatment of the chosen Ca(2+) chelator/channel blockers/antagonist. Following the treatments, cell death and DNA damage were investigated in the root cells by comet assay. Furthermore, genotoxicity in the root meristems was determined after 18-30h of recovery. These results revealed that Al(3+) (800μM) significantly induced DNA damage and cell death in the root cells of A. cepa. On the other hand, conditioning of the root cells with Al(3+) at low concentrations (5 or 10μM) offered adaptive response leading to the protection against genotoxic stress induced by MMCl and EMS. Pre-treatment of root cells with the Ca(2+) chelator/channel blockers/antagonist not only alleviated Al(3+)-induced DNA damage and cell death induced but also blocked the Al(3+)-mediated adaptive response to genotoxic stress induced by MMCl and EMS. For the first time, the results of the present study highlighted the role of Ca(2+) signalling underlying the biphasic mode of action of Al(3+) that induced DNA damage and cell death at high doses and offered adaptation to genotoxic response in plants at low doses. PMID:23313746
Focusing of truncated Gaussian beams
NASA Astrophysics Data System (ADS)
Horváth, Zoltán L.; Bor, Zsolt
2003-07-01
It is shown that the focusing of truncated Gaussian beams can be treated by the same manner as uniform spherical waves, i.e., the diffraction integral can be expressed by the Lommel functions, which offers a very efficient way for the calculation of the three-dimensional light distribution near focus. All the expressions for the uniform spherical waves hold good for Gaussian beams if the first variable in the Lommel functions is extended to the complex domain. The intensity distribution depending on the Fresnel number and the truncation coefficient is calculated. The location of the first few minima and maxima of the intensity in focal plane is given for different values of the truncation coefficient. The phase behavior depending on the truncation coefficient is studied.
A Truncated Waveguide Phase Shifter
NASA Technical Reports Server (NTRS)
Lourie, Nathan P.; Chuss, D. T.; Henry, R.; Wollack, E. J.
2011-01-01
The design, fabrication and performance of a simple phase shifter based upon truncated circular and square waveguides is presented. An emphasis is placed upon validation of simple analytical formulae that describe the propagation properties of the structure. A test device is prototyped at approximately 40GHz; however, the concepts explored can be directly extended to millimeter and submillimeter applications.
Truncated States Obtained by Iteration
NASA Astrophysics Data System (ADS)
Cardoso B., W.; Almeida G. de, N.
2008-02-01
We introduce the concept of truncated states obtained via iterative processes (TSI) and study its statistical features, making an analogy with dynamical systems theory (DST). As a specific example, we have studied TSI for the doubling and the logistic functions, which are standard functions in studying chaos. TSI for both the doubling and logistic functions exhibit certain similar patterns when their statistical features are compared from the point of view of DST.
Broom, Donald M
2006-01-01
The term adaptation is used in biology in three different ways. It may refer to changes which occur at the cell and organ level, or at the individual level, or at the level of gene action and evolutionary processes. Adaptation by cells, especially nerve cells helps in: communication within the body, the distinguishing of stimuli, the avoidance of overload and the conservation of energy. The time course and complexity of these mechanisms varies. Adaptive characters of organisms, including adaptive behaviours, increase fitness so this adaptation is evolutionary. The major part of this paper concerns adaptation by individuals and its relationships to welfare. In complex animals, feed forward control is widely used. Individuals predict problems and adapt by acting before the environmental effect is substantial. Much of adaptation involves brain control and animals have a set of needs, located in the brain and acting largely via motivational mechanisms, to regulate life. Needs may be for resources but are also for actions and stimuli which are part of the mechanism which has evolved to obtain the resources. Hence pigs do not just need food but need to be able to carry out actions like rooting in earth or manipulating materials which are part of foraging behaviour. The welfare of an individual is its state as regards its attempts to cope with its environment. This state includes various adaptive mechanisms including feelings and those which cope with disease. The part of welfare which is concerned with coping with pathology is health. Disease, which implies some significant effect of pathology, always results in poor welfare. Welfare varies over a range from very good, when adaptation is effective and there are feelings of pleasure or contentment, to very poor. A key point concerning the concept of individual adaptation in relation to welfare is that welfare may be good or poor while adaptation is occurring. Some adaptation is very easy and energetically cheap and
Greenough, Jeffrey A.; de Supinski, Bronis R.; Yates, Robert K.; Rendleman, Charles A.; Skinner, David; Beckner, Vince; Lijewski, Mike; Bell, John; Sexton, James C.
2005-04-25
We describe the performance of the block-structured Adaptive Mesh Refinement (AMR) code Raptor on the 32k node IBM BlueGene/L computer. This machine represents a significant step forward towards petascale computing. As such, it presents Raptor with many challenges for utilizing the hardware efficiently. In terms of performance, Raptor shows excellent weak and strong scaling when running in single level mode (no adaptivity). Hardware performance monitors show Raptor achieves an aggregate performance of 3:0 Tflops in the main integration kernel on the 32k system. Results from preliminary AMR runs on a prototype astrophysical problem demonstrate the efficiency of the current software when running at large scale. The BG/L system is enabling a physics problem to be considered that represents a factor of 64 increase in overall size compared to the largest ones of this type computed to date. Finally, we provide a description of the development work currently underway to address our inefficiencies.
NASA Astrophysics Data System (ADS)
Bargatze, L. F.
2015-12-01
Active Data Archive Product Tracking (ADAPT) is a collection of software routines that permits one to generate XML metadata files to describe and register data products in support of the NASA Heliophysics Virtual Observatory VxO effort. ADAPT is also a philosophy. The ADAPT concept is to use any and all available metadata associated with scientific data to produce XML metadata descriptions in a consistent, uniform, and organized fashion to provide blanket access to the full complement of data stored on a targeted data server. In this poster, we present an application of ADAPT to describe all of the data products that are stored by using the Common Data File (CDF) format served out by the CDAWEB and SPDF data servers hosted at the NASA Goddard Space Flight Center. These data servers are the primary repositories for NASA Heliophysics data. For this purpose, the ADAPT routines have been used to generate data resource descriptions by using an XML schema named Space Physics Archive, Search, and Extract (SPASE). SPASE is the designated standard for documenting Heliophysics data products, as adopted by the Heliophysics Data and Model Consortium. The set of SPASE XML resource descriptions produced by ADAPT includes high-level descriptions of numerical data products, display data products, or catalogs and also includes low-level "Granule" descriptions. A SPASE Granule is effectively a universal access metadata resource; a Granule associates an individual data file (e.g. a CDF file) with a "parent" high-level data resource description, assigns a resource identifier to the file, and lists the corresponding assess URL(s). The CDAWEB and SPDF file systems were queried to provide the input required by the ADAPT software to create an initial set of SPASE metadata resource descriptions. Then, the CDAWEB and SPDF data repositories were queried subsequently on a nightly basis and the CDF file lists were checked for any changes such as the occurrence of new, modified, or deleted
Demontis, G C; Ratto, G M; Bisti, S; Cervetto, L
1995-01-01
Membrane current and light response were recorded from rods of monkey and guinea pig by means of suction electrodes. The correlation between adaptation and the Na+/K+ pump was investigated by measuring light-dependent changes in sensitivity with and without inhibition of Na+/K+ ATPase by strophanthidin. Strophanthidin was found to reduce the dark current, to slow the time course of the photoresponse, and to increase light sensitivity. At concentrations between 20 and 500 nM, the pump inhibitor suppressed in a reversible way the current re-activation occurring during prolonged illumination and modified the light-dependent decrease in sensitivity, which in control conditions approximates to a Weber-Fechner function. The effects of the pump inhibitor on the adaptive properties of rods are associated with an increased time constant of the membrane current attributed to the operation of the Na+:Ca2+,K+ exchanger. The effects of rapid application of the pump inhibitor on the current re-activation are consistent with the idea that significant changes in the internal sodium occur in rods of mammals during background illumination and that they play an important role in the process of light adaptation. PMID:8527658
Phase behavior of a family of truncated hard cubes.
Gantapara, Anjan P; de Graaf, Joost; van Roij, René; Dijkstra, Marjolein
2015-02-01
In continuation of our work in Gantapara et al., [Phys. Rev. Lett. 111, 015501 (2013)], we investigate here the thermodynamic phase behavior of a family of truncated hard cubes, for which the shape evolves smoothly from a cube via a cuboctahedron to an octahedron. We used Monte Carlo simulations and free-energy calculations to establish the full phase diagram. This phase diagram exhibits a remarkable richness in crystal and mesophase structures, depending sensitively on the precise particle shape. In addition, we examined in detail the nature of the plastic crystal (rotator) phases that appear for intermediate densities and levels of truncation. Our results allow us to probe the relation between phase behavior and building-block shape and to further the understanding of rotator phases. Furthermore, the phase diagram presented here should prove instrumental for guiding future experimental studies on similarly shaped nanoparticles and the creation of new materials. PMID:25662665
Phase behavior of a family of truncated hard cubes
Gantapara, Anjan P. Dijkstra, Marjolein; Graaf, Joost de; Roij, René van
2015-02-07
In continuation of our work in Gantapara et al., [Phys. Rev. Lett. 111, 015501 (2013)], we investigate here the thermodynamic phase behavior of a family of truncated hard cubes, for which the shape evolves smoothly from a cube via a cuboctahedron to an octahedron. We used Monte Carlo simulations and free-energy calculations to establish the full phase diagram. This phase diagram exhibits a remarkable richness in crystal and mesophase structures, depending sensitively on the precise particle shape. In addition, we examined in detail the nature of the plastic crystal (rotator) phases that appear for intermediate densities and levels of truncation. Our results allow us to probe the relation between phase behavior and building-block shape and to further the understanding of rotator phases. Furthermore, the phase diagram presented here should prove instrumental for guiding future experimental studies on similarly shaped nanoparticles and the creation of new materials.
Lamp with a truncated reflector cup
Li, Ming; Allen, Steven C.; Bazydola, Sarah; Ghiu, Camil-Daniel
2013-10-15
A lamp assembly, and method for making same. The lamp assembly includes first and second truncated reflector cups. The lamp assembly also includes at least one base plate disposed between the first and second truncated reflector cups, and a light engine disposed on a top surface of the at least one base plate. The light engine is configured to emit light to be reflected by one of the first and second truncated reflector cups.
Reducing Truncation Error In Integer Processing
NASA Technical Reports Server (NTRS)
Thomas, J. Brooks; Berner, Jeffrey B.; Graham, J. Scott
1995-01-01
Improved method of rounding off (truncation of least-significant bits) in integer processing of data devised. Provides for reduction, to extremely low value, of numerical bias otherwise generated by accumulation of truncation errors from many arithmetic operations. Devised for use in integer signal processing, in which rescaling and truncation usually performed to reduce number of bits, which typically builds up in sequence of operations. Essence of method to alternate direction of roundoff (plus, then minus) on alternate occurrences of truncated values contributing to bias.
Bilaloglu, Seda; Lu, Ying; Geller, Daniel; Rizzo, John Ross; Aluru, Viswanath; Gardner, Esther P; Raghavan, Preeti
2016-03-01
Adaptation of fingertip forces to friction at the grasping surface is necessary to prevent use of inadequate or excessive grip forces. In the current study we investigated the effect of blocking tactile information from the fingertips noninvasively on the adaptation and efficiency of grip forces to surface friction during precision grasp. Ten neurologically intact subjects grasped and lifted an instrumented grip device with 18 different frictional surfaces under three conditions: with bare hands or with a thin layer of plastic (Tegaderm) or an additional layer of foam affixed to the fingertips. The coefficient of friction at the finger-object interface of each surface was obtained for each subject with bare hands and Tegaderm by measuring the slip ratio (grip force/load force) at the moment of slip. We found that the foam layer reduced sensibility for two-point discrimination and pressure sensitivity at the fingertips, but Tegaderm did not. However, Tegaderm reduced static, but not dynamic, tactile discrimination. Adaptation of fingertip grip forces to surface friction measured by the rate of change of peak grip force, and grip force efficiency measured by the grip-load force ratio at lift, showed a proportional relationship with bare hands but were impaired with Tegaderm and foam. Activation of muscles engaged in precision grip also varied with the frictional surface with bare hands but not with Tegaderm and foam. The results suggest that sensitivity for static tactile discrimination is necessary for feedforward and feedback control of grip forces and for adaptive modulation of muscle activity during precision grasp. PMID:26655820
Perspective on rainbow-ladder truncation
NASA Astrophysics Data System (ADS)
Eichmann, G.; Alkofer, R.; Cloët, I. C.; Krassnigg, A.; Roberts, C. D.
2008-04-01
Prima facie the systematic implementation of corrections to the rainbow-ladder truncation of QCD's Dyson-Schwinger equations will uniformly reduce in magnitude those calculated mass-dimensioned results for pseudoscalar and vector meson properties that are not tightly constrained by symmetries. The aim and interpretation of studies employing rainbow-ladder truncation are reconsidered in this light.
Perspective on rainbow-ladder truncation
Eichmann, G.; Alkofer, R.; Krassnigg, A.; Cloeet, I. C.; Roberts, C. D.
2008-04-15
Prima facie the systematic implementation of corrections to the rainbow-ladder truncation of QCD's Dyson-Schwinger equations will uniformly reduce in magnitude those calculated mass-dimensioned results for pseudoscalar and vector meson properties that are not tightly constrained by symmetries. The aim and interpretation of studies employing rainbow-ladder truncation are reconsidered in this light.
Li, Henry Y; Appelbaum, Frederick R; Willman, Cheryl L; Zager, Richard A; Banker, Deborah E
2003-05-01
The mevalonate pathway produces many critical substances in cells, including sterols essential for membrane structure and isoprenoids vital to the function of many membrane proteins. 3-Hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase is a rate-limiting enzyme in the mevalonate pathway. Because cholesterol is a product of this pathway, HMG-CoA reductase inhibitors (statins) are used to treat hypercholesterolemia. Statins are also toxic to several malignancies, including acute myeloid leukemia (AML). Although this toxicity has been attributed to the inhibition of Ras/Rho isoprenylation, we have previously shown that statin toxicity in primary AML cells (AMLs) does not correlate with Ras isoprenylation or with activating Ras mutations. In other studies, we have shown that hypoxic and oxidant injuries induce cholesterol increments in renal tubule cells and that statins sensitize these cells to injury by blocking protective cholesterol responses. We now demonstrate that exposing particular AMLs to radiochemotherapy induces much greater cellular cholesterol increments than those seen in similarly treated normal bone marrow. Treatment of these AMLs with mevastatin or zaragozic acid (which inhibits cholesterol synthesis but not isoprenoid synthesis) attenuates the cholesterol increments and sensitizes cells to radiochemotherapy. The extent of toxicity is affected by the availability of extracellular lipoproteins, further suggesting that cellular cholesterol is critical to cell survival in particular AMLs. Because zaragozic acid does not inhibit isoprenoid synthesis, these data suggest that cholesterol modulation is an important mechanism whereby statins exert toxic effects on some AMLs and that cholesterol modulators may improve therapeutic ratios in AML by impacting cholesterol-dependent cytoresistance. PMID:12506040
... Block Explore Heart Block What Is... Electrical System & EKG Results Types Causes Who Is at Risk Signs & ... heart block. Doctors use a test called an EKG (electrocardiogram) to help diagnose heart block. This test ...
Evolutionary and Functional Relationships in the Truncated Hemoglobin Family
Bustamante, Juan P.; Radusky, Leandro; Boechi, Leonardo; Estrin, Darío A.; ten Have, Arjen; Martí, Marcelo A.
2016-01-01
Predicting function from sequence is an important goal in current biological research, and although, broad functional assignment is possible when a protein is assigned to a family, predicting functional specificity with accuracy is not straightforward. If function is provided by key structural properties and the relevant properties can be computed using the sequence as the starting point, it should in principle be possible to predict function in detail. The truncated hemoglobin family presents an interesting benchmark study due to their ubiquity, sequence diversity in the context of a conserved fold and the number of characterized members. Their functions are tightly related to O2 affinity and reactivity, as determined by the association and dissociation rate constants, both of which can be predicted and analyzed using in-silico based tools. In the present work we have applied a strategy, which combines homology modeling with molecular based energy calculations, to predict and analyze function of all known truncated hemoglobins in an evolutionary context. Our results show that truncated hemoglobins present conserved family features, but that its structure is flexible enough to allow the switch from high to low affinity in a few evolutionary steps. Most proteins display moderate to high oxygen affinities and multiple ligand migration paths, which, besides some minor trends, show heterogeneous distributions throughout the phylogenetic tree, again suggesting fast functional adaptation. Our data not only deepens our comprehension of the structural basis governing ligand affinity, but they also highlight some interesting functional evolutionary trends. PMID:26788940
Evolutionary and Functional Relationships in the Truncated Hemoglobin Family.
Bustamante, Juan P; Radusky, Leandro; Boechi, Leonardo; Estrin, Darío A; Ten Have, Arjen; Martí, Marcelo A
2016-01-01
Predicting function from sequence is an important goal in current biological research, and although, broad functional assignment is possible when a protein is assigned to a family, predicting functional specificity with accuracy is not straightforward. If function is provided by key structural properties and the relevant properties can be computed using the sequence as the starting point, it should in principle be possible to predict function in detail. The truncated hemoglobin family presents an interesting benchmark study due to their ubiquity, sequence diversity in the context of a conserved fold and the number of characterized members. Their functions are tightly related to O2 affinity and reactivity, as determined by the association and dissociation rate constants, both of which can be predicted and analyzed using in-silico based tools. In the present work we have applied a strategy, which combines homology modeling with molecular based energy calculations, to predict and analyze function of all known truncated hemoglobins in an evolutionary context. Our results show that truncated hemoglobins present conserved family features, but that its structure is flexible enough to allow the switch from high to low affinity in a few evolutionary steps. Most proteins display moderate to high oxygen affinities and multiple ligand migration paths, which, besides some minor trends, show heterogeneous distributions throughout the phylogenetic tree, again suggesting fast functional adaptation. Our data not only deepens our comprehension of the structural basis governing ligand affinity, but they also highlight some interesting functional evolutionary trends. PMID:26788940
Truncated Moment Analysis of Nucleon Structure Functions
A. Psaker; W. Melnitchouk; M. E. Christy; C. E. Keppel
2007-11-16
We employ a novel new approach using "truncated" moments, or integrals of structure functions over restricted regions of x, to study local quark-hadron duality, and the degree to which individual resonance regions are dominated by leading twists. Because truncated moments obey the same Q^2 evolution equations as the leading twist parton distributions, this approach makes possible for the first time a description of resonance region data and the phenomenon of quark-hadron duality directly from QCD.
NASA Technical Reports Server (NTRS)
Glocer, A.; Toth, G.; Ma, Y.; Gombosi, T.; Zhang, J.-C.; Kistler, L. M.
2009-01-01
The magnetosphere contains a significant amount of ionospheric O+, particularly during geomagnetically active times. The presence of ionospheric plasma in the magnetosphere has a notable impact on magnetospheric composition and processes. We present a new multifluid MHD version of the Block-Adaptive-Tree Solar wind Roe-type Upwind Scheme model of the magnetosphere to track the fate and consequences of ionospheric outflow. The multifluid MHD equations are presented as are the novel techniques for overcoming the formidable challenges associated with solving them. Our new model is then applied to the May 4, 1998 and March 31, 2001 geomagnetic storms. The results are juxtaposed with traditional single-fluid MHD and multispecies MHD simulations from a previous study, thereby allowing us to assess the benefits of using a more complex model with additional physics. We find that our multifluid MHD model (with outflow) gives comparable results to the multispecies MHD model (with outflow), including a more strongly negative Dst, reduced CPCP, and a drastically improved magnetic field at geosynchronous orbit, as compared to single-fluid MHD with no outflow. Significant differences in composition and magnetic field are found between the multispecies and multifluid approach further away from the Earth. We further demonstrate the ability to explore pressure and bulk velocity differences between H+ and O+, which is not possible when utilizing the other techniques considered
Müller, Achim; Gouzerh, Pierre
2012-11-21
Following Nature's lessons, today chemists can cross the boundary of the small molecule world to construct multifunctional and highly complex molecular nano-objects up to protein size and even cell-like nanosystems showing responsive sensing. Impressive examples emerge from studies of the solutions of some oxoanions of the early transition metals especially under reducing conditions which enable the controlled linking of metal-oxide building blocks. The latter are available from constitutional dynamic libraries, thus providing the option to generate multifunctional unique nanoscale molecular systems with exquisite architectures, which even opens the way towards adaptive and evolutive (Darwinian) chemistry. The present review presents the first comprehensive report of current knowledge (including synthesis aspects not discussed before) regarding the related giant metal-oxide clusters mainly of the type {Mo(57)M'(6)} (M' = Fe(III), V(IV)) (torus structure), {M(72)M'(30)} (M = Mo, M' = V(IV), Cr(III), Fe(III), Mo(V)), {M(72)Mo(60)} (M = Mo, W) (Keplerates), {Mo(154)}, {Mo(176)}, {Mo(248)} ("big wheels"), and {Mo(368)} ("blue lemon") - all having the important transferable pentagonal {(M)M(5)} groups in common. These discoveries expanded the frontiers of inorganic chemistry to the mesoscopic world, while there is probably no collection of discrete inorganic compounds which offers such a versatile chemistry and the option to study new phenomena of interdisciplinary interest. The variety of different properties of the sphere- and wheel-type metal-oxide-based clusters can directly be related to their unique architectures: The spherical Keplerate-type capsules having 20 crown-ether-type pores and tunable internal functionalities allow the investigation of confined matter as well as that of sphere-surface-supramolecular and encapsulation chemistry - including related new aspects of the biologically important hydrophobic effects - but also of nanoscale ion transport and
Testing block subdivision algorithms on block designs
NASA Astrophysics Data System (ADS)
Wiseman, Natalie; Patterson, Zachary
2016-01-01
Integrated land use-transportation models predict future transportation demand taking into account how households and firms arrange themselves partly as a function of the transportation system. Recent integrated models require parcels as inputs and produce household and employment predictions at the parcel scale. Block subdivision algorithms automatically generate parcel patterns within blocks. Evaluating block subdivision algorithms is done by way of generating parcels and comparing them to those in a parcel database. Three block subdivision algorithms are evaluated on how closely they reproduce parcels of different block types found in a parcel database from Montreal, Canada. While the authors who developed each of the algorithms have evaluated them, they have used their own metrics and block types to evaluate their own algorithms. This makes it difficult to compare their strengths and weaknesses. The contribution of this paper is in resolving this difficulty with the aim of finding a better algorithm suited to subdividing each block type. The proposed hypothesis is that given the different approaches that block subdivision algorithms take, it's likely that different algorithms are better adapted to subdividing different block types. To test this, a standardized block type classification is used that consists of mutually exclusive and comprehensive categories. A statistical method is used for finding a better algorithm and the probability it will perform well for a given block type. Results suggest the oriented bounding box algorithm performs better for warped non-uniform sites, as well as gridiron and fragmented uniform sites. It also produces more similar parcel areas and widths. The Generalized Parcel Divider 1 algorithm performs better for gridiron non-uniform sites. The Straight Skeleton algorithm performs better for loop and lollipop networks as well as fragmented non-uniform and warped uniform sites. It also produces more similar parcel shapes and patterns.
Dualising consistent IIA/IIB truncations
NASA Astrophysics Data System (ADS)
Malek, Emanuel; Samtleben, Henning
2015-12-01
We use exceptional field theory to establish a duality between certain consistent 7-dimensional truncations with maximal SUSY from IIA to IIB. We use this technique to obtain new consistent truncations of IIB on S 3 and H p,q and work out the explicit reduction formulas in the internal sector. We also present uplifts for other gaugings of 7-d maximal SUGRA, including theories with a trombone gauging. Some of the latter can only be obtained by a non-geometric compactification.
Jang, Hyesun; Ngunjiri, John M; Lee, Chang-Won
2016-01-01
Influenza virus mutants that encode C-terminally truncated NS1 proteins (NS1-truncated mutants) are attractive candidates for avian live attenuated influenza vaccine (LAIV) development because they are both attenuated and immunogenic in chickens. We previously showed that a high protective efficacy of NS1-truncated LAIV in chickens corresponds with induction of high levels of type I interferon (IFN) responses in chicken embryonic fibroblast cells. In this study, we investigated the relationship between induction of IFN and IFN-stimulated gene responses in vivo and the immunogenicity and protective efficacy of NS1-truncated LAIV. Our data demonstrates that accelerated antibody induction and protective efficacy of NS1-truncated LAIV correlates well with upregulation of IFN-stimulated genes. Further, through oral administration of recombinant chicken IFN alpha in drinking water, we provide direct evidence that type I IFN can promote rapid induction of adaptive immune responses and protective efficacy of influenza vaccine in chickens. PMID:27257989
Jang, Hyesun; Ngunjiri, John M.; Lee, Chang-Won
2016-01-01
Influenza virus mutants that encode C-terminally truncated NS1 proteins (NS1-truncated mutants) are attractive candidates for avian live attenuated influenza vaccine (LAIV) development because they are both attenuated and immunogenic in chickens. We previously showed that a high protective efficacy of NS1-truncated LAIV in chickens corresponds with induction of high levels of type I interferon (IFN) responses in chicken embryonic fibroblast cells. In this study, we investigated the relationship between induction of IFN and IFN-stimulated gene responses in vivo and the immunogenicity and protective efficacy of NS1-truncated LAIV. Our data demonstrates that accelerated antibody induction and protective efficacy of NS1-truncated LAIV correlates well with upregulation of IFN-stimulated genes. Further, through oral administration of recombinant chicken IFN alpha in drinking water, we provide direct evidence that type I IFN can promote rapid induction of adaptive immune responses and protective efficacy of influenza vaccine in chickens. PMID:27257989
Canine MPV17 truncation without clinical manifestations
Hänninen, Reetta L.; Ahonen, Saija; Màrquez, Merce; Myöhänen, Maarit J.; Hytönen, Marjo K.; Lohi, Hannes
2015-01-01
ABSTRACT Mitochondrial DNA depletion syndromes (MDS) are often serious autosomal recessively inherited disorders characterized by tissue-specific mtDNA copy number reduction. Many genes, including MPV17, are associated with the hepatocerebral form of MDS. MPV17 encodes for a mitochondrial inner membrane protein with a poorly characterized function. Several MPV17 mutations have been reported in association with a heterogeneous group of early-onset manifestations, including liver disease and neurological problems. Mpv17-deficient mice present renal and hearing defects. We describe here a MPV17 truncation mutation in dogs. We found a 1-bp insertion in exon 4 of the MPV17 gene, resulting in a frameshift and early truncation of the encoded protein. The mutation halves MPV17 expression in the lymphocytes of the homozygous dogs and the truncated protein is not translated in transfected cells. The insertion mutation is recurrent and exists in many unrelated breeds, although is highly enriched in the Boxer breed. Unexpectedly, despite the truncation of MPV17, we could not find any common phenotypes in the genetically affected dogs. The lack of observable phenotype could be due to a late onset, mild symptoms or potential tissue-specific compensatory mechanisms. This study suggests species-specific differences in the manifestation of the MPV17 defects and establishes a novel large animal model to further study MPV17 function and role in mitochondrial biology. PMID:26353863
Family Therapy for the "Truncated" Nuclear Family.
ERIC Educational Resources Information Center
Zuk, Gerald H.
1980-01-01
The truncated nuclear family consists of a two-generation group in which conflict has produced a polarization of values. The single-parent family is at special risk. Go-between process enables the therapist to depolarize sharply conflicted values and reduce pathogenic relating. (Author)
Irregularly Shaped Space-Filling Truncated Octahedra
ERIC Educational Resources Information Center
Hanson, John Robert
2008-01-01
For any parent tetrahedron ABCD, centroids of selected sub-tetrahedra form the vertices of an irregularly shaped space-filling truncated octahedron. To reflect these properties, such a figure will be called an ISTO. Each edge of the ISTO is parallel to and one-eighth the length of one of the edges of tetrahedron ABCD and the volume of the ISTO is…
Fast and accurate matrix completion via truncated nuclear norm regularization.
Hu, Yao; Zhang, Debing; Ye, Jieping; Li, Xuelong; He, Xiaofei
2013-09-01
Recovering a large matrix from a small subset of its entries is a challenging problem arising in many real applications, such as image inpainting and recommender systems. Many existing approaches formulate this problem as a general low-rank matrix approximation problem. Since the rank operator is nonconvex and discontinuous, most of the recent theoretical studies use the nuclear norm as a convex relaxation. One major limitation of the existing approaches based on nuclear norm minimization is that all the singular values are simultaneously minimized, and thus the rank may not be well approximated in practice. In this paper, we propose to achieve a better approximation to the rank of matrix by truncated nuclear norm, which is given by the nuclear norm subtracted by the sum of the largest few singular values. In addition, we develop a novel matrix completion algorithm by minimizing the Truncated Nuclear Norm. We further develop three efficient iterative procedures, TNNR-ADMM, TNNR-APGL, and TNNR-ADMMAP, to solve the optimization problem. TNNR-ADMM utilizes the alternating direction method of multipliers (ADMM), while TNNR-AGPL applies the accelerated proximal gradient line search method (APGL) for the final optimization. For TNNR-ADMMAP, we make use of an adaptive penalty according to a novel update rule for ADMM to achieve a faster convergence rate. Our empirical study shows encouraging results of the proposed algorithms in comparison to the state-of-the-art matrix completion algorithms on both synthetic and real visual datasets. PMID:23868774
Phase diagram of a truncated tetrahedral model.
Krcmar, Roman; Gendiar, Andrej; Nishino, Tomotoshi
2016-08-01
Phase diagram of a discrete counterpart of the classical Heisenberg model, the truncated tetrahedral model, is analyzed on the square lattice, when the interaction is ferromagnetic. Each spin is represented by a unit vector that can point to one of the 12 vertices of the truncated tetrahedron, which is a continuous interpolation between the tetrahedron and the octahedron. Phase diagram of the model is determined by means of the statistical analog of the entanglement entropy, which is numerically calculated by the corner transfer matrix renormalization group method. The obtained phase diagram consists of four different phases, which are separated by five transition lines. In the parameter region, where the octahedral anisotropy is dominant, a weak first-order phase transition is observed. PMID:27627273
Truncated Dual-Cap Nucleation Site Development
NASA Technical Reports Server (NTRS)
Matson, Douglas M.; Sander, Paul J.
2012-01-01
During heterogeneous nucleation within a metastable mushy-zone, several geometries for nucleation site development must be considered. Traditional spherical dual cap and crevice models are compared to a truncated dual cap to determine the activation energy and critical cluster growth kinetics in ternary Fe-Cr-Ni steel alloys. Results of activation energy results indicate that nucleation is more probable at grain boundaries within the solid than at the solid-liquid interface.
Unquenched Studies Using the Truncated Determinant Algorithm
A. Duncan, E. Eichten and H. Thacker
2001-11-29
A truncated determinant algorithm is used to study the physical effects of the quark eigenmodes associated with eigenvalues below 420 MeV. This initial high statistics study focuses on coarse (6{sup 4}) lattices (with O(a{sup 2}) improved gauge action), light internal quark masses and large physical volumes. Three features of full QCD are examined: topological charge distributions, string breaking as observed in the static energy and the eta prime mass.
Accurate basis set truncation for wavefunction embedding
NASA Astrophysics Data System (ADS)
Barnes, Taylor A.; Goodpaster, Jason D.; Manby, Frederick R.; Miller, Thomas F.
2013-07-01
Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size of the MO virtual space. In this study, we extend a recently introduced projection-based embedding method [F. R. Manby, M. Stella, J. D. Goodpaster, and T. F. Miller III, J. Chem. Theory Comput. 8, 2564 (2012)], 10.1021/ct300544e to allow for the systematic and accurate truncation of the embedded subsystem basis set. The approach is applied to both covalently and non-covalently bound test cases, including water clusters and polypeptide chains, and it is demonstrated that errors associated with basis set truncation are controllable to well within chemical accuracy. Furthermore, we show that this approach allows for switching between accurate projection-based embedding and DFT embedding with approximate kinetic energy (KE) functionals; in this sense, the approach provides a means of systematically improving upon the use of approximate KE functionals in DFT embedding.
ERIC Educational Resources Information Center
Smith, Martin H.
1992-01-01
Describes an educational game called "Population Blocks" that is designed to illustrate the concept of exponential growth of the human population and some potential effects of overpopulation. The game material consists of wooden blocks; 18 blocks are painted green (representing land), 7 are painted blue (representing water); and the remaining…
Turbulence excited frequency domain damping measurement and truncation effects
NASA Technical Reports Server (NTRS)
Soovere, J.
1976-01-01
Existing frequency domain modal frequency and damping analysis methods are discussed. The effects of truncation in the Laplace and Fourier transform data analysis methods are described. Methods for eliminating truncation errors from measured damping are presented. Implications of truncation effects in fast Fourier transform analysis are discussed. Limited comparison with test data is presented.
Performance of an artificial absorber for truncating FEM meshes
NASA Astrophysics Data System (ADS)
Gong, Jian; Volakis, John L.
1995-01-01
We investigate the effectiveness of an artificial absorber for truncating finite element (FE) meshes. Specifically, we present the implementation of a novel mesh truncation approach using a perfectly matched anisotropic absorber for waveguides and stripline circuits. This truncation scheme is useful in many applications, including antennas, scattering, and microwave circuits.
Xiao, Kai; Yu, Xiang; Chen, Jihua; Lavrik, Nickolay V; Hong, Kunlun; Sumpter, Bobby; Geohegan, David B
2011-01-01
The self-assembly process and resulting structure of a series of conductive diblock copolymer thin films of Poly(3-hexylthiophene)-b-Polystyrene (P3HT-b-PS) have been studied by TEM, SAED, GIXD and AFM and additionally by first principles modeling and simulation. By varying the molecular weight of the P3HT segment, these block copolymers undergo microphase separation and self-assemble into nanostructured sphere, lamellae, nanofiber, and nanoribbon in the films. Within the diblock copolymer thin film, the convalently bonded PS blocks segregated to form amorphous domains, however, the conductive P3HT blocks were crystalline, exhibiting highly-ordered molecular packing with their alkyl side chains aligned along to the normal to the substrate and the - stacking direction of the thiophene rings aligned parallel to the substrate. The conductive P3HY block copolymers exhibited significant improvements in organic feild-effect transistor (OFET) performance and environmental stability as compared to P3HT homopolymers, with up to a factor of two increase in measured moblity (0.08 cm2/Vs ) for the P4 (85 wt% P3HT). Overall, this work demonstrates that the high degree of molecular order induced by bock copolymer phase separation can improve the transport properties and stability of conductive polymer critical for high-performance OFET s.
Tibial hemimelia associated with GLI3 truncation.
Deimling, Steven; Sotiropoulos, Chris; Lau, Kimberly; Chaudhry, Sonia; Sturgeon, Kendra; Kelley, Simon; Narayanan, Unni; Howard, Andrew; Hui, Chi-Chung; Hopyan, Sevan
2016-05-01
Tibial hemimelia is a rare, debilitating and often sporadic congenital deficiency. In syndromic cases, mutations of a Sonic hedgehog (SHH) enhancer have been identified. Here we describe an ~5 kb deletion within the SHH repressor GLI3 in two patients with bilateral tibial hemimelia. This deletion results in a truncated GLI3 protein that lacks a DNA-binding domain and cannot repress hedgehog signaling. These findings strengthen the concept that tibial hemimelia arises because of failure to restrict SHH activity to the posterior aspect of the limb bud. PMID:26791356
ERIC Educational Resources Information Center
Sevcik, Richard S.; Gamble, Rex; Martinez, Elizabet; Schultz, Linda D.; Alexander, Susan V.
2008-01-01
"Ionic Blocks" is a teaching tool designed to help middle school students visualize the concepts of ions, ionic compounds, and stoichiometry. It can also assist high school students in reviewing their subject mastery. Three dimensional blocks are used to represent cations and anions, with color indicating charge (positive or negative) and size…
Vortex breakdown in a truncated conical bioreactor
NASA Astrophysics Data System (ADS)
Balci, Adnan; Brøns, Morten; Herrada, Miguel A.; Shtern, Vladimir N.
2015-12-01
This numerical study explains the eddy formation and disappearance in a slow steady axisymmetric air-water flow in a vertical truncated conical container, driven by the rotating top disk. Numerous topological metamorphoses occur as the water height, Hw, and the bottom-sidewall angle, α, vary. It is found that the sidewall convergence (divergence) from the top to the bottom stimulates (suppresses) the development of vortex breakdown (VB) in both water and air. At α = 60°, the flow topology changes eighteen times as Hw varies. The changes are due to (a) competing effects of AMF (the air meridional flow) and swirl, which drive meridional motions of opposite directions in water, and (b) feedback of water flow on AMF. For small Hw, the AMF effect dominates. As Hw increases, the swirl effect dominates and causes VB. The water flow feedback produces and modifies air eddies. The results are of fundamental interest and can be relevant for aerial bioreactors.
Entanglement entropy from the truncated conformal space
NASA Astrophysics Data System (ADS)
Palmai, T.
2016-08-01
A new numerical approach to entanglement entropies of the Rényi type is proposed for one-dimensional quantum field theories. The method extends the truncated conformal spectrum approach and we will demonstrate that it is especially suited to study the crossover from massless to massive behavior when the subsystem size is comparable to the correlation length. We apply it to different deformations of massless free fermions, corresponding to the scaling limit of the Ising model in transverse and longitudinal fields. For massive free fermions the exactly known crossover function is reproduced already in very small system sizes. The new method treats ground states and excited states on the same footing, and the applicability for excited states is illustrated by reproducing Rényi entropies of low-lying states in the transverse field Ising model.
Mycobacterial truncated hemoglobins: from genes to functions.
Ascenzi, Paolo; Bolognesi, Martino; Milani, Mario; Guertin, Michel; Visca, Paolo
2007-08-15
Infections caused by bacteria belonging to genus Mycobacterium are among the most challenging threats for human health. The ability of mycobacteria to persist in vivo in the presence of reactive nitrogen and oxygen species implies the presence in these bacteria of effective detoxification mechanisms. Mycobacterial truncated hemoglobins (trHbs) have recently been implicated in scavenging of reactive nitrogen species. Individual members from each trHb family (N, O, and P) can be present in the same mycobacterial species. The distinct features of the heme active site structure combined with different ligand binding properties and in vivo expression patterns of mycobacterial trHbs suggest that these globins may accomplish diverse functions. Here, recent genomic, structural and biochemical information on mycobacterial trHbs is reviewed, with the aim of providing further insights into the role of these globins in mycobacterial physiology. PMID:17532149
NASA Astrophysics Data System (ADS)
Ameri, Mohsen; Samavat, Feridoun; Mohajerani, Ezeddin; Fathollahi, Mohammad-Reza
2016-06-01
In the present research, the effect of \\text{ZnO} -based blocking layers on the operational features of \\text{Ti}{{\\text{O}}2} -based dye-sensitized solar cells is investigated. A facile solution-based coating method is applied to prepare an interfacial highly transparent \\text{ZnO} compact blocking layer (CBL) to enhance the efficiency of dye-sensitized solar cells. Different precursor molar concentration were tested to find the optimum concentration. Optical and electrical measurements were carried out to confirm the operation of the CBLs. Morphological characterizations were performed by scanning electron microscopy (SEM) and atomic force microscopy (AFM) to investigate the structure of the compact layers. We have also developed a set of modeling procedures to extract the effective electrical parameters including the parasitic resistances and charged carrier profiles to investigate the effect of CBLs on the dye-sensitized solar cell (DSSC) performance. The adopted modeling approach should establish a versatile framework for diagnosis of DSSCs and facilitates the exploration of critical factors influencing device performance.
A method for Hamiltonian truncation: a four-wave example
NASA Astrophysics Data System (ADS)
Viscondi, Thiago F.; Caldas, Iberê L.; Morrison, Philip J.
2016-04-01
A method for extracting finite-dimensional Hamiltonian systems from a class of 2 + 1 Hamiltonian mean field theories is presented. These theories possess noncanonical Poisson brackets, which normally resist Hamiltonian truncation, but a process of beatification by coordinate transformation near a reference state is described in order to perturbatively overcome this difficulty. Two examples of four-wave truncation of Euler’s equation for scalar vortex dynamics are given and compared: one a direct non-Hamiltonian truncation of the equations of motion, the other obtained by beatifying the Poisson bracket and then truncating.
Farshadpour, Fatemeh; Makvandi, Manoochehr; Taherkhani, Reza
2015-01-01
Background: Hepatitis E Virus (HEV) is the causative agent of enterically transmitted acute hepatitis and has high mortality rate of up to 30% among pregnant women. Therefore, development of a novel vaccine is a desirable goal. Objectives: The aim of this study was to construct tPAsp-PADRE-truncated open reading frame 2 (ORF2) and truncated ORF2 DNA plasmid, which can assist future studies with the preparation of an effective vaccine against Hepatitis E Virus. Materials and Methods: A synthetic codon-optimized gene cassette encoding tPAsp-PADRE-truncated ORF2 protein was designed, constructed and analyzed by some bioinformatics software. Furthermore, a codon-optimized truncated ORF2 gene was amplified by the polymerase chain reaction (PCR), with a specific primer from the previous construct. The constructs were sub-cloned in the pVAX1 expression vector and finally expressed in eukaryotic cells. Results: Sequence analysis and bioinformatics studies of the codon-optimized gene cassette revealed that codon adaptation index (CAI), GC content, and frequency of optimal codon usage (Fop) value were improved, and performance of the secretory signal was confirmed. Cloning and sub-cloning of the tPAsp-PADRE-truncated ORF2 gene cassette and truncated ORF2 gene were confirmed by colony PCR, restriction enzymes digestion and DNA sequencing of the recombinant plasmids pVAX-tPAsp-PADRE-truncated ORF2 (aa 112-660) and pVAX-truncated ORF2 (aa 112-660). The expression of truncated ORF2 protein in eukaryotic cells was approved by an Immunoﬂuorescence assay (IFA) and the reverse transcriptase polymerase chain reaction (RT-PCR) method. Conclusions: The results of this study demonstrated that the tPAsp-PADRE-truncated ORF2 gene cassette and the truncated ORF2 gene in recombinant plasmids are successfully expressed in eukaryotic cells. The immunogenicity of the two recombinant plasmids with different formulations will be evaluated as a novel DNA vaccine in future investigations. PMID
Minimizing the angular divergence of high-order harmonics by truncating the truncated Bessel beam
NASA Astrophysics Data System (ADS)
Ye, Peng; Teng, Hao; He, Xin-Kui; Zhong, Shi-Yang; Wang, Li-Feng; Zhan, Min-Jie; Zhang, Wei; Yun, Chen-Xia; Wei, Zhi-Yi
2014-12-01
We have experimentally investigated high-order-harmonic generation driven by a few-cycle truncated Bessel (TB) laser beam which propagates through optical elements of finite aperture sizes. The TB beam was first investigated by Nisoli et al. [Phys. Rev. Lett. 88, 033902 (2002), 10.1103/PhysRevLett.88.033902], who assumed an infinite size for the optical elements so they concluded that the phase and intensity of the laser field oscillate dramatically around the laser focus in space. However, in all real experiments, the optical elements are always finite in size and would further truncate the TB beam, and so the oscillations would dwindle substantially. In this paper we take the finite size of the optical elements into account. We find that the further truncated TB beam has two intensity peaks around the focus. In front of the second peak position the curvatures of the laser phase front and the atomic-dipole phase front have the same absolute values but opposite signs, so the generated harmonic has a flat wavefront and hence a minimized angular divergence. In addition, at this position the pump intensity is not much less than its maximal value. This result is of significant importance in practical applications due to the finite aperture size of all real optical elements.
Stringy Schrödinger truncations
NASA Astrophysics Data System (ADS)
Detournay, Stéphane; Guica, Monica
2013-08-01
Motivated by the desire to better understand finite-temperature holography for three-dimensional Schrödinger spacetimes, we: i) construct a four-parameter family of warped black string solutions of type IIB supergravity and ii) find the first consistent truncations of type IIB string theory to three dimensions that admit both supersymmetric Schrödinger solutions and warped generalizations of the BTZ black hole. Our analysis reveals a number of interesting features. One is that the thermodynamic properties of all the warped black strings, as well as the asymptotic symmetry group data, are identical to those of BTZ, in an appropriate parametrization. A more striking feature is that the spectrum of linearized perturbations around the various supersymmetric Schrödinger vacua oftentimes contains modes that carry energy flux through the spacetime boundary, which are usually believed to be unstable. A preliminary analysis indicates that, at least in the case of most interest, these modes do not lead to an instability.
BCFT moduli space in level truncation
NASA Astrophysics Data System (ADS)
Kudrna, Matěj; Maccaferri, Carlo
2016-04-01
We propose a new non-perturbative method to search for marginal deformations in level truncated open string field theory. Instead of studying the flatness of the effective potential for the marginal field (which is not expected to give a one-to-one parametrization of the BCFT moduli space), we identify a new non-universal branch of the tachyon potential which, from known analytic examples, is expected to parametrize the marginal flow in a much larger region of the BCFT moduli space. By a level 18 computation in Siegel gauge we find an increasingly flat effective potential in the non-universal sector, connected to the perturbative vacuum and we confirm that the coefficient of the marginal field ( λ SFT) has a maximum compatible with the value where the solutions stop existing in the standard Sen-Zwiebach approach. At the maximal reachable level the effective potential still deviates from flatness for large values of the tachyon, but the Ellwood invariants stay close to the correct BCFT values on the whole branch and the full periodic moduli space of the cosine deformation is covered.
Efficient Generation of Truncated Bessel Beams using Cylindrical Waveguides
NASA Technical Reports Server (NTRS)
Ilchenko, Vladimir S.; Mohageg, Makan; Savchenkov, Anatoliy A.; Matsko, Andrey B.; Maleki, Lute
2007-01-01
In this paper we address efficient conversion between a Gaussian beam (a truncated plane wave) and a truncated Bessel beam of agiven order, using cylindrical optical waveguides and whispering gallery mode resonators. Utilizing a generator based on waveguides combined with whispering gallery mode resonators, we have realized Bessel beams of the order of 200 with a conversion efficiency exceeding 10 %.
Kim, So-Youn; Zhu, Jie; Woodruff, Teresa K
2011-08-01
The receptor-regulated protein Smad3 is key player in the signaling cascade stimulated by the binding of activin to its cell surface receptor. Upon phosphorylation, Smad3 forms a heterocomplex with Smad2 and Smad4, translocates to the nucleus and acts as a transcriptional co-activator. We have identified a unique isoform of Smad3 that is expressed in mature pituitary gonadotropes. 5' RACE revealed that this truncated Smad3 isoform is transcribed from an ATG site within exon 4 and consists of 7 exons encoding half of the linker region and the MH2 region. In pituitary cells, the truncated Smad3 isoform was phosphorylated upon activin treatment, in a manner that was temporally distinct from the phosphorylation of full-length Smad3. Activin-induced phosphorylation of Smad3 and the truncated Smad3 isoform was blocked by both follistatin and siRNA-mediated knockdown of Smad3. The truncated Smad3 isoform antagonized Smad3-mediated, activin-responsive promoter activity. We propose that the pituitary gonadotrope contains an ultra-short, activin-responsive feedback loop utilizing two different isoforms of Smad3, one which acts as an agonist (Smad3) and another that acts as an intracrine antagonist (truncated Smad3 isoform) to regulate FSHβ production. PMID:21664424
A Shifted Block Lanczos Algorithm 1: The Block Recurrence
NASA Technical Reports Server (NTRS)
Grimes, Roger G.; Lewis, John G.; Simon, Horst D.
1990-01-01
In this paper we describe a block Lanczos algorithm that is used as the key building block of a software package for the extraction of eigenvalues and eigenvectors of large sparse symmetric generalized eigenproblems. The software package comprises: a version of the block Lanczos algorithm specialized for spectrally transformed eigenproblems; an adaptive strategy for choosing shifts, and efficient codes for factoring large sparse symmetric indefinite matrices. This paper describes the algorithmic details of our block Lanczos recurrence. This uses a novel combination of block generalizations of several features that have only been investigated independently in the past. In particular new forms of partial reorthogonalization, selective reorthogonalization and local reorthogonalization are used, as is a new algorithm for obtaining the M-orthogonal factorization of a matrix. The heuristic shifting strategy, the integration with sparse linear equation solvers and numerical experience with the code are described in a companion paper.
Self-equilibrium and stability of regular truncated tetrahedral tensegrity structures
NASA Astrophysics Data System (ADS)
Zhang, J. Y.; Ohsaki, M.
2012-10-01
This paper presents analytical conditions of self-equilibrium and super-stability for the regular truncated tetrahedral tensegrity structures, nodes of which have one-to-one correspondence to the tetrahedral group. These conditions are presented in terms of force densities, by investigating the block-diagonalized force density matrix. The block-diagonalized force density matrix, with independent sub-matrices lying on its leading diagonal, is derived by making use of the tetrahedral symmetry via group representation theory. The condition for self-equilibrium is found by enforcing the force density matrix to have the necessary number of nullities, which is four for three-dimensional structures. The condition for super-stability is further presented by guaranteeing positive semi-definiteness of the force density matrix.
A Truncated Nef Peptide from SIVcpz Inhibits the Production of HIV-1 Infectious Progeny.
Sabino Cunha, Marcela; Lima Sampaio, Thatiane; Peterlin, B Matija; Jesus da Costa, Luciana
2016-01-01
Nef proteins from all primate Lentiviruses, including the simian immunodeficiency virus of chimpanzees (SIVcpz), increase viral progeny infectivity. However, the function of Nef involved with the increase in viral infectivity is still not completely understood. Nonetheless, until now, studies investigating the functions of Nef from SIVcpz have been conducted in the context of the HIV-1 proviruses. In an attempt to investigate the role played by Nef during the replication cycle of an SIVcpz, a Nef-defective derivative was obtained from the SIVcpzWTGab2 clone by introducing a frame shift mutation at a unique restriction site within the nef sequence. This nef-deleted clone expresses an N-terminal 74-amino acid truncated peptide of Nef and was named SIVcpz-tNef. We found that the SIVcpz-tNef does not behave as a classic nef-deleted HIV-1 or simian immunodeficiency virus of macaques SIVmac. Markedly, SIVcpz-tNef progeny from both Hek-293T and Molt producer cells were completely non-infectious. Moreover, the loss in infectivity of SIVcpz-tNef correlated with the inhibition of Gag and GagPol processing. A marked accumulation of Gag and very low levels of reverse transcriptase were detected in viral lysates. Furthermore, these observations were reproduced once the tNef peptide was expressed in trans both in SIVcpzΔNef and HIV-1WT expressing cells, demonstrating that the truncated peptide is a dominant negative for viral processing and infectivity for both SIVcpz and HIV-1. We demonstrated that the truncated Nef peptide binds to GagPol outside the protease region and by doing so probably blocks processing of both GagPol and Gag precursors at a very early stage. This study demonstrates for the first time that naturally-occurring Nef peptides can potently block lentiviral processing and infectivity. PMID:27399760
Tailor-made dimensions of diblock copolymer truncated micelles on a solid by UV irradiation.
Liou, Jiun-You; Sun, Ya-Sen
2015-09-28
We investigated the structural evolution of truncated micelles in ultrathin films of polystyrene-block-poly(2-vinylpyridine), PS-b-P2VP, of monolayer thickness on bare silicon substrates (SiOx/Si) upon UV irradiation in air- (UVIA) and nitrogen-rich (UVIN) environments. The structural evolution of micelles upon UV irradiation was monitored using GISAXS measurements in situ, while the surface morphology was probed using atomic force microscopy ex situ and the chemical composition using X-ray photoelectron spectroscopy (XPS). This work provides clear evidence for the interpretation of the relationship between the structural evolution and photochemical reactions in PS-b-P2VP truncated micelles upon UVIA and UVIN. Under UVIA treatment, photolysis and cross-linking reactions coexisted within the micelles; photolysis occurred mainly at the top of the micelles, whereas cross-linking occurred preferentially at the bottom. The shape and size of UVIA-treated truncated micelles were controlled predominantly by oxidative photolysis reactions, which depended on the concentration gradient of free radicals and oxygen along the micelle height. Because of an interplay between photolysis and photo-crosslinking, the scattering length densities (SLD) of PS and P2VP remained constant. In contrast, UVIN treatments enhanced the contrast in SLD between the PS shell and the P2VP core as cross-linking dominated over photolysis in the presence of nitrogen. The enhancement of the SLD contrast was due to the various degrees of cross-linking under UVIN for the PS and P2VP blocks. PMID:26251976
A Truncated Nef Peptide from SIVcpz Inhibits the Production of HIV-1 Infectious Progeny
Sabino Cunha, Marcela; Lima Sampaio, Thatiane; Peterlin, B. Matija; Jesus da Costa, Luciana
2016-01-01
Nef proteins from all primate Lentiviruses, including the simian immunodeficiency virus of chimpanzees (SIVcpz), increase viral progeny infectivity. However, the function of Nef involved with the increase in viral infectivity is still not completely understood. Nonetheless, until now, studies investigating the functions of Nef from SIVcpz have been conducted in the context of the HIV-1 proviruses. In an attempt to investigate the role played by Nef during the replication cycle of an SIVcpz, a Nef-defective derivative was obtained from the SIVcpzWTGab2 clone by introducing a frame shift mutation at a unique restriction site within the nef sequence. This nef-deleted clone expresses an N-terminal 74-amino acid truncated peptide of Nef and was named SIVcpz-tNef. We found that the SIVcpz-tNef does not behave as a classic nef-deleted HIV-1 or simian immunodeficiency virus of macaques SIVmac. Markedly, SIVcpz-tNef progeny from both Hek-293T and Molt producer cells were completely non-infectious. Moreover, the loss in infectivity of SIVcpz-tNef correlated with the inhibition of Gag and GagPol processing. A marked accumulation of Gag and very low levels of reverse transcriptase were detected in viral lysates. Furthermore, these observations were reproduced once the tNef peptide was expressed in trans both in SIVcpzΔNef and HIV-1WT expressing cells, demonstrating that the truncated peptide is a dominant negative for viral processing and infectivity for both SIVcpz and HIV-1. We demonstrated that the truncated Nef peptide binds to GagPol outside the protease region and by doing so probably blocks processing of both GagPol and Gag precursors at a very early stage. This study demonstrates for the first time that naturally-occurring Nef peptides can potently block lentiviral processing and infectivity. PMID:27399760
ERIC Educational Resources Information Center
Black, Susan
2001-01-01
Studies show that deteriorating school facilities take their toll on students' and teachers' health and morale. Classrooms should be accessible to the outdoors; clustered around a commons; adaptable and flexible; and aesthetically pleasing. Architects say natural lighting and noise reduction are routine parts of their job. Research studies support…
Enhanced light trapping in periodically truncated cone silicon nanowire structure
NASA Astrophysics Data System (ADS)
Kai, Qiu; Yuhua, Zuo; Tianwei, Zhou; Zhi, Liu; Jun, Zheng; Chuanbo, Li; Buwen, Cheng
2015-10-01
Light trapping plays an important role in improving the conversion efficiency of thin-film solar cells. The good wideband light trapping is achieved using our periodically truncated cone Si nanowire (NW) structures, and their inherent mechanism is analyzed and simulated by FDTD solution software. Ordered cylinder Si NW structure with initial size of 80 nm and length of 200 nm is grown by pattern transfer and selective epitaxial growth. Truncated cone Si NW array is then obtained by thermal oxidation treatment. Its mean reflection in the range of 300-900 nm is lowered to be 5% using 140 nm long truncated cone Si NW structure, compared with that of 20% using cylinder counterparts. It indicates that periodically truncated Si cone structures trap the light efficiently to enhance the light harvesting in a wide spectral range and have the potential application in highly efficient NW solar cells. Project supported by the National Natural Science Foundation of China (Nos. 51072194, 61021003, 61036001, 61376057).
Refractive turbulence effects on truncated Gaussian beam heterodyne lidar
NASA Technical Reports Server (NTRS)
Murty, R.
1984-01-01
A monostatic heterodyne lidar performance model is formulated to study the combined effects of beam truncation and refractive turbulence in the weak scintillation regime. The results show that there is a loss of signal power due to beam truncation and coherence loss, but there is also an enhancement of signal power due to log-amplitude covariance in suitable conditions of long paths with weak turbulence.
The effect of truncation on very small cardiac SPECT camerasystems
Rohmer, Damien; Eisner, Robert L.; Gullberg, Grant T.
2006-08-01
Background: The limited transaxial field-of-view (FOV) of avery small cardiac SPECT camera system causes view-dependent truncationof the projection of structures exterior to, but near the heart. Basictomographic principles suggest that the reconstruction of non-attenuatedtruncated data gives a distortion-free image in the interior of thetruncated region, but the DC term of the Fourier spectrum of thereconstructed image is incorrect, meaning that the intensity scale of thereconstruction is inaccurate. The purpose of this study was tocharacterize the reconstructed image artifacts from truncated data, andto quantify their effects on the measurement of tracer uptake in themyocardial. Particular attention was given to instances where the heartwall is close to hot structures (structures of high activity uptake).Methods: The MCAT phantom was used to simulate a 2D slice of the heartregion. Truncated and non-truncated projections were formed both with andwithout attenuation. The reconstructions were analyzed for artifacts inthe myocardium caused by truncation, and for the effect that attenuationhas relative to increasing those artifacts. Results: The inaccuracy dueto truncation is primarily caused by an incorrect DC component. Forvisualizing theleft ventricular wall, this error is not worse than theeffect of attenuation. The addition of a small hot bowel-like structurenear the left ventricle causes few changes in counts on the wall. Largerartifacts due to the truncation are located at the boundary of thetruncation and can be eliminated by sinogram interpolation. Finally,algebraic reconstruction methods are shown to give better reconstructionresults than an analytical filtered back-projection reconstructionalgorithm. Conclusion: Small inaccuracies in reconstructed images fromsmall FOV camera systems should have little effect on clinicalinterpretation. However, changes in the degree of inaccuracy in countsfrom slice toslice are due to changes in the truncated structures
An algorithm to estimate the object support in truncated images
Hsieh, Scott S.; Nett, Brian E.; Cao, Guangzhi; Pelc, Norbert J.
2014-07-15
Purpose: Truncation artifacts in CT occur if the object to be imaged extends past the scanner field of view (SFOV). These artifacts impede diagnosis and could possibly introduce errors in dose plans for radiation therapy. Several approaches exist for correcting truncation artifacts, but existing correction algorithms do not accurately recover the skin line (or support) of the patient, which is important in some dose planning methods. The purpose of this paper was to develop an iterative algorithm that recovers the support of the object. Methods: The authors assume that the truncated portion of the image is made up of soft tissue of uniform CT number and attempt to find a shape consistent with the measured data. Each known measurement in the sinogram is interpreted as an estimate of missing mass along a line. An initial estimate of the object support is generated by thresholding a reconstruction made using a previous truncation artifact correction algorithm (e.g., water cylinder extrapolation). This object support is iteratively deformed to reduce the inconsistency with the measured data. The missing data are estimated using this object support to complete the dataset. The method was tested on simulated and experimentally truncated CT data. Results: The proposed algorithm produces a better defined skin line than water cylinder extrapolation. On the experimental data, the RMS error of the skin line is reduced by about 60%. For moderately truncated images, some soft tissue contrast is retained near the SFOV. As the extent of truncation increases, the soft tissue contrast outside the SFOV becomes unusable although the skin line remains clearly defined, and in reformatted images it varies smoothly from slice to slice as expected. Conclusions: The support recovery algorithm provides a more accurate estimate of the patient outline than thresholded, basic water cylinder extrapolation, and may be preferred in some radiation therapy applications.
Non-perturbative Renormalization in Truncated Yukawa Model
NASA Astrophysics Data System (ADS)
Karmanov, V. A.
2016-06-01
An approach to non-perturbative calculations in the light-front quantum field theory and its new developments are briefly reviewed. We start with the decomposition of the state vector in Fock components. After truncation of this decomposition (main approximation in this approach), the eigenvalue equation for the light-front Hamiltonian generates, in Minkowski space, a finite system of integral equations for the Fock components. Solving this system numerically and performing the non-perturbative renormalization, we find the state vector of fermion in the quenched scalar Yukawa model, up to the four-body truncation (one fermion + three bosons), for rather large values of the coupling constant. With the state vector, found in this way, the fermion electromagnetic form factors are calculated. Comparing results obtained in the four-body truncation with those found in the previous, three-body truncation, we discover very good convergence relative to truncation, that indicates that we are close to the exact non-perturbative solution in this field-theoretical model. The approach can be extended to more realistic field theories and, after further development, it could constitute an alternative to the lattice calculations.
Dish antenna having switchable beamwidth. [with truncated concave ellipsoid subreflector
NASA Technical Reports Server (NTRS)
Schmidt, R. F. (Inventor)
1975-01-01
A switchable beamwidth antenna includes a concave parabolic main reflecting dish which has a central circular region and a surrounding coaxial annular region. A feed means selectively excites only the central region of the main dish via a truncated subreflector for wide beamwidth or substantially the entire main dish for narrow beamwidth. In one embodiment, the feed means comprises a truncated concave ellipsoid subreflector and separate feed terminations located at two foci of the ellipsoid. One feed termination directly views all of the main dish while the other feed termination, exciting the main dish via the subreflector, excites only the central region because of the subreflector truncation. In the another embodiment, the feed means comprises one feed termination and a convex hyperboloid subreflector via which the feed excites the main dish.
Effects of truncation in modal representations of thermal convection
NASA Technical Reports Server (NTRS)
Marcus, P. S.
1979-01-01
The Galerkin (including single-mode and Lorenz) equations were examined for convection in a sphere to determine which physical processes are neglected when the equations of motion are truncated too severely. The conclusions were tested by calculating solutions to the equations of motion for different values of the Rayleigh number and for different values of the limit of the horizontal spatial resolution. It was shown that the transitions from steady state to periodic, then to aperiodic convection depend not only on the Rayleigh number but also very strongly on the horizontal resolution. One of the effects of truncation is to enhance the high wavenumber end of the kinetic energy and thermal variance spectra. The numerical examples indicate that as long as the kinetic energy spectrum decreases with wavenumber, a truncation gives a qualitatively correct solution.
Truncated Long-Range Percolation on Oriented Graphs
NASA Astrophysics Data System (ADS)
van Enter, A. C. D.; de Lima, B. N. B.; Valesin, D.
2016-07-01
We consider different problems within the general theme of long-range percolation on oriented graphs. Our aim is to settle the so-called truncation question, described as follows. We are given probabilities that certain long-range oriented bonds are open; assuming that the sum of these probabilities is infinite, we ask if the probability of percolation is positive when we truncate the graph, disallowing bonds of range above a possibly large but finite threshold. We give some conditions in which the answer is affirmative. We also translate some of our results on oriented percolation to the context of a long-range contact process.
A Flexible Variable Truncated Power Series Algebra in Zlib
Yan, Y.T.; /SLAC
2011-08-25
Zlib is a numerical library for Truncated Power Series Algebra (TPSA) and Lie Algebra for application to nonlinear analysis of single particle dynamics. The first version was developed in 1990 with the use of the One-Step Index Pointers (OSIP's). The OSIP's form the Zlib nerve that offers optimal computation and alloworder grading as well as flexible initialization of the global number of variables for the TPSA. While the OSIP's are still kept for minimum index passing to achieve efficient computation, Zlib has been being upgraded to allow flexible and gradable local number of variables in each C++ object of the Truncated Power Series (Tps) class. Possible applications using Zlib are discussed.
Real-time low-energy fall detection algorithm with a programmable truncated MAC.
de la Guia Solaz, Manuel; Bourke, Alan; Conway, Richard; Nelson, John; Olaighin, Gearoid
2010-01-01
The ability to discriminate between falls and activities of daily living (ADL) has been investigated by using tri-axial accelerometer sensors, mounted on the trunk and using simulated falls performed by young healthy subjects under supervised conditions and ADL performed by elderly subjects. In this paper we propose a power-aware real-time fall detection integrated circuit (IC) that can distinguish Falls from ADL by processing the accelerations measured during 240 falls and 240 ADL. In the proposed fixed point custom DSP architecture, a threshold algorithm was implemented to analyze the effectiveness of Programmable Truncated Multiplication regarding power reduction while maintaining a high output accuracy. The presented system runs a real time implementation of the algorithm on a low power architecture that allows up to 23% power savings through its digital blocks when compared to a standard implementation, without any accuracy loss. PMID:21095956
SOUTHERLY STRETCH OF MILLBURY PORTION; CLOSER VIEW OF TRUNCATED NORTHERLY ...
SOUTHERLY STRETCH OF MILLBURY PORTION; CLOSER VIEW OF TRUNCATED NORTHERLY END OF TOWPATH BERM (RIGHT) AND CANAL PRISM (LEFT); VIEW TO SOUTH FROM LATER BORROW PIT - Blackstone Canal Worcester-Millbury Segment, Eastern bank of Blackstone River, Millbury, Worcester County, MA
The truncation model of the derivative nonlinear Schroedinger equation
Sanchez-Arriaga, G.; Hada, T.; Nariyuki, Y.
2009-04-15
The derivative nonlinear Schroedinger (DNLS) equation is explored using a truncation model with three resonant traveling waves. In the conservative case, the system derives from a time-independent Hamiltonian function with only one degree of freedom and the solutions can be written using elliptic functions. In spite of its low dimensional order, the truncation model preserves some features from the DNLS equation. In particular, the modulational instability criterion fits with the existence of two hyperbolic fixed points joined by a heteroclinic orbit that forces the exchange of energy between the three waves. On the other hand, numerical integrations of the DNLS equation show that the truncation model fails when wave energy is increased or left-hand polarized modulational unstable modes are present. When dissipative and growth terms are added the system exhibits a very complex dynamics including appearance of several attractors, period doubling bifurcations leading to chaos as well as other nonlinear phenomenon. In this case, the validity of the truncation model depends on the strength of the dissipation and the kind of attractor investigated.
Two truncated forms of rat insulin receptor-related receptor.
Itoh, N; Jobo, K; Tsujimoto, K; Ohta, M; Kawasaki, T
1993-08-25
The insulin receptor-related receptor (IRR) (1271 amino acids) is expected to have unique functions as a novel member of the insulin receptor family. In this paper, we report two alternatively spliced variants of rat IRR mRNA, which are predicted to encode two truncated forms of IRR, sIRR-1 (410 amino acids) and sIRR-2 (469 amino acids). The amino acid sequence of sIRR-1 is identical to the N-terminal 410-amino acid sequence of IRR. sIRR-2 has an additional 59-amino acid insertion in the C-terminal region. Both truncated forms retain the N-terminal and cysteine-rich domains but lack the transmembrane and intracellular tyrosine kinase domains, indicating that the truncated forms are the secreted forms. The translation products of the truncated form mRNAs were detected in the stomach and kidney by Western analysis. However, the physiological significance of the secreted forms remains to be elucidated. PMID:7688734
Truncation selection and payoff distributions applied to the replicator equation.
Morsky, B; Bauch, C T
2016-09-01
The replicator equation has been frequently used in the theoretical literature to explain a diverse array of biological phenomena. However, it makes several simplifying assumptions, namely complete mixing, an infinite population, asexual reproduction, proportional selection, and mean payoffs. Here, we relax the conditions of mean payoffs and proportional selection by incorporating payoff distributions and truncation selection into extensions of the replicator equation and agent-based models. In truncation selection, replicators with fitnesses above a threshold survive. The reproduction rate is equal for all survivors and is sufficient to replace the replicators that did not survive. We distinguish between two types of truncation: independent and dependent with respect to the fitness threshold. If the payoff variances from all strategy pairing are the same, then we recover the replicator equation from the independent truncation equation. However, if all payoff variances are not equal, then any boundary fixed point can be made stable (or unstable) if only the fitness threshold is chosen appropriately. We observed transient and complex dynamics in our models, which are not observed in replicator equations incorporating the same games. We conclude that the assumptions of mean payoffs and proportional selection in the replicator equation significantly impact replicator dynamics. PMID:27343031
12. DOUBLEDAY AVENUE NEAR MUMMASBURG ROAD. NOTE TRUNCATED OBSERVATION TOWER ...
12. DOUBLEDAY AVENUE NEAR MUMMASBURG ROAD. NOTE TRUNCATED OBSERVATION TOWER AND ROAD SIGN VARIATIONS (CAST IRON PLACE NAME AT LEFT / AUTO TOUR SIGN AT RIGHT). ALSO NOTE CONCRETE BOLLARDS TO CONTROL PARKING. VIEW S. - Gettysburg National Military Park Tour Roads, Gettysburg, Adams County, PA
78 FR 6273 - IRS Truncated Taxpayer Identification Numbers; Correction
Federal Register 2010, 2011, 2012, 2013, 2014
2013-01-30
...This document contains corrections to a notice of proposed rulemaking (REG-148873-09) and notice of public hearing that was published in the Federal Register on Monday, January 7, 2013 (78 FR 913). The proposed regulation provides guidance regarding creating a new taxpayer identifying number known as an IRS truncated taxpayer identification number, a...
Mediation of opioid analgesia by a truncated 6-transmembrane GPCR
Lu, Zhigang; Xu, Jin; Rossi, Grace C.; Majumdar, Susruta; Pasternak, Gavril W.; Pan, Ying-Xian
2015-01-01
The generation of potent opioid analgesics that lack the side effects of traditional opioids may be possible by targeting truncated splice variants of the μ-opioid receptor. μ-Opioids act through GPCRs that are generated from the Oprm1 gene, which undergoes extensive alternative splicing. The most abundant set of Oprm1 variants encode classical full-length 7 transmembrane domain (7TM) μ-opioid receptors that mediate the actions of the traditional μ-opioid drugs morphine and methadone. In contrast, 3-iodobenzoyl-6β-naltrexamide (IBNtxA) is a potent analgesic against thermal, inflammatory, and neuropathic pain that acts independently of 7TM μ-opioid receptors but has no activity in mice lacking a set of 6TM truncated μ-opioid receptor splice variants. Unlike traditional opioids, IBNtxA does not depress respiration or result in physical dependence or reward behavior, suggesting it acts through an alternative μ-opioid receptor target. Here we demonstrated that a truncated 6TM splice variant, mMOR-1G, can rescue IBNtxA analgesia in a μ-opioid receptor–deficient mouse that lacks all Oprm1 splice variants, ablating μ-opioid activity in these animals. Intrathecal administration of lentivirus containing the 6TM variant mMOR-1G restored IBNtxA, but not morphine, analgesia in Oprm1-deficient animals. Together, these results confirm that a truncated 6TM GPCR is both necessary and sufficient for IBNtxA analgesia. PMID:26011641
On the ijk forms of the truncated LU decomposition
NASA Astrophysics Data System (ADS)
Mohsen, A.
2009-11-01
Matrix LU decomposition has six ijk forms. Different forms have different computational complexities and storage requirements, particularly on vector and parallel computers. Other factors governing the choice of a particular form are considered. For treating Fredholm integral equations of the first kind, the truncated LU decomposition of the resulting system matrix is recommended. Required modifications to selected known ijk forms are presented.
Assessing association between protein truncating variants and quantitative traits
Rivas, Manuel A.; Pirinen, Matti; Neville, Matthew J.; Gaulton, Kyle J.; Moutsianas, Loukas; Lindgren, Cecilia M.; Karpe, Fredrik; McCarthy, Mark I.; Donnelly, Peter
2013-01-01
Motivation: In sequencing studies of common diseases and quantitative traits, power to test rare and low frequency variants individually is weak. To improve power, a common approach is to combine statistical evidence from several genetic variants in a region. Major challenges are how to do the combining and which statistical framework to use. General approaches for testing association between rare variants and quantitative traits include aggregating genotypes and trait values, referred to as ‘collapsing’, or using a score-based variance component test. However, little attention has been paid to alternative models tailored for protein truncating variants. Recent studies have highlighted the important role that protein truncating variants, commonly referred to as ‘loss of function’ variants, may have on disease susceptibility and quantitative levels of biomarkers. We propose a Bayesian modelling framework for the analysis of protein truncating variants and quantitative traits. Results: Our simulation results show that our models have an advantage over the commonly used methods. We apply our models to sequence and exome-array data and discover strong evidence of association between low plasma triglyceride levels and protein truncating variants at APOC3 (Apolipoprotein C3). Availability: Software is available from http://www.well.ox.ac.uk/~rivas/mamba Contact: donnelly@well.ox.ac.uk PMID:23860716
Consistent N=8 truncation of massive IIA on S 6
NASA Astrophysics Data System (ADS)
Guarino, Adolfo; Varela, Oscar
2015-12-01
Massive type IIA supergravity is shown to admit a consistent truncation on the six-sphere to maximal supergravity in four dimensions with a dyonic ISO(7) gauging. We obtain the complete, non-linear embedding of all the D = 4 fields into the IIA metric and form potentials, and show its consistency. We first rewrite the IIA theory in an SO(1 , 3) × SL(7)-covariant way. Then, we employ an N=8 SL(7)-covariant restriction of the D = 4 tensor hierarchy in order to find the full embedding. The redundant D = 4 degrees of freedom introduced by the tensor hierarchy can be eliminated by writing the embedding in terms of the field strengths and exploiting the restricted duality hierarchy. In particular, closed expressions for the Freund-Rubin term are found using this technique which reveal a pattern valid for other truncations. Finally, we show that the present N=8 truncation of massive IIA on S 6 and the N=2 truncation obtained when S 6 is equipped with its nearly-Kähler structure, overlap in the N=1 , G2-invariant sector of the former.
NASA Astrophysics Data System (ADS)
Yamakawa, Keisuke; Kojima, Shinichi
2014-03-01
Iteratively reconstructing data only inside the region of interest (ROI) is widely used to acquire CT images in less computation time while maintaining high spatial resolution. A method that subtracts projected data outside the ROI from full-coverage measured data has been proposed. A serious problem with this method is that the accuracy of the measured data confined inside the ROI decreases according to the truncation error outside the ROI. We propose a two-step iterative method that reconstructs image inside the full-coverage in addition to a conventional iterative method inside the ROI to reduce the truncation error inside full-coverage images. Statistical information (e.g., quantum-noise distributions) acquired by detected X-ray photons is generally used in iterative methods as a photon weight to efficiently reduce image noise. Our proposed method applies one of two kinds of weights (photon or constant weights) chosen adaptively by taking into consideration the influence of truncation error. The effectiveness of the proposed method compared with that of the conventional method was evaluated in terms of simulated CT values by using elliptical phantoms and an abdomen phantom. The standard deviation of error and the average absolute error of the proposed method on the profile curve were respectively reduced from 3.4 to 0.4 [HU] and from 2.8 to 0.8 [HU] compared with that of the conventional method. As a result, applying a suitable weight on the basis of a target object made it possible to effectively reduce the errors in CT images.
Truncation and use of model-coordinate data
NASA Astrophysics Data System (ADS)
Trenberth, Kevin E.
1995-05-01
The advantages and disadvantages of using global analyses on pressure level surfaces versus model (sigma or hybrid) level surfaces are explored. Model levels consist of a terrain-following coordinate in the lowest levels but may gradually transition to pressure with height. One major issue is that the model surface often does not correspond with the earth's real surface. Another is that a change in horizontal resolution is not well defined because the vertical coordinate also changes in the process. However, such changes are required as comparison of analyses from one center with another or with model output requires a common vertical coordinate. Also, a reduction from high resolution with 106 waves (T106 resolution) to a moderate resolution with, say, 42 waves (T42), so as to reduce the size of datasets by a factor of about 6, is often desirable. Another issue involves the meaning and use of time averages on model surfaces and their relationship to corresponding time averages on pressure surfaces. The traditional representation on constant pressure surfaces has much to recommend it and is widely used and familiar to the community, but suffers from errors arising from interpolation to the pressure surfaces and the need to properly treat regions of those surfaces that are below ground (in regions of high topography). Spectral truncation and resolution changes are well defined on pressure surfaces. Test results are presented for cases where T106 analyses on model surfaces are (1) transformed to pressure and then truncated, (2) truncated and then transformed to pressure levels, and (3) then compared at comparable resolutions. The differences arise mainly from the ill-posed truncation on model surfaces, but also from vertical interpolations. These tests are also applied to a heat budget calculation involving nonlinear terms for one month. However, the latter comparison also brings in considerations of how best to do time averaging. Fortunately, in practical terms
Block 3, People in Cities: An Ecological Approach.
ERIC Educational Resources Information Center
Oates, John
An Open University course text, People in Cities--An Ecological Approach (Block 3), is presented. Three sections of the block are: the ecology of urban life, socialization and some implications for the urban child, and the compensatory debate. Some of the adaptive processes and ways in which failures of adaptation are distributed in different…
Exploring Quantum Many-Body Spin Dynamics with Truncated Wigner Methods
NASA Astrophysics Data System (ADS)
Schachenmayer, Johannes
Recent experiments in atomic, molecular, and optical physics offer controlled and clean environments to experimentally study non-equilibrium dynamics of large many-body quantum spin-models with variable range interactions. Thus, efficient computation of such dynamics is of great importance. While in one dimension, time-dependent density matrix renormalization group methods (t-DMRG) have proven effective under certain conditions, computing dynamics in higher dimensional systems remains an outstanding challenge. Recently we formulated the discrete truncated Wigner approximation (DTWA), a semiclassical method based on the truncated Wigner approximation (TWA) that has been proven to be surprisingly accurate in predicting quench dynamics in high-dimensional lattices with up to tens of thousands of quantum spins. Here, we introduce the DTWA and show how it can compute time-evolution of quantum states in experiments that engineer spin-models with polar molecules in optical lattices or with ions in two-dimensional Penning traps. We show, how the DTWA can provide results for the time-evolution of classical and quantum correlations in quench experiments in regimes where other numerical methods are generally unreliable. We report on progress of how to incorporate higher order corrections to the method, and how to adapt it to systems with both spin and bosonic degrees of freedom.
Zhao, Zhilong; Shi, Ting; Xu, Min; Brock, Nelson L; Zhao, Yi-Lei; Wang, Yemin; Deng, Zixin; Pang, Xiuhua; Tao, Meifeng
2016-02-01
Heterologous expression of bacterial artificial chromosome (BAC) clones from the genomic library of Streptomyces variabilis Snt24 in Streptomyces lividans SBT5 which carried a truncated undecylprodigiosin biosynthetic gene cluster led to the identification of hybrubins A-C. The hybrubins represent a new carbon skeleton in which a tetramic acid moiety is fused to a 2,2'-dipyrrole building block. Gene knockout experiments confirmed that hybrubins are derived from two convergent biosynthetic pathways including the remaining genomic red genes of S. lividans SBT5 as well as the BAC encoded hbn genes for the production of 5-ethylidenetetramic acid. A possible biosynthetic pathway was also proposed. PMID:26800378
... Block Explore Heart Block What Is... Electrical System & EKG Results Types Causes Who Is at Risk Signs & ... the P and the R waves on the EKG (electrocardiogram). First-degree heart block may not cause ...
Data consistency conditions for truncated fanbeam and parallel projections
Clackdoyle, Rolf; Desbat, Laurent
2015-02-15
Purpose: In image reconstruction from projections, data consistency conditions (DCCs) are mathematical relationships that express the overlap of information between ideal projections. DCCs have been incorporated in image reconstruction procedures for positron emission tomography, single photon emission computed tomography, and x-ray computed tomography (CT). Building on published fanbeam DCCs for nontruncated projections along a line, the authors recently announced new DCCs that can be applied to truncated parallel projections in classical (two-dimensional) image reconstruction. These DCCs take the form of polynomial expressions for a weighted backprojection of the projections. The purpose of this work was to present the new DCCs for truncated parallel projections, to extend these conditions to truncated fanbeam projections on a circular trajectory, to verify the conditions with numerical examples, and to present a model of how DCCs could be applied with a toy problem in patient motion estimation with truncated projections. Methods: A mathematical derivation of the new parallel DCCs was performed by substituting the underlying imaging equation into the mathematical expression for the weighted backprojection and demonstrating the resulting polynomial form. This DCC result was extended to fanbeam projections by a substitution of parallel to fanbeam variables. Ideal fanbeam projections of a simple mathematical phantom were simulated and the DCCs for these projections were evaluated by fitting polynomials to the weighted backprojection. For the motion estimation problem, a parametrized motion was simulated using a dynamic version of the mathematical phantom, and both noiseless and noisy fanbeam projections were simulated for a full circular trajectory. The fanbeam DCCs were applied to extract the motion parameters, which allowed the motion contamination to be removed from the projections. A reconstruction was performed from the corrected projections. Results: The
Caspase-3-mediated Cleavage of Cdc6 Induces Nuclear Localization of p49-truncated Cdc6 and Apoptosis
Yim, Hyungshin; Jin, Ying Hua; Park, Byoung Duck; Choi, Hye Jin; Lee, Seung Ki
2003-01-01
We show that Cdc6, an essential initiation factor for DNA replication, undergoes caspase-3–mediated cleavage in the early stages of apoptosis in HeLa cells and SK-HEP-1 cells induced by etoposide, paclitaxel, ginsenoside Rh2, or tumor necrosis factor-related apoptosis-inducing ligand. The cleavage occurs at the SEVD442/G motif and generates an N-terminal truncated Cdc6 fragment (p49-tCdc6) that lacks the carboxy-terminal nuclear export sequence. Cdc6 is known to be phosphorylated by cyclin A-cyclin dependent kinase 2 (Cdk2), an event that promotes its exit from the nucleus and probably blocks it from initiating inappropriate DNA replication. In contrast, p49-tCdc6 translocation to the cytoplasm is markedly reduced under the up-regulated conditions of Cdk2 activity, which is possibly due to the loss of nuclear export sequence. Thus, truncation of Cdc6 results in an increased nuclear retention of p49-tCdc6 that could act as a dominant negative inhibitor of DNA replication and its accumulation in the nucleus could promote apoptosis. Supporting this is that the ectopic expression of p49-tCdc6 not only promotes apoptosis of etoposide-induced HeLa cells but also induces apoptosis in untreated cells. Thus, the caspase-mediated cleavage of Cdc6 creates a truncated Cdc6 fragment that is retained in the nucleus and induces apoptosis. PMID:14517333
He, Shanshan; Zhao, Zhen; Yang, Yongfei; O'Connell, Douglas; Zhang, Xiaowei; Oh, Soohwan; Ma, Binyun; Lee, Joo-Hyung; Zhang, Tian; Varghese, Bino; Yip, Janae; Dolatshahi Pirooz, Sara; Li, Ming; Zhang, Yong; Li, Guo-Min; Ellen Martin, Sue; Machida, Keigo; Liang, Chengyu
2015-01-01
Autophagy-related factors are implicated in metabolic adaptation and cancer metastasis. However, the role of autophagy factors in cancer progression and their effect in treatment response remain largely elusive. Recent studies have shown that UVRAG, a key autophagic tumour suppressor, is mutated in common human cancers. Here we demonstrate that the cancer-related UVRAG frameshift (FS), which does not result in a null mutation, is expressed as a truncated UVRAGFS in colorectal cancer (CRC) with microsatellite instability (MSI), and promotes tumorigenesis. UVRAGFS abrogates the normal functions of UVRAG, including autophagy, in a dominant-negative manner. Furthermore, expression of UVRAGFS can trigger CRC metastatic spread through Rac1 activation and epithelial-to-mesenchymal transition, independently of autophagy. Interestingly, UVRAGFS expression renders cells more sensitive to standard chemotherapy regimen due to a DNA repair defect. These results identify UVRAG as a new MSI target gene and provide a mechanism for UVRAG participation in CRC pathogenesis and treatment response. PMID:26234763
Estimators for the truncated beta-binomial distribution
Atwood, C.L.
1980-01-01
Let X have a beta-binomial(m,p,theta) distribution, truncated such that X > t for t = 0 or 1. Suppose that independent observations of X are available. A consistent estimator of (p,theta) is given, based on the first three sample moments. This may be used as a start for maximum likelihood estimation or jackknifing. The standard assumptions for a C(..cap alpha..) is truncated binomial do not hold; however, a test is proposed based on jackknifing the sample variance of X. Some Monte Carlo comparisons are given. For moderately small data sets, these comparisons show that the moment estimator is often superior to the MLE, and the C(..cap alpha..) test is superior to other proposed tests, in spite of its lack of theoretical justification. 3 figures, 5 tables.
Reconstructions from parallel- and fan-beam data with truncations
NASA Astrophysics Data System (ADS)
Xia, Dan; Zou, Yu; Pan, Xiaochuan
2006-03-01
A formula was recently described by Clackdoyle et. al. for image reconstruction within a region of interest (ROI) from knowledge of its truncated 2D Radon transform. In this work, we present an alternative, simple derivation of the formula by using the well-known relationship between the parallel-beam and fan-beam geometries. Based upon our derivation, the role of parameter t in the formula in ROI-image reconstruction can be clearly identified. We show that the parameter t determines the size of a reconstructible ROI from parallel-beam data containing truncations. Numerical studies were performed to by use of the formula with different t. We show that the formula yields ROI images with smaller sizes and lower quality than does our backprojection filtration algorithm.
A truncation error injection approach to viscous-inviscid interaction
NASA Technical Reports Server (NTRS)
Goble, B. D.; Fung, K.-Y.
1987-01-01
An approach to viscous-inviscid interaction which is based on truncation error injection is presented in the context of solving flow over an airfoil. A two-dimensional interpolation scheme is used to restrict the fine grid solutions to the global coarse grid. Details on the current implementation of the approach are given, and the boundary conditions being used are discussed. Inviscid results from a NACA0012 airfoil test case and the viscous results are presented.
Truncation artifact and boundary artifact reduction in breast tomosynthesis reconstruction
NASA Astrophysics Data System (ADS)
Zhang, Yiheng; Chan, Heang-Ping; Wu, Yi-Ta; Sahiner, Berkman; Zhou, Chuan; Wei, Jun; Ge, Jun; Hadjiiski, Lubomir M.; Shi, Jiazheng
2008-03-01
Digital Tomosynthesis Mammography (DTM) is an emerging technique that has the potential to improve breast cancer detection. DTM acquires low-dose mammograms at a number of projection angles over a limited angular range and reconstructs the 3D breast volume. Due to the limited number of projections within a limited angular range and the finite size of the detector, DTM reconstruction contains boundary and truncation artifacts that degrade the image quality of the tomosynthesized slices, especially that of the boundary and truncated regions. In this work, we developed artifact reduction methods that make use of both 2D and 3D breast boundary information and local intensity-equalization and tissue-compensation techniques. A breast phantom containing test objects and a selected DTM patient case were used to evaluate the effects of artifact reduction. The contrast-to-noise ratio (CNR), the normalized profiles of test objects, and a non-uniformity error index were used as performance measures. A GE prototype DTM system was used to acquire 21 PVs in 3° increments over a +/-30° angular range. The Simultaneous Algebraic Reconstruction Technique (SART) was used for DTM reconstruction. Our results demonstrated that the proposed methods can improve the image quality both qualitatively and quantitatively, resulting in increased CNR value, background uniformity and an overall reconstruction quality comparable to that without truncation. For the selected DTM patient case, the obscured breast structural information near the truncated regions was essentially recovered. In addition, restricting SART reconstruction to be performed within the estimated 3D breast volume increased the computation efficiency.
Some new applications of truncated Gauss-Laguerre quadrature formulas
NASA Astrophysics Data System (ADS)
Mastroianni, G.; Monegato, G.
2008-12-01
We show how truncated Gauss-Laguerre quadrature formulas can be used to produce accurate approximations and high rates of convergence, also when they are applied to integrand functions having only an algebraic type decay to zero at infinity. The approach presented in the paper is proposed for the computation of integrals and for the construction of Nyström type interpolants for some second kind integral equations.
Power conservation for reflector antennas with truncated feed patterns
NASA Technical Reports Server (NTRS)
Rush, W. V. T.; Cramer, P.
1976-01-01
Reflector-antenna calculations using idealised truncated feed patterns can lead to incorrect values of total secondary radiated power. It is demonstrated that this discrepancy is due to the presence of higher-order spherical modes incident on the reflector. When a proper spherical-wave expansion of the incident field is used, in conjunction with the physical-optics technique, to determine the scattered field, the total power of the scattered field will equal the power radiated by the feed.
Technical Pitfalls of Signal Truncation in Perfusion MRI of Glioblastoma
Wong, Kelvin K.; Fung, Steve H.; New, Pamela Z.; Wong, Stephen T. C.
2016-01-01
Dynamic susceptibility contrast (DSC) perfusion-weighted imaging (PWI) is widely used in clinical settings for the radiological diagnosis of brain tumor. The signal change in brain tissue in gradient echo-based DSC PWI is much higher than in spin echo-based DSC PWI. Due to its exquisite sensitivity, gradient echo-based sequence is the preferred method for imaging of all tumors except those near the base of the skull. However, high sensitivity also comes with a dynamic range problem. It is not unusual for blood volume to increase in gene-mediated cytotoxic immunotherapy-treated glioblastoma patients. The increase of fractional blood volume sometimes saturates the MRI signal during first-pass contrast bolus arrival and presents signal truncation artifacts of various degrees in the tumor when a significant amount of blood exists in the image pixels. It presents a hidden challenge in PWI, as this signal floor can be either close to noise level or just above and can go no lower. This signal truncation in the signal intensity time course is a significant issue that deserves attention in DSC PWI. In this paper, we demonstrate that relative cerebral blood volume and relative cerebral blood flow (rCBF) are underestimated due to signal truncation in DSC perfusion, in glioblastoma patients. We propose the use of second-pass tissue residue function in rCBF calculation using least-absolute-deviation deconvolution to avoid the underestimation problem. PMID:27531989
Technical Pitfalls of Signal Truncation in Perfusion MRI of Glioblastoma.
Wong, Kelvin K; Fung, Steve H; New, Pamela Z; Wong, Stephen T C
2016-01-01
Dynamic susceptibility contrast (DSC) perfusion-weighted imaging (PWI) is widely used in clinical settings for the radiological diagnosis of brain tumor. The signal change in brain tissue in gradient echo-based DSC PWI is much higher than in spin echo-based DSC PWI. Due to its exquisite sensitivity, gradient echo-based sequence is the preferred method for imaging of all tumors except those near the base of the skull. However, high sensitivity also comes with a dynamic range problem. It is not unusual for blood volume to increase in gene-mediated cytotoxic immunotherapy-treated glioblastoma patients. The increase of fractional blood volume sometimes saturates the MRI signal during first-pass contrast bolus arrival and presents signal truncation artifacts of various degrees in the tumor when a significant amount of blood exists in the image pixels. It presents a hidden challenge in PWI, as this signal floor can be either close to noise level or just above and can go no lower. This signal truncation in the signal intensity time course is a significant issue that deserves attention in DSC PWI. In this paper, we demonstrate that relative cerebral blood volume and relative cerebral blood flow (rCBF) are underestimated due to signal truncation in DSC perfusion, in glioblastoma patients. We propose the use of second-pass tissue residue function in rCBF calculation using least-absolute-deviation deconvolution to avoid the underestimation problem. PMID:27531989
Importance-truncated large-scale shell model
NASA Astrophysics Data System (ADS)
Stumpf, Christina; Braun, Jonas; Roth, Robert
2016-02-01
We propose an importance-truncation scheme for the large-scale nuclear shell model that extends its range of applicability to larger valence spaces and midshell nuclei. It is based on a perturbative measure for the importance of individual basis states that acts as an additional truncation for the many-body model space in which the eigenvalue problem of the Hamiltonian is solved numerically. Through a posteriori extrapolations of all observables to vanishing importance threshold, the full shell-model results can be recovered. In addition to simple threshold extrapolations, we explore extrapolations based on the energy variance. We apply the importance-truncated shell model for the study of 56Ni in the p f valence space and of 60Zn and 64Ge in the p f g9 /2 space. We demonstrate the efficiency and accuracy of the approach, which pave the way for future applications of valence-space interactions derived in ab initio approaches in larger valence spaces.
Incremental truncation of PHA synthases results in altered product specificity.
Wang, Qian; Xia, Yongzhen; Chen, Quan; Qi, Qingsheng
2012-05-10
PHA synthase is the key enzyme involved in the biosynthesis of microbial polymers, polyhydroxyalkanoates (PHA). In this study, we created a hybrid library of PHA synthase gene with different crossover points by an incremental truncation method between the C-terminal fragments of the phaC(Cn) (phaC from Cupriavidus necator) and the N-terminal fragments of the phaC1(Pa) (phaC from Pseudomonas aeruginosa). As the truncation of the hybrid enzyme increased, the in vivo PHB synthesis ability of the hybrids declined gradually. PHA synthase PhaC(Cn) with a deletion on N-terminal up to 83 amino acid residues showed no synthase activity. While with the removal of up to 270 amino acids from the N-terminus, the activity of the truncated PhaC(Cn) could be complemented by the N-terminus of PhaC1(Pa). Three of the hybrid enzymes W188, W235 and W272 (named by the deleted nucleic acid number) were found to have altered product specificities. PMID:22500895
Parameterizing the power spectrum: Beyond the truncated Taylor expansion
Abazajian, Kevork; Kadota, Kenji; Stewart, Ewan D.; /KAIST, Taejon /Canadian Inst. Theor. Astrophys.
2005-07-01
The power spectrum is traditionally parameterized by a truncated Taylor series: ln P(k) = ln P{sub *} + (n{sub *} - 1) ln(k/k{sub *}) + 1/2 n'{sub *} ln{sup 2} (k/k{sub *}). It is reasonable to truncate the Taylor series if |n'{sub *} ln(k/k{sub *})| << |n{sub *} - 1|, but it is not if |n'{sub *} ln(k/k{sub *})| {approx}> |n{sub *} - 1|. We argue that there is no good theoretical reason to prefer |n'{sub *}| << |n{sub *} - 1|, and show that current observations are consistent with |n*{sub *} ln(k/k{sub *})| {approx} |n{sub *} - 1| even for |ln(k/k{sub *})| {approx} 1. Thus, there are regions of parameter space, which are both theoretically and observationally relevant, for which the traditional truncated Taylor series parameterization is inconsistent, and hence it can lead to incorrect parameter estimations. Motivated by this, we propose a simple extension of the traditional parameterization, which uses no extra parameters, but that, unlike the traditional approach, covers well motivated inflationary spectra with |n'{sub *}| {approx} |n{sub *} - 1|. Our parameterization therefore covers not only standard-slow-roll inflation models but also a much wider class of inflation models. We use this parameterization to perform a likelihood analysis for the cosmological parameters.
Two distinct truncated variants of ankyrin associated with hereditary spherocytosis.
Hayette, S; Carré, G; Bozon, M; Alloisio, N; Maillet, P; Wilmotte, R; Pascal, O; Reynaud, J; Reman, O; Stéphan, J L; Morlé, L; Delaunay, J
1998-05-01
We present two distinct truncated variants of ankyrin associated with mild to moderate hereditary spherocytosis. Ankyrin Saint-Etienne 1 was manifested by an additional band located between bands 2.1 and 2.2. It was associated with a nonsense mutation in exon 39: TGG-->TGA; W1721X. Ankyrin Saint-Etienne 2 appeared as two faint bands underlining bands 2.1 and 2.2. It was associated with a nonsense mutation in exon 41: CGA-->TGA; R1833X. Overall ankyrin was diminished in splenectomized patients. Messenger RNAs Saint-Etienne 1 and 2 amounted to 20 and 37% of the total ankyrin mRNA, respectively. Ankyrin molecules truncated in their C-terminal region retain some ability to bind to the membrane whereas the bulk of nonsense mutations, located in more upstream regions, result in the mere disappearance of one haploid set of ankyrin. In the present cases, it was not possible to apportion the roles of ankyrin reduction and truncation in the pathogenesis of hereditary spherocytosis. PMID:9590147
Frequency domain FIR and IIR adaptive filters
NASA Technical Reports Server (NTRS)
Lynn, D. W.
1990-01-01
A discussion of the LMS adaptive filter relating to its convergence characteristics and the problems associated with disparate eigenvalues is presented. This is used to introduce the concept of proportional convergence. An approach is used to analyze the convergence characteristics of block frequency-domain adaptive filters. This leads to a development showing how the frequency-domain FIR adaptive filter is easily modified to provide proportional convergence. These ideas are extended to a block frequency-domain IIR adaptive filter and the idea of proportional convergence is applied. Experimental results illustrating proportional convergence in both FIR and IIR frequency-domain block adaptive filters is presented.
Games, Dora; Valera, Elvira; Spencer, Brian; Rockenstein, Edward; Mante, Michael; Adame, Anthony; Patrick, Christina; Ubhi, Kiren; Nuber, Silke; Sacayon, Patricia; Zago, Wagner; Seubert, Peter; Barbour, Robin; Schenk, Dale; Masliah, Eliezer
2014-07-01
Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are common neurodegenerative disorders of the aging population, characterized by progressive and abnormal accumulation of α-synuclein (α-syn). Recent studies have shown that C-terminus (CT) truncation and propagation of α-syn play a role in the pathogenesis of PD/DLB. Therefore, we explored the effect of passive immunization against the CT of α-syn in the mThy1-α-syn transgenic (tg) mouse model, which resembles the striato-nigral and motor deficits of PD. Mice were immunized with the new monoclonal antibodies 1H7, 5C1, or 5D12, all directed against the CT of α-syn. CT α-syn antibodies attenuated synaptic and axonal pathology, reduced the accumulation of CT-truncated α-syn (CT-α-syn) in axons, rescued the loss of tyrosine hydroxylase fibers in striatum, and improved motor and memory deficits. Among them, 1H7 and 5C1 were most effective at decreasing levels of CT-α-syn and higher-molecular-weight aggregates. Furthermore, in vitro studies showed that preincubation of recombinant α-syn with 1H7 and 5C1 prevented CT cleavage of α-syn. In a cell-based system, CT antibodies reduced cell-to-cell propagation of full-length α-syn, but not of the CT-α-syn that lacked the 118-126 aa recognition site needed for antibody binding. Furthermore, the results obtained after lentiviral expression of α-syn suggest that antibodies might be blocking the extracellular truncation of α-syn by calpain-1. Together, these results demonstrate that antibodies against the CT of α-syn reduce levels of CT-truncated fragments of the protein and its propagation, thus ameliorating PD-like pathology and improving behavioral and motor functions in a mouse model of this disease. PMID:25009275
Games, Dora; Valera, Elvira; Spencer, Brian; Rockenstein, Edward; Mante, Michael; Adame, Anthony; Patrick, Christina; Ubhi, Kiren; Nuber, Silke; Sacayon, Patricia; Zago, Wagner; Seubert, Peter; Barbour, Robin; Schenk, Dale
2014-01-01
Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are common neurodegenerative disorders of the aging population, characterized by progressive and abnormal accumulation of α-synuclein (α-syn). Recent studies have shown that C-terminus (CT) truncation and propagation of α-syn play a role in the pathogenesis of PD/DLB. Therefore, we explored the effect of passive immunization against the CT of α-syn in the mThy1-α-syn transgenic (tg) mouse model, which resembles the striato-nigral and motor deficits of PD. Mice were immunized with the new monoclonal antibodies 1H7, 5C1, or 5D12, all directed against the CT of α-syn. CT α-syn antibodies attenuated synaptic and axonal pathology, reduced the accumulation of CT-truncated α-syn (CT-α-syn) in axons, rescued the loss of tyrosine hydroxylase fibers in striatum, and improved motor and memory deficits. Among them, 1H7 and 5C1 were most effective at decreasing levels of CT-α-syn and higher-molecular-weight aggregates. Furthermore, in vitro studies showed that preincubation of recombinant α-syn with 1H7 and 5C1 prevented CT cleavage of α-syn. In a cell-based system, CT antibodies reduced cell-to-cell propagation of full-length α-syn, but not of the CT-α-syn that lacked the 118–126 aa recognition site needed for antibody binding. Furthermore, the results obtained after lentiviral expression of α-syn suggest that antibodies might be blocking the extracellular truncation of α-syn by calpain-1. Together, these results demonstrate that antibodies against the CT of α-syn reduce levels of CT-truncated fragments of the protein and its propagation, thus ameliorating PD-like pathology and improving behavioral and motor functions in a mouse model of this disease. PMID:25009275
Identification of target genes for wild type and truncated HMGA2 in mesenchymal stem-like cells
2010-01-01
Background The HMGA2 gene, coding for an architectural transcription factor involved in mesenchymal embryogenesis, is frequently deranged by translocation and/or amplification in mesenchymal tumours, generally leading to over-expression of shortened transcripts and a truncated protein. Methods To identify pathways that are affected by sarcoma-associated variants of HMGA2, we have over-expressed wild type and truncated HMGA2 protein in an immortalized mesenchymal stem-like cell (MSC) line, and investigated the localisation of these proteins and their effects on differentiation and gene expression patterns. Results Over-expression of both transgenes blocked adipogenic differentiation of these cells, and microarray analysis revealed clear changes in gene expression patterns, more pronounced for the truncated protein. Most of the genes that showed altered expression in the HMGA2-overexpressing cells fell into the group of NF-κB-target genes, suggesting a central role for HMGA2 in this pathway. Of particular interest was the pronounced up-regulation of SSX1, already implicated in mesenchymal oncogenesis and stem cell functions, only in cells expressing the truncated protein. Furthermore, over-expression of both HMGA2 forms was associated with a strong repression of the epithelial marker CD24, consistent with the reported low level of CD24 in cancer stem cells. Conclusions We conclude that the c-terminal part of HMGA2 has important functions at least in mesenchymal cells, and the changes in gene expression resulting from overexpressing a protein lacking this domain may add to the malignant potential of sarcomas. PMID:20576167
LGI2 Truncation Causes a Remitting Focal Epilepsy in Dogs
Seppälä, Eija H.; Jokinen, Tarja S.; Fukata, Masaki; Fukata, Yuko; Webster, Matthew T.; Karlsson, Elinor K.; Kilpinen, Sami K.; Steffen, Frank; Dietschi, Elisabeth; Leeb, Tosso; Eklund, Ranja; Zhao, Xiaochu; Rilstone, Jennifer J.; Lindblad-Toh, Kerstin; Minassian, Berge A.; Lohi, Hannes
2011-01-01
One quadrillion synapses are laid in the first two years of postnatal construction of the human brain, which are then pruned until age 10 to 500 trillion synapses composing the final network. Genetic epilepsies are the most common neurological diseases with onset during pruning, affecting 0.5% of 2–10-year-old children, and these epilepsies are often characterized by spontaneous remission. We previously described a remitting epilepsy in the Lagotto romagnolo canine breed. Here, we identify the gene defect and affected neurochemical pathway. We reconstructed a large Lagotto pedigree of around 34 affected animals. Using genome-wide association in 11 discordant sib-pairs from this pedigree, we mapped the disease locus to a 1.7 Mb region of homozygosity in chromosome 3 where we identified a protein-truncating mutation in the Lgi2 gene, a homologue of the human epilepsy gene LGI1. We show that LGI2, like LGI1, is neuronally secreted and acts on metalloproteinase-lacking members of the ADAM family of neuronal receptors, which function in synapse remodeling, and that LGI2 truncation, like LGI1 truncations, prevents secretion and ADAM interaction. The resulting epilepsy onsets at around seven weeks (equivalent to human two years), and remits by four months (human eight years), versus onset after age eight in the majority of human patients with LGI1 mutations. Finally, we show that Lgi2 is expressed highly in the immediate post-natal period until halfway through pruning, unlike Lgi1, which is expressed in the latter part of pruning and beyond. LGI2 acts at least in part through the same ADAM receptors as LGI1, but earlier, ensuring electrical stability (absence of epilepsy) during pruning years, preceding this same function performed by LGI1 in later years. LGI2 should be considered a candidate gene for common remitting childhood epilepsies, and LGI2-to-LGI1 transition for mechanisms of childhood epilepsy remission. PMID:21829378
Universal microscopic correlation functions for products of truncated unitary matrices
NASA Astrophysics Data System (ADS)
Akemann, Gernot; Burda, Zdzislaw; Kieburg, Mario; Nagao, Taro
2014-06-01
We investigate the spectral properties of the product of M complex non-Hermitian random matrices that are obtained by removing L rows and columns of larger unitary random matrices uniformly distributed on the group U(N + L). Such matrices are called truncated unitary matrices or random contractions. We first derive the joint probability distribution for the complex eigenvalues of the product matrix for fixed N, L, and M, given by a standard determinantal point process in the complex plane. The weight however is non-standard and can be expressed in terms of the Meijer G-function. The explicit knowledge of all eigenvalue correlation functions and the corresponding kernel allows us to take various large N (and L) limits at fixed M. At strong non-unitarity, with L/N finite, the eigenvalues condense on a domain inside the unit circle. At the edge and in the bulk we find the same universal microscopic kernel as for a single complex non-Hermitian matrix from the Ginibre ensemble. At the origin we find the same new universality classes labeled by M as for the product of M matrices from the Ginibre ensemble. Keeping a fixed size of truncation, L, when N goes to infinity leads to weak non-unitarity, with most eigenvalues on the unit circle as for unitary matrices. Here we find a new microscopic edge kernel that generalizes the known results for M = 1. We briefly comment on the case when each product matrix results from a truncation of different size Lj.
Prevalence of Titin Truncating Variants in General Population
Akinrinade, Oyediran; Koskenvuo, Juha W.; Alastalo, Tero-Pekka
2015-01-01
Background Truncating titin (TTN) mutations, especially in A-band region, represent the most common cause of dilated cardiomyopathy (DCM). Clinical interpretation of these variants can be challenging, as these variants are also present in reference populations. We carried out systematic analyses of TTN truncating variants (TTNtv) in publicly available reference populations, including, for the first time, data from Exome Aggregation Consortium (ExAC). The goal was to establish more accurate estimate of prevalence of different TTNtv to allow better clinical interpretation of these findings. Methods and Results Using data from 1000 Genomes Project, Exome Sequencing Project (ESP) and ExAC, we estimated the prevalence of TTNtv in the population. In the three population datasets, 52–54% of TTNtv were not affecting all TTN transcripts. The frequency of truncations affecting all transcripts in ExAC was 0.36% (0.32% - 0.41%, 95% CI) and 0.19% (0.16% - 0.23%, 95% CI) for those affecting the A-band. In the A-band region, the prevalences of frameshift, nonsense and essential splice site variants were 0.057%, 0.090%, and 0.047% respectively. Cga/Tga (arginine/nonsense–R/*) transitional change at CpG mutation hotspots was the most frequent type of TTN nonsense mutation accounting for 91.3% (21/23) of arginine residue nonsense mutation (R/*) at TTN A-band region. Non-essential splice-site variants had significantly lower proportion of private variants and higher proportion of low-frequency variants compared to essential splice-site variants (P = 0.01; P = 5.1 X 10−4, respectively). Conclusion A-band TTNtv are more rare in the general population than previously reported. Based on this analysis, one in 500 carries a truncation in TTN A-band suggesting the penetrance of these potentially harmful variants is still poorly understood, and some of these variants do not manifest as autosomal dominant DCM. This calls for caution when interpreting TTNtv in individuals and families
Mistargeting hippocampal axons by expression of a truncated Eph receptor
Yue, Yong; Chen, Zhi-Yong; Gale, Nick W.; Blair-Flynn, Jan; Hu, Tian-Jing; Yue, Xin; Cooper, Margaret; Crockett, David P.; Yancopoulos, George D.; Tessarollo, Lino; Zhou, Renping
2002-01-01
Topographic mapping of axon terminals is a general principle of neural architecture that underlies the interconnections among many neural structures. The Eph family tyrosine kinase receptors and their ligands, the ephrins, have been implicated in the formation of topographic projection maps. We show that multiple Eph receptors and ligands are expressed in the hippocampus and its major subcortical projection target, the lateral septum, and that expression of a truncated Eph receptor in the mouse brain results in a pronounced alteration of the hippocamposeptal topographic map. Our observations provide strong support for a critical role of Eph family guidance factors in regulating ontogeny of hippocampal projections. PMID:12124402
Equalization of loudspeaker response using balanced model truncation.
Li, Xiansheng; Cai, Zhibo; Zheng, Chengshi; Li, Xiaodong
2015-04-01
Traditional loudspeaker equalization algorithms cannot decide the order of an equalizer before the whole equalization procedure has been completed. Designers have to try many times before they determine a proper order of the equalization filter. A method which solves this drawback is presented for loudspeaker equalization using balanced model truncation. The order of the equalizer can be easily decided using this algorithm and the error between the model and the loudspeaker can also be readily controlled. Examples are presented and the performance of the proposed method is discussed with comparative experiments. PMID:25920872
Quark propagator in a truncation scheme beyond the rainbow approximation
NASA Astrophysics Data System (ADS)
Fu, Hui-Feng; Wang, Qing
2016-01-01
The quark propagator is studied under a truncation scheme beyond the rainbow approximation by dressing the quark-gluon vertex nonperturbatively. It is found that, in the chiral limit with dynamical symmetry breaking, the dynamical quark mass and the quark condensate are significantly enhanced due to the non-Abelian contribution arising from the three-gluon interaction compared to those under the rainbow approximation, and the critical strength of the dynamical chiral symmetry breaking is much lowered. The Abelian contribution is much smaller than the non-Abelian contribution. A technical issue on removing the ultraviolet divergences, including the overlapping divergences, is discussed.
Simulating Hamiltonian dynamics with a truncated Taylor series.
Berry, Dominic W; Childs, Andrew M; Cleve, Richard; Kothari, Robin; Somma, Rolando D
2015-03-01
We describe a simple, efficient method for simulating Hamiltonian dynamics on a quantum computer by approximating the truncated Taylor series of the evolution operator. Our method can simulate the time evolution of a wide variety of physical systems. As in another recent algorithm, the cost of our method depends only logarithmically on the inverse of the desired precision, which is optimal. However, we simplify the algorithm and its analysis by using a method for implementing linear combinations of unitary operations together with a robust form of oblivious amplitude amplification. PMID:25793789
Relevance of truncating titin mutations in dilated cardiomyopathy.
Akinrinade, O; Alastalo, T-P; Koskenvuo, J W
2016-07-01
Dilated cardiomyopathy (DCM), a genetically heterogeneous cardiac disease characterized by left ventricular dilatation and systolic dysfunction, is caused majorly by truncations of titin (TTN), especially in A-band region. Clinical interpretation of TTN-truncating variants (TTNtv) has been challenged by the existing inaccurate variant assessment strategies and uncertainty in the true frequency of TTNtv across the general population. We aggregated TTNtv identified in 1788 DCM patients and compared the variants with those reported in over 60,000 Exome Aggregation Consortium reference population. We implemented our current variant assessment strategy that prioritizes TTNtv affecting all transcripts of the gene, and observed a decline in the prevalence of TTNtv in DCM. Despite this decline, TTNtv are more prevalent in DCM patients compared with reference population (p = 4.1 × 10(-295) ). Moreover, our extended analyses confirmed the enrichment of TTNtv not only in the A-band but also in the I/A-band junction of TTN. We estimated the probability of pathogenicity of TTNtv affecting all transcripts of TTN, identified in unselected DCM patients to be 97.8% (likelihood ratio (LR) = 42.2). We emphasize that identifying a TTNtv, especially in the A-band region, has a higher risk of being disease-causing than previously anticipated, and recommend prioritizing TTNtv affecting at least five transcripts of the gene. PMID:26777568
Excess of rare, inherited truncating mutations in autism
Krumm, Niklas; Turner, Tychele N.; Baker, Carl; Vives, Laura; Mohajeri, Kiana; Witherspoon, Kali; Raja, Archana; Coe, Bradley P.; Stessman, Holly A.; He, Zong-Xiao; Leal, Suzanne M.; Bernier, Raphael; Eichler, Evan E.
2015-01-01
To assess the relative impact of inherited and de novo variants on autism risk, we generated a comprehensive set of exonic single nucleotide variants (SNVs) and copy number variants (CNVs) from 2,377 autism families. We find that private, inherited truncating SNVs in conserved genes are enriched in probands (odds ratio=1.14, p=0.0002) compared to unaffected siblings, an effect with significant maternal transmission bias to sons. We also observe a bias for inherited CNVs, specifically for small (<100 kbp), maternally inherited events (p=0.01) that are enriched in CHD8 target genes (p=7.4×10−3). Using a logistic regression model, we show that private truncating SNVs and rare, inherited CNVs are statistically independent autism risk factors, with odds ratios of 1.11 (p=0.0002) and 1.23 (p=0.01), respectively. This analysis identifies a second class of candidate genes (e.g., RIMS1, CUL7, and LZTR1) where transmitted mutations may create a sensitized background but are unlikely to be completely penetrant. PMID:25961944
Projection-free approximate balanced truncation of large unstable systems
NASA Astrophysics Data System (ADS)
Flinois, Thibault L. B.; Morgans, Aimee S.; Schmid, Peter J.
2015-08-01
In this article, we show that the projection-free, snapshot-based, balanced truncation method can be applied directly to unstable systems. We prove that even for unstable systems, the unmodified balanced proper orthogonal decomposition algorithm theoretically yields a converged transformation that balances the Gramians (including the unstable subspace). We then apply the method to a spatially developing unstable system and show that it results in reduced-order models of similar quality to the ones obtained with existing methods. Due to the unbounded growth of unstable modes, a practical restriction on the final impulse response simulation time appears, which can be adjusted depending on the desired order of the reduced-order model. Recommendations are given to further reduce the cost of the method if the system is large and to improve the performance of the method if it does not yield acceptable results in its unmodified form. Finally, the method is applied to the linearized flow around a cylinder at Re = 100 to show that it actually is able to accurately reproduce impulse responses for more realistic unstable large-scale systems in practice. The well-established approximate balanced truncation numerical framework therefore can be safely applied to unstable systems without any modifications. Additionally, balanced reduced-order models can readily be obtained even for large systems, where the computational cost of existing methods is prohibitive.
A conformal truncation framework for infinite-volume dynamics
NASA Astrophysics Data System (ADS)
Katz, Emanuel; Khandker, Zuhair U.; Walters, Matthew T.
2016-07-01
We present a new framework for studying conformal field theories deformed by one or more relevant operators. The original CFT is described in infinite volume using a basis of states with definite momentum, P , and conformal Casimir, C. The relevant deformation is then considered using lightcone quantization, with the resulting Hamiltonian expressed in terms of this CFT basis. Truncating to states with C ≤ C_{max } , one can numerically find the resulting spectrum, as well as other dynamical quantities, such as spectral densities of operators. This method requires the introduction of an appropriate regulator, which can be chosen to preserve the conformal structure of the basis. We check this framework in three dimensions for various perturbative deformations of a free scalar CFT, and for the case of a free O( N ) CFT deformed by a mass term and a non-perturbative quartic interaction at large- N . In all cases, the truncation scheme correctly reproduces known analytic results. We also discuss a general procedure for generating a basis of Casimir eigenstates for a free CFT in any number of dimensions.
Simulating Hamiltonian Dynamics with a Truncated Taylor Series
NASA Astrophysics Data System (ADS)
Somma, Rolando
2015-03-01
One of the main motivations for quantum computers is their ability to efficiently simulate the dynamics of quantum systems. Since the mid-1990s, many algorithms have been developed to simulate Hamiltonian dynamics on a quantum computer, with applications to problems such as simulating spin models and quantum chemistry. While it is now well known that quantum computers can efficiently simulate Hamiltonian dynamics, ongoing work has improved the performance and expanded the scope of such simulations. In this talk, I will describe a very simple and efficient algorithm for simulating Hamiltonian dynamics on a quantum computer by approximating the truncated Taylor series of the evolution operator. This algorithm can simulate the time evolution of a wide variety of physical systems. The cost of this algorithm depends only logarithmically on the inverse of the desired precision, and can be shown to be optimal. Such a cost also represents an exponential improvement over known methods for Hamiltonian simulation based on, e.g., Trotter-Suzuki approximations. Roughly speaking, doubling the number of digits of accuracy of the simulation only doubles the complexity. The new algorithm and its analysis are highly simplified due to a technique for implementing linear combinations of unitary operations to directly apply the truncated Taylor series. This is joint work with Dominic Berry, Andrew Childs, Richard Cleve, and Robin Kothari.
... combination produces a unique effect, blocking pain-sensing neurons without impairing signals from other cells. In contrast, ... surgical procedures block activity in all types of neurons. This can cause numbness, paralysis, and other nervous ...
Adaptive EAGLE dynamic solution adaptation and grid quality enhancement
NASA Technical Reports Server (NTRS)
Luong, Phu Vinh; Thompson, J. F.; Gatlin, B.; Mastin, C. W.; Kim, H. J.
1992-01-01
In the effort described here, the elliptic grid generation procedure in the EAGLE grid code was separated from the main code into a subroutine, and a new subroutine which evaluates several grid quality measures at each grid point was added. The elliptic grid routine can now be called, either by a computational fluid dynamics (CFD) code to generate a new adaptive grid based on flow variables and quality measures through multiple adaptation, or by the EAGLE main code to generate a grid based on quality measure variables through static adaptation. Arrays of flow variables can be read into the EAGLE grid code for use in static adaptation as well. These major changes in the EAGLE adaptive grid system make it easier to convert any CFD code that operates on a block-structured grid (or single-block grid) into a multiple adaptive code.
The Block Scheduling Handbook.
ERIC Educational Resources Information Center
Queen, J. Allen
Block scheduling encourages increased comprehensive immersion into subject matter, improved teacher-student relationships, and decreased disciplinary problems. While block scheduling may offer many advantages, moving to a block schedule from conventional scheduling can be a major adjustment for both students and teachers. This guide is intended to…
Block Scheduling. Research Brief
ERIC Educational Resources Information Center
Muir, Mike
2003-01-01
What are the effects of block scheduling? Results of transitioning from traditional to block scheduling are mixed. Some studies indicate no change in achievement results, nor change in teachers' opinions about instructional strategies. Other studies show that block scheduling doesn't work well for Advanced Placement or Music courses, that "hard to…
Defying Gravity Using Jenga[TM] Blocks
ERIC Educational Resources Information Center
Tan, Yin-Soo; Yap, Kueh-Chin
2007-01-01
This paper describes how Jenga[TM] blocks can be used to demonstrate the physics of an overhanging tower that appears to defy gravity. We also propose ideas for how this demonstration can be adapted for the A-level physics curriculum. (Contains 8 figures and 1 table.)
Properties of permuted-block randomization in clinical trials.
Matts, J P; Lachin, J M
1988-12-01
selection bias only when the investigator is able to discern the next assignment with certainty. This type of bias is reduced by the use of random block sizes and is eliminated only if the possible block sizes are unknown to the investigators. Finally, the Efron model for accidental bias is used to assess the potential for bias in the estimation of treatment effects due to covariate imbalances. For the permuted-block design, the variance of this bias approaches that of complete randomization as the half-block length m----infinity.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:3203524
Blocking Delaunay triangulations
Aichholzer, Oswin; Fabila-Monroy, Ruy; Hackl, Thomas; van Kreveld, Marc; Pilz, Alexander; Ramos, Pedro; Vogtenhuber, Birgit
2013-01-01
Given a set B of n black points in general position, we say that a set of white points W blocks B if in the Delaunay triangulation of B∪W there is no edge connecting two black points. We give the following bounds for the size of the smallest set W blocking B: (i) 3n/2 white points are always sufficient to block a set of n black points, (ii) if B is in convex position, 5n/4 white points are always sufficient to block it, and (iii) at least n−1 white points are always necessary to block a set of n black points. PMID:23483043
Blocking Delaunay triangulations.
Aichholzer, Oswin; Fabila-Monroy, Ruy; Hackl, Thomas; van Kreveld, Marc; Pilz, Alexander; Ramos, Pedro; Vogtenhuber, Birgit
2013-02-01
Given a set B of n black points in general position, we say that a set of white points W blocks B if in the Delaunay triangulation of [Formula: see text] there is no edge connecting two black points. We give the following bounds for the size of the smallest set W blocking B: (i) [Formula: see text] white points are always sufficient to block a set of n black points, (ii) if B is in convex position, [Formula: see text] white points are always sufficient to block it, and (iii) at least [Formula: see text] white points are always necessary to block a set of n black points. PMID:23483043
Adaptive Mesh Refinement in CTH
Crawford, David
1999-05-04
This paper reports progress on implementing a new capability of adaptive mesh refinement into the Eulerian multimaterial shock- physics code CTH. The adaptivity is block-based with refinement and unrefinement occurring in an isotropic 2:1 manner. The code is designed to run on serial, multiprocessor and massive parallel platforms. An approximate factor of three in memory and performance improvements over comparable resolution non-adaptive calculations has-been demonstrated for a number of problems.
NASA Technical Reports Server (NTRS)
Demmel, James W.; Higham, Nicholas J.; Schreiber, Robert S.
1992-01-01
Many of the currently popular 'block algorithms' are scalar algorithms in which the operations have been grouped and reordered into matrix operations. One genuine block algorithm in practical use is block LU factorization, and this has recently been shown by Demmel and Higham to be unstable in general. It is shown here that block LU factorization is stable if A is block diagonally dominant by columns. Moreover, for a general matrix the level of instability in block LU factorization can be founded in terms of the condition number kappa(A) and the growth factor for Gaussian elimination without pivoting. A consequence is that block LU factorization is stable for a matrix A that is symmetric positive definite or point diagonally dominant by rows or columns as long as A is well-conditioned.
Remanent state studies of truncated conical magnetic particles
Hwang, M.; Redjdal, M.; Humphrey, F. B.; Ross, C. A.
2001-06-01
The remanent state of truncated conical particles is investigated as a function of their size, aspect ratio, and anisotropy, using a micromagnetic model based on the Landau{endash}Lifshitz{endash}Gilbert equation. Particles with a base diameter smaller than three times the exchange length show a {open_quotes}flower{close_quotes} state, while larger particles show a {open_quotes}vortex{close_quotes} magnetization state. The critical size for this transition increases with increasing anisotropy. Small flower-state particles show abrupt reorientation from out-of-plane to in-plane magnetization at a critical aspect ratio of 0.9. For vortex-state particles, the axial remanence gradually increases as the aspect ratio increases, and high aspect ratio particles have significant remanence even at larger diameters. {copyright} 2001 American Institute of Physics.
Truncated-correlation photothermal coherence tomography for deep subsurface analysis
NASA Astrophysics Data System (ADS)
Kaiplavil, Sreekumar; Mandelis, Andreas
2014-08-01
Photothermal diffusion-wave imaging is a promising technique for the analysis of a range of media. However, traditional diffusion-wave techniques are limited by the physics of parabolic diffusion and can only produce depth-integrated planar images. Here, we report a depth-resolved photothermal imaging modality, henceforth termed truncated-correlation photothermal coherence tomography (TC-PCT). This enables three-dimensional visualization of subsurface features, which is not possible with known optical or photothermal imaging techniques. Examples include imaging of solids with intricate subsurface structures and discontinuities, such as holes in steel, burn depth profiles in tissues, and the structure of bone. It is compatible with regulations concerning maximum permissible exposure and is the photothermal analogue of optical coherence tomography. Axial and lateral resolutions in bone are measured to be ~25 and 100 µm, respectively, with a depth range of ~3.2 mm (approximately four thermal diffusion lengths).
Truncated CASK does not alter skeletal muscle or protein interactors.
Sanford, Jamie L; Mays, Tessily A; Varian, Kenneth D; Wilson, Joanna B; Janssen, Paul M L; Rafael-Fortney, Jill A
2008-09-01
CASK (Ca2+, calmodulin-associated serine/threonine kinase) is an essential mammalian cell junction protein and is also crucial at Drosophila neuromuscular synapses. We have shown that CASK is present in mammalian skeletal muscle at the postsynaptic membrane of the neuromuscular junction. CASK interacts biochemically with channels at central synapses, and studies in cultured cells have led to proposed functions for CASK. However, in vivo functions of CASK in skeletal muscle remain unknown. To test hypotheses of CASK functions, we generated two lines of transgenic mice, which overexpress full-length and truncated CASK protein in skeletal muscle. Extensive analyses showed that overexpression of CASK protein did not affect the morphology or physiology of skeletal muscle, the morphology of the neuromuscular junction, or the levels or distribution of protein interactors. These results contrast with previous cell culture experiments and emphasize the importance of in vivo analysis of protein function. PMID:18642383
Simulating strongly correlated multiparticle systems in a truncated Hilbert space
Ernst, Thomas; Hallwood, David W.; Gulliksen, Jake; Brand, Joachim; Meyer, Hans-Dieter
2011-08-15
Representing a strongly interacting multiparticle wave function in a finite product basis leads to errors. Simple rescaling of the contact interaction can preserve the low-lying energy spectrum and long-wavelength structure of wave functions in one-dimensional systems and thus correct for the basis set truncation error. The analytic form of the rescaling is found for a two-particle system where the rescaling is exact. A detailed comparison between finite Hilbert space calculations and exact results for up to five particles show that rescaling can significantly improve the accuracy of numerical calculations in various external potentials. In addition to ground-state energies, the low-lying excitation spectrum, density profile, and correlation functions are studied. The results give a promising outlook for numerical simulations of trapped ultracold atoms.
Exact Interior Reconstruction from Truncated Limited-Angle Projection Data
Ye, Yangbo; Yu, Hengyong; Wang, Ge
2008-01-01
Using filtered backprojection (FBP) and an analytic continuation approach, we prove that exact interior reconstruction is possible and unique from truncated limited-angle projection data, if we assume a prior knowledge on a subregion or subvolume within an object to be reconstructed. Our results show that (i) the interior region-of-interest (ROI) problem and interior volume-of-interest (VOI) problem can be exactly reconstructed from a limited-angle scan of the ROI/VOI and a 180 degree PI-scan of the subregion or subvolume and (ii) the whole object function can be exactly reconstructed from nontruncated projections from a limited-angle scan. These results improve the classical theory of Hamaker et al. (1980). PMID:18490957
Pair truncation for rotational nuclei: j=(17/2 model
NASA Astrophysics Data System (ADS)
Halse, P.; Jaqua, L.; Barrett, B. R.
1989-08-01
The suitability of the pair condensate approach for rotational states is studied in a single j=(17/2 shell of identical nucleons interacting through a quadrupole-quadrupole Hamiltonian. The ground band and a K=2 excited band are both studied in detail. A direct comparison of the exact states with those constituting the SD and SDG subspaces is used to identify the important degrees of freedom for these levels. The range of pairs necessary for a good description is found to be highly state dependent; S and D pairs are the major constituents of the low-spin ground-band levels, while G pairs are needed for those in the γ band. Energy spectra are obtained for each truncated subspace. SDG pairs allow accurate reproduction of the binding energy and K=2 excitation energy, but still give a moment of inertia which is about 30% too small even for the lowest levels.
Modified Truncated Cone Target Hyperthermal Atomic Oxygen Test Results
NASA Technical Reports Server (NTRS)
Vaughn, J. A.; Kamenetsky, R. R.; Finckenor, M. M.
1999-01-01
The modified truncated cone target is a docking target planned for use on the International Space Station. The current design consists of aluminum treated with a black dye anodize, then crosshairs are laser etched for a silvery color. Samples of the treated aluminum were exposed to laboratory simulation of atomic oxygen and ultraviolet radiation to determine if significant degradation might occur. Durability was evaluated based on the contrast ratio between the black and silvery white areas of the target. Degradation of optical properties appeared to level off after an initial period of exposure to atomic oxygen. The sample that was not alodined according to MIL-C-5541, type 1A, performed better than alodined samples.
Characterization of a Truncated Lipoarabinomannan from the Actinomycete Turicella otitidis
Gilleron, Martine; Garton, Natalie J.; Nigou, Jérôme; Brando, Thérèse; Puzo, Germain; Sutcliffe, Iain C.
2005-01-01
Lipoarabinomannan (LAM) lipoglycans have been characterized from a range of mycolic acid-containing actinomycetes and from the amycolate actinomycete Amycolatopsis sulphurea. To further understand the structural diversity of this family, we have characterized the lipoglycan of the otic commensal Turicella otitidis. T. otitidis LAM (TotLAM) has been determined to consist of a mannosyl phosphatidylinositol anchor unit carrying an (α 1→6)-linked mannan core and substituted with terminal-arabinosyl branches. Thus, TotLAM has a novel truncated LAM structure. Using the human monocytic THP-1 cell line, it was found that TotLAM exhibited only minimal ability to induce tumor necrosis factor alpha. These findings contribute further to our understanding of actinomycete LAM diversity and allow further speculation as to the correlation between LAM structure and the immunomodulatory activities of these lipoglycans. PMID:15659663
Administering truncated receive functions in a parallel messaging interface
Archer, Charles J; Blocksome, Michael A; Ratterman, Joseph D; Smith, Brian E
2014-12-09
Administering truncated receive functions in a parallel messaging interface (`PMI`) of a parallel computer comprising a plurality of compute nodes coupled for data communications through the PMI and through a data communications network, including: sending, through the PMI on a source compute node, a quantity of data from the source compute node to a destination compute node; specifying, by an application on the destination compute node, a portion of the quantity of data to be received by the application on the destination compute node and a portion of the quantity of data to be discarded; receiving, by the PMI on the destination compute node, all of the quantity of data; providing, by the PMI on the destination compute node to the application on the destination compute node, only the portion of the quantity of data to be received by the application; and discarding, by the PMI on the destination compute node, the portion of the quantity of data to be discarded.
Growth of pentatwinned gold nanorods into truncated decahedra.
Carbó-Argibay, Enrique; Rodríguez-González, Benito; Pastoriza-Santos, Isabel; Pérez-Juste, Jorge; Liz-Marzán, Luis M
2010-11-01
The growth mechanism from pentatwinned (PTW) gold nanorods into truncated quasi-decahedral particles when a gold salt (HAuCl₄) is reduced by N, N-dimethylformamide (DMF) in the presence of poly(vinylpyrrolidone), was elucidated through a combination of different techniques, including transmission and scanning electron microscopy, high resolution TEM and selected area electron diffraction. Particles with intermediate shapes between the original pentatwinned Au nanorods, used as seeds, and the final quasi-decahedral particles were obtained by simply tuning the [HAuCl₄] to [seeds] ratio. From the thorough structural analysis of all the intermediate morphologies obtained, it was concluded that gradual morphology changes are related to the preferential growth of higher energy crystallographic facets. As a result of the particle growth and concomitant decreased anisotropy, a progressive blue-shift of the surface plasmon resonance bands of the nanoparticles was registered by vis-NIR extinction spectroscopy. PMID:20714650
PHOTOEVAPORATION AS A TRUNCATION MECHANISM FOR CIRCUMPLANETARY DISKS
Mitchell, Tyler R.; Stewart, Glen R.
2011-11-15
We investigate the conditions under which the regular satellites of Jupiter and Saturn formed. The final stage of giant planet accretion is thought to occur slowly over a relatively long, 10 Myr, timescale. Gas accretion during this stage, through a completely or partially opened gap in the solar nebula, occurs slowly, allowing for the condensation of ices and incomplete differentiation seen in the regular satellites of the giant planets. Furthermore, the dichotomy seen in the Jovian and Saturnian systems may be explained as this infall wanes or is completely shutoff as a result of gaps opening or global depletion of gas in the solar nebula. We present one-dimensional simulations of circumplanetary disks that couple the viscous transport of material with the loss of mass at the disk outer edge by ultraviolet photoevaporation as well as the infall of material from the solar nebula. We find that the circumplanetary disks of these protoplanets are truncated as a result of photoevaporation at a range of values with the mean corresponding to Almost-Equal-To 0.16 Hill radii. These truncation radii are broadly consistent with the current locations of the regular satellite systems of Jupiter and Saturn. We also find that photoevaporation can successfully act as a clearing mechanism for circumplanetary nebulae on the potentially short timescales, 10{sup 2}-10{sup 4} yr, over which mass accretion from the solar nebula wanes as a result of a gap opening. Such a rapid clearing of the circum-Jovian disk may be required to explain the survival of the Galilean satellites.
Growth of pentatwinned gold nanorods into truncated decahedra
NASA Astrophysics Data System (ADS)
Carbó-Argibay, Enrique; Rodríguez-González, Benito; Pastoriza-Santos, Isabel; Pérez-Juste, Jorge; Liz-Marzán, Luis M.
2010-11-01
The growth mechanism from pentatwinned (PTW) gold nanorods into truncated quasi-decahedral particles when a gold salt (HAuCl4) is reduced by N,N-dimethylformamide (DMF) in the presence of poly(vinylpyrrolidone), was elucidated through a combination of different techniques, including transmission and scanning electron microscopy, high resolution TEM and selected area electron diffraction. Particles with intermediate shapes between the original pentatwinned Au nanorods, used as seeds, and the final quasi-decahedral particles were obtained by simply tuning the [HAuCl4] to [seeds] ratio. From the thorough structural analysis of all the intermediate morphologies obtained, it was concluded that gradual morphology changes are related to the preferential growth of higher energy crystallographic facets. As a result of the particle growth and concomitant decreased anisotropy, a progressive blue-shift of the surface plasmon resonance bands of the nanoparticles was registered by vis-NIR extinction spectroscopy.The growth mechanism from pentatwinned (PTW) gold nanorods into truncated quasi-decahedral particles when a gold salt (HAuCl4) is reduced by N,N-dimethylformamide (DMF) in the presence of poly(vinylpyrrolidone), was elucidated through a combination of different techniques, including transmission and scanning electron microscopy, high resolution TEM and selected area electron diffraction. Particles with intermediate shapes between the original pentatwinned Au nanorods, used as seeds, and the final quasi-decahedral particles were obtained by simply tuning the [HAuCl4] to [seeds] ratio. From the thorough structural analysis of all the intermediate morphologies obtained, it was concluded that gradual morphology changes are related to the preferential growth of higher energy crystallographic facets. As a result of the particle growth and concomitant decreased anisotropy, a progressive blue-shift of the surface plasmon resonance bands of the nanoparticles was registered by vis
Blocked randomization with randomly selected block sizes.
Efird, Jimmy
2011-01-01
When planning a randomized clinical trial, careful consideration must be given to how participants are selected for various arms of a study. Selection and accidental bias may occur when participants are not assigned to study groups with equal probability. A simple random allocation scheme is a process by which each participant has equal likelihood of being assigned to treatment versus referent groups. However, by chance an unequal number of individuals may be assigned to each arm of the study and thus decrease the power to detect statistically significant differences between groups. Block randomization is a commonly used technique in clinical trial design to reduce bias and achieve balance in the allocation of participants to treatment arms, especially when the sample size is small. This method increases the probability that each arm will contain an equal number of individuals by sequencing participant assignments by block. Yet still, the allocation process may be predictable, for example, when the investigator is not blind and the block size is fixed. This paper provides an overview of blocked randomization and illustrates how to avoid selection bias by using random block sizes. PMID:21318011
Torices, Silvia; Alvarez-Rodríguez, Lorena; Grande, Lara; Varela, Ignacio; Muñoz, Pedro; Pascual, Dora; Balsa, Alejandro; López-Hoyos, Marcos; Martinez-Taboada, Víctor; Fernández-Luna, Jose L
2015-12-01
Loss of the regulatory mechanisms that avoid excessive or constitutive activation of NF-κB may be associated with chronic inflammatory disorders, including rheumatoid arthritis (RA). After massive sequencing of 158 regulators of the NF-κB pathway in RA patients, we focused on a scarcely known gene, ASCC1, and showed that it potently inhibits the expression of NF-κB target genes (TRAIL, TNF-α, cIAP-1, IL8) and blocks activation of a NF-κB-luciferase reporter construct in five different human cell lines. Therefore, ASCC1 may contribute to avoiding a pathologic activation of this transcription factor. A truncated variant of ASCC1 (p.S78*) was found in RA patients and control individuals. Functional in vitro studies revealed that truncation abrogated the NF-κB inhibition capacity of ASCC1. In contrast with full-length protein, truncated ASCC1 did not reduce the transcriptional activation of NF-κB and the secretion of TNF-α in response to inflammatory stimuli. We analyzed the clinical impact of p.S78* variant in 433 patients with RA and found that heterozygous carriers of this variant needed more disease-modifying antirheumatic drugs, and more patients with this genotype needed treatment with corticoids and biologic agents. Moreover, the truncated allele-carrier group had lower rates of remission compared with the full-length variant carriers. Overall, our findings show for the first time, to our knowledge, that ASCC1 inhibits NF-κB activation and that a truncated and inactive variant of ASCC1 is associated with a more severe disease, which could have clinical value for assessing the progression and prognosis of RA. PMID:26503956
Propagation of time-truncated Airy-type pulses in media with quadratic and cubic dispersion.
Borda-Hernández, José A; Zamboni-Rached, Michel; Shaarawi, Amr; Besieris, Ioannis M
2015-10-01
In this paper, we describe analytically the propagation of Airy-type pulses truncated by a finite-time aperture when second- and third-order dispersion effects are considered. The mathematical method presented here, which is based on the superposition of exponentially truncated Airy pulses, is very effective and allows us to avoid the use of time-consuming numerical simulations. We analyze the behavior of the time-truncated ideal Airy pulse and also the interesting case of a time-truncated Airy pulse with a "defect" in its initial profile, which reveals the self-healing property of this kind of pulse solution. PMID:26479932
Reduction of truncation artifacts in CT images via a discriminative dictionary representation method
NASA Astrophysics Data System (ADS)
Chen, Yang; Li, Ke; Li, Yinsheng; Hsieh, Jiang; Chen, Guang-Hong
2016-04-01
When the scan field of view (SFOV) of a CT system is not large enough to enclose the entire cross-section of a patient, or the patient needs to be intentionally positioned partially outside the SFOV for certain clinical CT scans, truncation artifacts are often observed in the reconstructed CT images. Conventional wisdom to reduce truncation artifacts is to complete the truncated projection data via data extrapolation with different a priori assumptions. This paper presents a novel truncation artifact reduction method that directly works in the CT image domain. Specifically, a discriminative dictionary that includes a sub-dictionary of truncation artifacts and a sub-dictionary of non-artifact image information was used to separate a truncation artifact-contaminated image into two sub-images, one with reduced truncation artifacts, and the other one containing only the truncation artifacts. Both experimental phantom and retrospective human subject studies have been performed to characterize the performance of the proposed truncation artifact reduction method.
Protein based Block Copolymers
Rabotyagova, Olena S.; Cebe, Peggy; Kaplan, David L.
2011-01-01
Advances in genetic engineering have led to the synthesis of protein-based block copolymers with control of chemistry and molecular weight, resulting in unique physical and biological properties. The benefits from incorporating peptide blocks into copolymer designs arise from the fundamental properties of proteins to adopt ordered conformations and to undergo self-assembly, providing control over structure formation at various length scales when compared to conventional block copolymers. This review covers the synthesis, structure, assembly, properties, and applications of protein-based block copolymers. PMID:21235251
NASA Astrophysics Data System (ADS)
Thériault Lauzier, Pascal; Tang, Jie; Chen, Guang-Hong
2012-05-01
C-arm cone-beam CT could replace preoperative multi-detector CT scans in the cardiac interventional setting. However, cardiac gating results in view angle undersampling and the small size of the detector results in projection data truncation. These problems are incompatible with conventional tomographic reconstruction algorithms. In this paper, the prior image constrained compressed sensing (PICCS) reconstruction method was adapted to solve these issues. The performance of the proposed method was compared to that of FDK, FDK with extrapolated projection data (E-FDK), and total variation-based compressed sensing. A canine projection dataset acquired using a clinical C-arm imaging system supplied realistic cardiac motion and anatomy for this evaluation. Three different levels of truncation were simulated. The relative root mean squared error and the universal image quality index were used to quantify the reconstruction accuracy. Three main conclusions were reached. (1) The adapted version of the PICCS algorithm offered the highest image quality and reconstruction accuracy. (2) No meaningful variation in performance was observed when the amount of truncation was changed. (3) This study showed evidence that accurate interior tomography with an undersampled acquisition is possible for realistic objects if a prior image with minimal artifacts is available.
Truncated Thermal Equilibrium Distribution for Intense Beam Propagation
Ronald C. Davidson; Hong Qin; Steven M. Lund
2003-02-26
An intense charged-particle beam with directed kinetic energy ({lambda}{sub b}-1)m{sub b}c{sup 2} propagates in the z-direction through an applied focusing field with transverse focusing force modeled by F{sub foc} = -{lambda}{sub b}m{sub b}{omega}{sub beta}{sup 2} {perpendicular} x {perpendicular} in the smooth focusing approximation. This paper examines properties of the axisymmetric, truncated thermal equilibrium distribution F(sub)b(r,p perpendicular) = A exp (-H Perpendicular/T perpendicular (sub)b) = (H perpendicular-E(sub)b), where A, T perpendicular (sub)b, and E (sub)b are positive constants, and H perpendicular is the Hamiltonian for transverse particle motion. The equilibrium profiles for beam number density, n(sub)b(r) = * d{sup 2}pF(sub)b(r,p perpendicular), and transverse temperature, T perpendicular (sub)b(r) = * d{sup 2}p(p{sup 2} perpendicular/2 lambda (sbu)bm (sub)b)F(sub)b(r,p perpendicular), are calculated self-consistently including space-charge effects. Several properties of the equilibrium profiles are noteworthy. For example, the beam has a sharp outer edge radius r(sub)b with n(sub)b(r greater than or equal to rb) = 0, where r(sub)b depends on the value of E(sub)b/T (sub)perpendicular(sub)b. In addition, unlike the choice of a semi-Gaussian distribution, F{sup SG}(sub)b = A exp (-p{sup 2}(sub)perpendicular/2lambda(sub)bm(sub)bTperpendicular(sub)b) = (r-r(sub)b), the truncated thermal equilibrium distribution F(sub)b(r,p) depends on (r,p) only through the single-particle constant of the motion Hperpendiuclar and is therefore a true steady-state solution (*/*t = 0) of the nonlinear Vlasov-Maxwell equations.
ERIC Educational Resources Information Center
Foster, Michael
1989-01-01
Explains a method of block printing using styrofoam shapes to make high relief. Describes the creation of the block design as well as the actual printing process. Uses a range of paper types for printing so children can see the results of using different media. (LS)
ERIC Educational Resources Information Center
Haley, Marjorie
A discussion of block scheduling for second language instruction looks at the advantages and disadvantages and offers some suggestions for classroom management and course organization. It is argued that block scheduling may offer a potential solution to large classes, insufficient time for labs, too little individualized instruction; few…
ERIC Educational Resources Information Center
Queen, J. Allen
2000-01-01
Successful block scheduling depends on provision of initial and ongoing instructional training. Teaching strategies should vary and include cooperative learning, the case method, the socratic seminar, synectics, concept attainment, the inquiry method, and simulations. Recommendations for maximizing block scheduling are outlined. (Contains 52…
Thermally actuated wedge block
Queen, Jr., Charles C.
1980-01-01
This invention relates to an automatically-operating wedge block for maintaining intimate structural contact over wide temperature ranges, including cryogenic use. The wedging action depends on the relative thermal expansion of two materials having very different coefficients of thermal expansion. The wedge block expands in thickness when cooled to cryogenic temperatures and contracts in thickness when returned to room temperature.
Electrochemical studies of a truncated laccase produced in Pichia pastoris
Gelo-Pujic, M.; Kim, H.H.; Butlin, N.G.; Palmore, G.T.R.
1999-12-01
The cDNA that encodes an isoform is laccase from Trametes versicolor (LCCI), as well as a truncated version (LCCIa), was subcloned and expressed by using the yeast Pichia pastoris as the heterologous host. The amino acid sequence of LCCIa is identical to that of LCCI except that the final 11 amino acids at the C terminus of LCCI are replaced with a single cysteine residue. This modification was introduced for the purpose of improving the kinetics of electron transfer between an electrode and the copper-containing active site of laccase. The two laccases (LCCI and LCCIa) are compared in terms of their relative activity with two substrates that have different redox potentials. Results from electrochemical studies on solutions containing LCCI and LCCIa indicate that the redox potential of the active site of LCCIa is shifted to more negative values (411 mV versus normal hydrogen electrode voltage) than that found in other fungal laccases. In addition, replacing the 11 codons at the C terminus of the laccase gene with a single cysteine codon influences the rate of heterogeneous electron transfer between and electrode and the copper-containing active site. These results demonstrate for the first time that the rate of electron transfer between an oxidoreductase and an electrode can be enhanced by changes to the primary structure of a protein via site-directed mutagenesis.
Transcriptional Truncation of the Long Coding Imprinted Gene Usp29
He, Hongzhi; Ye, An; Kim, Joomyeong
2016-01-01
Usp29 (Ubiquitin-specific protease 29) is a paternally expressed gene located upstream of another imprinted gene Peg3. In the current study, the transcription of this long coding gene spanning a 250-kb genomic distance was truncated using a knockin allele. According to the results, paternal transmission of the mutant allele resulted in reduced body and litter sizes whereas the maternal transmission caused no obvious effects. In the paternal mutant, the expression levels of Usp29 were reduced to 14–18% level of the wild-type littermates due to the Poly-A signal included in the knockin cassette. Expression analyses further revealed an unusual female-specific up-regulation of the adjacent imprinted gene Zfp264 in the mutant. Consistent with this, the promoter of Zfp264 was hypomethylated only in the female mutant. Interestingly, this female-specific hypomethylation by the knockin allele was not detected in the offspring of an interspecific crossing, indicating its sensitivity to genetic background. Overall, the results suggest that the transcription of Usp29 may be involved in DNA methylation setting of Zfp264 promoter in a sex-specific manner. PMID:27327533
Truncated γ-exponential models for tidal stellar systems
NASA Astrophysics Data System (ADS)
Gomez-Leyton, Y. J.; Velazquez, L.
2016-05-01
We introduce a parametric family of models to characterize the properties of astrophysical systems in a quasi-stationary evolution under the incidence evaporation. We start from an one-particle distribution fγ (q, p|β,ɛs) that considers an appropriate deformation of Maxwell-Boltzmann form with inverse temperature β, in particular, a power-law truncation at the scape energy ɛs with exponent γ > 0. This deformation is implemented using a generalized γ-exponential function obtained from the fractional integration of ordinary exponential. As shown in this work, this proposal generalizes models of tidal stellar systems that predict particles distributions with isothermal cores and polytropic haloes, e.g.: Michie-King models. We perform the analysis of thermodynamic features of these models and their associated distribution profiles. A nontrivial consequence of this study is that profiles with isothermal cores and polytropic haloes are only obtained for low energies whenever deformation parameter γ < γc ≃ 2.13. This study is a first approximation to characterize a self- gravitating system, so we consider equal to all the particles that constitute the system.
Crystallization and Preliminary Diffraction Analysis of Truncated Human Pleckstrin
S Jackson; S Sugiman-Marangos; K Cheung; M Junop
2011-12-31
Pleckstrin is a major substrate of protein kinase C in platelets and leukocytes and appears to play an important role in exocytosis through a currently unknown mechanism. Pleckstrin function is regulated by phosphorylation, which is thought to cause dissociation of pleckstrin dimers, thereby facilitating phosphoinositide interactions and membrane localization. Evidence also exists suggesting that phosphorylation causes a subtle conformational change in pleckstrin. Structural studies of pleckstrin have been initiated in order to characterize these structural changes and ultimately advance understanding of pleckstrin function. Here, the crystallization and preliminary X-ray diffraction analysis of a truncated version of pleckstrin consisting of the N-terminal PH domain, the protein kinase C phosphorylation sites and the DEP domain (NPHDEP) are reported. In addition, the oligomeric state and phospholipid-binding properties of NPHDEP were analyzed. This work demonstrates that NPHDEP behaves as a monomer in solution and suggests that all three pleckstrin domains contribute to the dimerization interface. Furthermore, based on the binding properties of NPHDEP, the C-terminal PH domain appears to increase the specificity of pleckstrin for phosphoinositides. This work represents a significant step towards determining the structure of pleckstrin.
Targeted radiosensitization of cells expressing truncated DNA polymerase {beta}.
Neijenhuis, Sari; Verwijs-Janssen, Manon; van den Broek, Lenie J; Begg, Adrian C; Vens, Conchita
2010-11-01
Ionizing radiation (IR) is an effective anticancer treatment, although failures still occur. To improve radiotherapy, tumor-targeted strategies are needed to increase radiosensitivity of tumor cells, without influencing normal tissue radiosensitivity. Base excision repair (BER) and single-strand break repair (SSBR) contribute to the determination of sensitivity to IR. A crucial protein in BER/SSBR is DNA polymerase β (polβ). Aberrant polβ expression is commonly found in human tumors and leads to inhibition of BER. Here, we show that truncated polβ variant (polβ-Δ)-expressing cells depend on homologous recombination (HR) for survival after IR, indicating that a considerable fraction of polβ-Δ-induced lesions are subject to repair by HR. Increased sensitization was found not to result from involvement in DNA-dependent protein kinase-dependent nonhomologous end joining, the other major double-strand break repair pathway. Caffeine and the ATM inhibitor Ku55933 cause polβ-Δ-dependent radiosensitization. Consistent with the observed HR dependence and the known HR-modulating activity of ATM, polβ-Δ-expressing cells showed increased radiosensitization after BRCA2 knockdown that is absent under ATM-inhibited conditions. Our data suggest that treatment with HR modulators is a promising therapeutic strategy for exploiting defects in the BER/SSBR pathway in human tumors. PMID:20978197
ERIC Educational Resources Information Center
Zhang, Junni L.; Rubin, Donald B.
2003-01-01
The topic of "truncation by death" in randomized experiments arises in many fields, such as medicine, economics and education. Traditional approaches addressing this issue ignore the fact that the outcome after the truncation is neither "censored" nor "missing," but should be treated as being defined on an extended sample space. Using an…
Code of Federal Regulations, 2014 CFR
2014-01-01
... 12 Banks and Banking 3 2014-01-01 2014-01-01 false Indorsement, Reconverting Bank Identification, and Truncating Bank Identification Standards D Appendix D to Part 229 Banks and Banking FEDERAL..., Reconverting Bank Identification, and Truncating Bank Identification Standards (1) The depositary bank...
Code of Federal Regulations, 2013 CFR
2013-01-01
... 12 Banks and Banking 3 2013-01-01 2013-01-01 false Indorsement, Reconverting Bank Identification, and Truncating Bank Identification Standards D Appendix D to Part 229 Banks and Banking FEDERAL..., Reconverting Bank Identification, and Truncating Bank Identification Standards (1) The depositary bank...
Reduction of truncation artifacts in fan beam transmission by using parallel beam emission data
Pan, T.S.; King, M.A.; Luo, D.S.; Case, J.A.; Penney, B.C.; Rajeevan, N.
1995-08-01
Transmission imaging has been demonstrated to be a promising technique to provide a patient specific attenuation map for attenuation correction of SPECT cardiac perfusion images. The authors describe a method which uses the measurement of both photopeak and Compton scatter energy window images from a parallel beam collimation to augment the truncated attenuation map reconstruction in a fan beam transmission system. The method first estimates the body and lung outlines from the reconstructed emission data and truncated attenuation map. Based on the outline information, an assigned attenuation map is created and reprojected to estimate the missed projection data, which are then combined with the truncated projection data for the set of complete data without truncation. Finally, a reconstruction using the combined complete data is performed to obtain the attenuation map with no truncation. The authors demonstrate that this method can significantly reduce the truncation artifacts in two phantom studies and one patient study. When some portion of the heart walls stays outside the densely sampled region (defined as the region of the object that has no truncation in any projection angle), the attenuation map estimated from this method can more effectively correct for the attenuation in the emission data than the truncated attenuation map.
Gantapara, Anjan P; de Graaf, Joost; van Roij, René; Dijkstra, Marjolein
2013-07-01
Using Monte Carlo simulations and free-energy calculations, we determine the phase diagram of a family of truncated hard cubes, where the shape evolves smoothly from a cube via a cuboctahedron to an octahedron. A remarkable diversity in crystal phases and close-packed structures is found, including a fully degenerate crystal structure, several plastic crystals, as well as vacancy-stabilized crystal phases, all depending sensitively on the precise particle shape. Our results illustrate the intricate relation between phase behavior and building-block shape, and can guide future experimental studies on polyhedral-shaped nanoparticles. PMID:23863011
Atmospheric Blocking in the Northern Hemisphere.
NASA Astrophysics Data System (ADS)
Knox, John Lewis
Blocking is generally understood as the obstruction on a large scale of the normal west - to - east motion of mid-latitude pressure systems. It is a persistent phenomenon lasting from one to several weeks and the resulting prolonged weather regimes may have serious economic and social consequences. The recent Northern Hemisphere winters, starting with 1976 -77, featured unusually large circulation anomalies, many of which can be directly related to prolonged episodes of large scale blocking. The intent of this study is to investigate the statistics and certain diagnostics of blocking in the Northern Hemisphere. The first of the three primary objectives is to present and interpret the spatial and temporal distribution of blocking during the past 33 years. We develop objective identification criteria, adaptable to machine processing methods, by relating the blocking anticyclone to its associated positive anomaly of 5-day mean 500MB height. Anomalies meeting the criteria are called 'blocking signatures.' We present the seasonal frequency of occurrence of these signatures by longitude and by area. The results are in good agreement with published studies for the oceans, but they also reveal a high frequency of blocking signatures over the Northeastern Canadian Archipelago. This result, dubbed the 'Baffin Island Paradox' is further investigated and rationalized. A catalogue has been prepared which identifies the date, centre location and magnitude of every blocking signature which occurred from January 1, 1946 to December 31, 1978. A supplementary Catalogue identifies sequences of these signatures corresponding to actual blocking episodes. The second objective is to investigate whether regions with high incidence of blocking, in either the developing or the mature stage, features non-Gaussian distributions of 5-day mean geopotential. During winter, fields of significantly low kurtosis are found in certain mid-latitude regions where the genesis and amplification of
Zhang, Chenggong; He, Wenqi; Wu, Jiachen; Peng, Xiang
2015-04-01
A novel optical cryptosystem based on phase-truncated Fresnel diffraction (PTFD) and transport of intensity equation (TIE) is proposed. By using the phase truncation technique, a phase-encoded plaintext could be encrypted into a real-valued noise-like intensity distribution by employing a random amplitude mask (RAM) and a random phase mask (RPM), which are regarded as two secret keys. For decryption, a generalized amplitude-phase retrieval (GAPR) algorithm combined with the TIE method are proposed to recover the plaintext with the help of two keys. Different from the current phase-truncated-based optical cryptosystems which need record the truncated phase as decryption keys, our scheme do not need the truncated phase because of the introducing of the TIE method. Moreover, the proposed scheme is expected to against existing attacks. A set of numerical simulation results show the feasibility and security of the proposed method. PMID:25968722
Dynamic Covalent Nanoparticle Building Blocks.
Kay, Euan R
2016-07-25
Rational and generalisable methods for engineering surface functionality will be crucial to realising the technological potential of nanomaterials. Nanoparticle-bound dynamic covalent exchange combines the error-correcting and environment-responsive features of equilibrium processes with the stability, structural precision, and vast diversity of covalent chemistry, defining a new and powerful approach for manipulating structure, function and properties at nanomaterial surfaces. Dynamic covalent nanoparticle (DCNP) building blocks thus present a whole host of possibilities for constructing adaptive systems, devices and materials that incorporate both nanoscale and molecular functional components. At the same time, DCNPs have the potential to reveal fundamental insights regarding dynamic and complex chemical systems confined to nanoscale interfaces. PMID:27312526
Truncation of NHEJ1 in a patient with polymicrogyria.
Cantagrel, Vincent; Lossi, Anne-Marie; Lisgo, Steven; Missirian, Chantal; Borges, Ana; Philip, Nicole; Fernandez, Carla; Cardoso, Carlos; Figarella-Branger, Dominique; Moncla, Anne; Lindsay, Susan; Dobyns, William B; Villard, Laurent
2007-04-01
Polymicrogyria (PMG) is a common malformation of the human cerebral cortex for which both acquired and genetic causes are known. Although genetic heterogeneity is documented, only one gene is currently known to cause isolated PMG. To clone new genes involved in this type of cerebral malformation, we studied a fetus presenting a defect of cortical organization consisting of a polymicrogyric cortex and neuronal heterotopia within the white matter. Karyotype analysis revealed that the fetus was carrier of a balanced, de novo, chromosomal translocation t(2;7)(q35;p22). Cloning and sequencing of the two translocation breakpoints reveals that the chromosomal rearrangement disrupts the coding region of a single gene, called NHEJ1, Cernunnos, or XLF, in 2q35. The NHEJ1 gene was recently identified as being responsible for autosomal recessive immunodeficiency with microcephaly. Using quantitative PCR experiments, we show that a truncated transcript is expressed in the polymicrogyric patient cells, suggesting a potential dominant negative effect possibly leading to a different phenotype. We performed in situ hybridization on human embryos and showed that the NHEJ1 transcript is preferentially expressed in the telencephalic ventricular and subventricular zones, consistent with the phenotype of the affected individual. In the human adult central nervous system (CNS), NHEJ1 is mainly expressed in the cerebral cortex and in the cerebellum. The association of PMG with the disruption of its transcript suggests that, in addition to its recently uncovered function in the immune system, the NHEJ1 protein may also play a role during development of the human cerebral cortex. PMID:17191205
A hemoglobin from plants homologous to truncated hemoglobins of microorganisms.
Watts, R A; Hunt, P W; Hvitved, A N; Hargrove, M S; Peacock, W J; Dennis, E S
2001-08-28
We have identified a nuclear-encoded Hb from plants (GLB3) that has a central domain similar to the "truncated" Hbs of bacteria, protozoa, and algae. The three-dimensional structure of these Hbs is a 2-on-2 arrangement of alpha-helices, distinct from the 3-on-3 arrangement of the standard globin fold [Pesce, A., Couture, M., Dewilde, S., Guertin, M., Yamauchi, K., Ascenzi, P., Moens, L. & Bolognesi, M. (2000) EMBO J. 19, 2424-2434]. GLB3-like genes are not found in animals or yeast, but our analysis reveals that they are present in a wide range of Angiosperms and a Bryophyte. Although cyanobacteria and Chlamydomonas have 2-on-2 Hbs (GLBN), GLB3 is more likely related to GLBO-type 2-on-2 Hbs from bacteria. Consequently, GLB3 is unlikely to have arisen from a horizontal transfer between the chloroplast and nuclear genomes. Arabidopsis thaliana GLB3 protein exhibits unusual concentration-independent binding of O(2) and CO. The absorbance spectrum of deoxy-GLB3 is unique; the protein forms a transient six-coordinate structure after reduction and deoxygenation, which slowly converts to a five-coordinate structure. In A. thaliana, GLB3 is expressed throughout the plant but responds to none of the treatments that induce plant 3-on-3 Hbs. Our analysis of the sequence, ligand interactions, and expression profile of GLB3 indicates that this protein has unique biochemical properties, evolutionary history, and, most likely, a function distinct from those of other plant Hbs. PMID:11526234
Functional and Spectroscopic Characterization of Chlamydomonas reinhardtii Truncated Hemoglobins
Droghetti, Enrica; Tundo, Grazia R.; Sanz-Luque, Emanuel; Polticelli, Fabio; Visca, Paolo; Smulevich, Giulietta; Ascenzi, Paolo; Coletta, Massimo
2015-01-01
The single-cell green alga Chlamydomonas reinhardtii harbors twelve truncated hemoglobins (Cr-TrHbs). Cr-TrHb1-1 and Cr-TrHb1-8 have been postulated to be parts of the nitrogen assimilation pathway, and of a NO-dependent signaling pathway, respectively. Here, spectroscopic and reactivity properties of Cr-TrHb1-1, Cr-TrHb1-2, and Cr-TrHb1-4, all belonging to clsss 1 (previously known as group N or group I), are reported. The ferric form of Cr-TrHb1-1, Cr-TrHb1-2, and Cr-TrHb1-4 displays a stable 6cLS heme-Fe atom, whereas the hexa-coordination of the ferrous derivative appears less strongly stabilized. Accordingly, kinetics of azide binding to ferric Cr-TrHb1-1, Cr-TrHb1-2, and Cr-TrHb1-4 are independent of the ligand concentration. Conversely, kinetics of CO or NO2− binding to ferrous Cr-TrHb1-1, Cr-TrHb1-2, and Cr-TrHb1-4 are ligand-dependent at low CO or NO2− concentrations, tending to level off at high ligand concentrations, suggesting the presence of a rate-limiting step. In agreement with the different heme-Fe environments, the pH-dependent kinetics for CO and NO2−binding to ferrous Cr-TrHb1-1, Cr-TrHb1-2, and Cr-TrHb1-4 are characterized by different ligand-linked protonation events. This raises the question of whether the simultaneous presence in C. reinhardtii of multiple TrHb1s may be related to different regulatory roles. PMID:25993270
Functional and Spectroscopic Characterization of Chlamydomonas reinhardtii Truncated Hemoglobins.
Ciaccio, Chiara; Ocaña-Calahorro, Francisco; Droghetti, Enrica; Tundo, Grazia R; Sanz-Luque, Emanuel; Polticelli, Fabio; Visca, Paolo; Smulevich, Giulietta; Ascenzi, Paolo; Coletta, Massimo
2015-01-01
The single-cell green alga Chlamydomonas reinhardtii harbors twelve truncated hemoglobins (Cr-TrHbs). Cr-TrHb1-1 and Cr-TrHb1-8 have been postulated to be parts of the nitrogen assimilation pathway, and of a NO-dependent signaling pathway, respectively. Here, spectroscopic and reactivity properties of Cr-TrHb1-1, Cr-TrHb1-2, and Cr-TrHb1-4, all belonging to clsss 1 (previously known as group N or group I), are reported. The ferric form of Cr-TrHb1-1, Cr-TrHb1-2, and Cr-TrHb1-4 displays a stable 6cLS heme-Fe atom, whereas the hexa-coordination of the ferrous derivative appears less strongly stabilized. Accordingly, kinetics of azide binding to ferric Cr-TrHb1-1, Cr-TrHb1-2, and Cr-TrHb1-4 are independent of the ligand concentration. Conversely, kinetics of CO or NO2- binding to ferrous Cr-TrHb1-1, Cr-TrHb1-2, and Cr-TrHb1-4 are ligand-dependent at low CO or NO2- concentrations, tending to level off at high ligand concentrations, suggesting the presence of a rate-limiting step. In agreement with the different heme-Fe environments, the pH-dependent kinetics for CO and NO2-binding to ferrous Cr-TrHb1-1, Cr-TrHb1-2, and Cr-TrHb1-4 are characterized by different ligand-linked protonation events. This raises the question of whether the simultaneous presence in C. reinhardtii of multiple TrHb1s may be related to different regulatory roles. PMID:25993270
Damping models in the truncated derivative nonlinear Schroedinger equation
Sanchez-Arriaga, G.; Sanmartin, J. R.; Elaskar, S. A.
2007-08-15
Four-dimensional flow in the phase space of three amplitudes of circularly polarized Alfven waves and one relative phase, resulting from a resonant three-wave truncation of the derivative nonlinear Schroedinger equation, has been analyzed; wave 1 is linearly unstable with growth rate {gamma}, and waves 2 and 3 are stable with damping {gamma}{sub 2} and {gamma}{sub 3}, respectively. The dependence of gross dynamical features on the damping model (as characterized by the relation between damping and wave-vector ratios, {gamma}{sub 2}/{gamma}{sub 3}, k{sub 2}/k{sub 3}), and the polarization of the waves, is discussed; two damping models, Landau ({gamma}{proportional_to}k) and resistive ({gamma}{proportional_to}k{sup 2}), are studied in depth. Very complex dynamics, such as multiple blue sky catastrophes and chaotic attractors arising from Feigenbaum sequences, and explosive bifurcations involving Intermittency-I chaos, are shown to be associated with the existence and loss of stability of certain fixed point P of the flow. Independently of the damping model, P may only exist for {gamma}<2({gamma}{sub 2}+{gamma}{sub 3})/3, as against flow contraction just requiring {gamma}<{gamma}{sub 2}+{gamma}{sub 3}. In the case of right-hand (RH) polarization, point P may exist for all models other than Landau damping; for the resistive model, P may exist for RH polarization only if {gamma}<({gamma}{sub 2}+{gamma}{sub 3})/2.
Cell block eleven (left) and cell block fifteen, looking from ...
Cell block eleven (left) and cell block fifteen, looking from cell block two into the "Death Row" exercise yard - Eastern State Penitentiary, 2125 Fairmount Avenue, Philadelphia, Philadelphia County, PA
View of cell block eight (left), cell block seven, and ...
View of cell block eight (left), cell block seven, and southwest guard tower, looking from cell block eight roof - Eastern State Penitentiary, 2125 Fairmount Avenue, Philadelphia, Philadelphia County, PA
... your baby may have an eye infection called conjunctivitis . ... increase the chance of other infections, such as conjunctivitis. ... be prevented. Proper treatment of nasal infections and conjunctivitis may reduce the risk of having a blocked ...
ERIC Educational Resources Information Center
Tompkins, Gail E.; Camp, Donna J.
1988-01-01
Describes four prewriting techniques that elementary and middle grade students can use to gather and organize ideas for writing, and by so doing, cure writer's block. Techniques discussed are: (1) brainstorming; (2) clustering; (3) freewriting; and (4) cubing.
Superalloy Lattice Block Structures
NASA Technical Reports Server (NTRS)
Nathal, M. V.; Whittenberger, J. D.; Hebsur, M. G.; Kantzos, P. T.; Krause, D. L.
2004-01-01
Initial investigations of investment cast superalloy lattice block suggest that this technology will yield a low cost approach to utilize the high temperature strength and environmental resistance of superalloys in lightweight, damage tolerant structural configurations. Work to date has demonstrated that relatively large superalloy lattice block panels can be successfully investment cast from both IN-718 and Mar-M247. These castings exhibited mechanical properties consistent with the strength of the same superalloys measured from more conventional castings. The lattice block structure also accommodates significant deformation without failure, and is defect tolerant in fatigue. The potential of lattice block structures opens new opportunities for the use of superalloys in future generations of aircraft applications that demand strength and environmental resistance at elevated temperatures along with low weight.
Block copolymer battery separator
Wong, David; Balsara, Nitash Pervez
2016-04-26
The invention herein described is the use of a block copolymer/homopolymer blend for creating nanoporous materials for transport applications. Specifically, this is demonstrated by using the block copolymer poly(styrene-block-ethylene-block-styrene) (SES) and blending it with homopolymer polystyrene (PS). After blending the polymers, a film is cast, and the film is submerged in tetrahydrofuran, which removes the PS. This creates a nanoporous polymer film, whereby the holes are lined with PS. Control of morphology of the system is achieved by manipulating the amount of PS added and the relative size of the PS added. The porous nature of these films was demonstrated by measuring the ionic conductivity in a traditional battery electrolyte, 1M LiPF.sub.6 in EC/DEC (1:1 v/v) using AC impedance spectroscopy and comparing these results to commercially available battery separators.
Perceptually-Based Adaptive JPEG Coding
NASA Technical Reports Server (NTRS)
Watson, Andrew B.; Rosenholtz, Ruth; Null, Cynthia H. (Technical Monitor)
1996-01-01
An extension to the JPEG standard (ISO/IEC DIS 10918-3) allows spatial adaptive coding of still images. As with baseline JPEG coding, one quantization matrix applies to an entire image channel, but in addition the user may specify a multiplier for each 8 x 8 block, which multiplies the quantization matrix, yielding the new matrix for the block. MPEG 1 and 2 use much the same scheme, except there the multiplier changes only on macroblock boundaries. We propose a method for perceptual optimization of the set of multipliers. We compute the perceptual error for each block based upon DCT quantization error adjusted according to contrast sensitivity, light adaptation, and contrast masking, and pick the set of multipliers which yield maximally flat perceptual error over the blocks of the image. We investigate the bitrate savings due to this adaptive coding scheme and the relative importance of the different sorts of masking on adaptive coding.
Chen, Chi-Jim; Pai, Tun-Wen; Cheng, Mox
2015-01-01
A sweeping fingerprint sensor converts fingerprints on a row by row basis through image reconstruction techniques. However, a built fingerprint image might appear to be truncated and distorted when the finger was swept across a fingerprint sensor at a non-linear speed. If the truncated fingerprint images were enrolled as reference targets and collected by any automated fingerprint identification system (AFIS), successful prediction rates for fingerprint matching applications would be decreased significantly. In this paper, a novel and effective methodology with low time computational complexity was developed for detecting truncated fingerprints in a real time manner. Several filtering rules were implemented to validate existences of truncated fingerprints. In addition, a machine learning method of supported vector machine (SVM), based on the principle of structural risk minimization, was applied to reject pseudo truncated fingerprints containing similar characteristics of truncated ones. The experimental result has shown that an accuracy rate of 90.7% was achieved by successfully identifying truncated fingerprint images from testing images before AFIS enrollment procedures. The proposed effective and efficient methodology can be extensively applied to all existing fingerprint matching systems as a preliminary quality control prior to construction of fingerprint templates. PMID:25835186
Chen, Chi-Jim; Pai, Tun-Wen; Cheng, Mox
2015-01-01
A sweeping fingerprint sensor converts fingerprints on a row by row basis through image reconstruction techniques. However, a built fingerprint image might appear to be truncated and distorted when the finger was swept across a fingerprint sensor at a non-linear speed. If the truncated fingerprint images were enrolled as reference targets and collected by any automated fingerprint identification system (AFIS), successful prediction rates for fingerprint matching applications would be decreased significantly. In this paper, a novel and effective methodology with low time computational complexity was developed for detecting truncated fingerprints in a real time manner. Several filtering rules were implemented to validate existences of truncated fingerprints. In addition, a machine learning method of supported vector machine (SVM), based on the principle of structural risk minimization, was applied to reject pseudo truncated fingerprints containing similar characteristics of truncated ones. The experimental result has shown that an accuracy rate of 90.7% was achieved by successfully identifying truncated fingerprint images from testing images before AFIS enrollment procedures. The proposed effective and efficient methodology can be extensively applied to all existing fingerprint matching systems as a preliminary quality control prior to construction of fingerprint templates. PMID:25835186
Unstructured mesh generation and adaptivity
NASA Technical Reports Server (NTRS)
Mavriplis, D. J.
1995-01-01
An overview of current unstructured mesh generation and adaptivity techniques is given. Basic building blocks taken from the field of computational geometry are first described. Various practical mesh generation techniques based on these algorithms are then constructed and illustrated with examples. Issues of adaptive meshing and stretched mesh generation for anisotropic problems are treated in subsequent sections. The presentation is organized in an education manner, for readers familiar with computational fluid dynamics, wishing to learn more about current unstructured mesh techniques.
Dimerization of truncated melittin analogues results in cytolytic peptides.
Rivett, D E; Kirkpatrick, A; Hewish, D R; Reilly, W; Werkmeister, J A
1996-01-01
A synthetic peptide with the sequence of the first 20 residues of melittin and terminating with an additional cysteine amide was found to have cytolytic activity similar to that of melittin. It was apparent from MS data that the cysteine-terminating peptides had formed disulphide dimers. A peptide in which the thiol was blocked by iodoacetate showed no activity, whereas the same peptide blocked by acetamidomethyl showed activity marginally less haemolytic than that of melittin. Cytolytic activity of melittin analogues comprising the full 26 residues could be obtained with wide sequence permutations providing that a general amphipathic helical structure was preserved. In contrast, the activity of the dimers was dependent not only on retention of an amphipathic helix but also on certain individual residues and a free positive charge. A free N-terminus was essential for haemolytic activity. In addition, a lysine or arginine residue at position 7 and a proline at position 14 were found to be necessary for activity, although it was apparent that additional residues are important for retention of the full lytic potential. PMID:8687396
Jennings, Matthew J; Barrios, Adam F; Tan, Song
2016-05-01
Undesirable truncated recombinant protein products pose a special expression and purification challenge because such products often share similar chromatographic properties as the desired full length protein. We describe here our observation of both full length and a truncated form of a yeast protein (Gcn5) expressed in Escherichia coli, and the reduction or elimination of the truncated form by mutating a cryptic Shine-Dalgarno or START codon within the Gcn5 coding region. Unsuccessful attempts to engineer in a cryptic translation initiation site into other recombinant proteins suggest that cryptic Shine-Dalgarno or START codon sequences are necessary but not sufficient for cryptic translation in E. coli. PMID:26739786
NASA Astrophysics Data System (ADS)
Accioly, Antonio; Gaete, Patricio; Helaÿel-Neto, José A.
We calculate the lowest-order corrections to the static potential for both the generalized Born-Infeld electrodynamics and an Euler-Heisenberg-like model, in the presence of a constant external magnetic field. Our analysis is carried out within the framework of the gauge-invariant but path-dependent variables formalism. The calculation reveals a long-range correction ((1)/(r5)-type) to the Coulomb potential for the generalized Born-Infeld electrodynamics. Interestingly enough, in the Euler-Heisenberg-like model, the static potential remains Coulombian. Therefore, contrary to popular belief, the quantized truncated action and the truncated quantized action do not commute at all.
Adaptations to training at the individual anaerobic threshold.
Keith, S P; Jacobs, I; McLellan, T M
1992-01-01
The individual anaerobic threshold (Th(an)) is the highest metabolic rate at which blood lactate concentrations can be maintained at a steady-state during prolonged exercise. The purpose of this study was to test the hypothesis that training at the Th(an) would cause a greater change in indicators of training adaptation than would training "around" the Th(an). Three groups of subjects were evaluated before, and again after 4 and 8 weeks of training: a control group, a group which trained continuously for 30 min at the Th(an) intensity (SS), and a group (NSS) which divided the 30 min of training into 7.5-min blocks at intensities which alternated between being below the Th(an) [Th(an) -30% of the difference between Th(an) and maximal oxygen consumption (VO2max)] and above the Th(an) (Th(an) +30% of the difference between Th(an) and VO2max). The VO2max increased significantly from 4.06 to 4.27 l.min-1 in SS and from 3.89 to 4.06 l.min-1 in NSS. The power output (W) at Th(an) increased from 70.5 to 79.8% VO2max in SS and from 71.1 to 80.7% VO2max in NSS. The magnitude of change in VO2max, W at Th(an), % VO2max at Th(an) and in exercise time to exhaustion at the pretraining Th(an) was similar in both trained groups. Vastus lateralis citrate synthase and 3-hydroxyacyl-CoA-dehydrogenase activities increased to the same extent in both trained groups. While all of these training-induced adaptations were statistically significant (P < 0.05), there were no significant changes in any of these variables for the control subjects.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1425631
Adaptive management is an approach to natural resource management that emphasizes learning through management where knowledge is incomplete, and when, despite inherent uncertainty, managers and policymakers must act. Unlike a traditional trial and error approach, adaptive managem...
Impression block with orientator
NASA Astrophysics Data System (ADS)
Brilin, V. I.; Ulyanova, O. S.
2015-02-01
Tool review, namely the impression block, applied to check the shape and size of the top of fish as well as to determine the appropriate tool for fishing operation was realized. For multiple application and obtaining of the impress depth of 3 cm and more, the standard volumetric impression blocks with fix rods are used. However, the registered impress of fish is not oriented in space and the rods during fishing are in the extended position. This leads to rods deformation and sinking due to accidental impacts of impression block over the borehole irregularity and finally results in faulty detection of the top end of fishing object in hole. The impression blocks with copy rods and fixed magnetic needle allow estimating the object configuration and fix the position of magnetic needle determining the position of the top end of object in hole. However, the magnetic needle fixation is realized in staged and the rods are in extended position during fishing operations as well as it is in standard design. The most efficient tool is the impression block with copy rods which directs the examined object in the borehole during readings of magnetic needles data from azimuth plate and averaging of readings. This significantly increases the accuracy of fishing toll direction. The rods during fishing are located in the body and extended only when they reach the top of fishing object.
Systematic renormalization scheme in light-front dynamics with Fock space truncation
Karmanov, V. A.; Smirnov, A. V.; Mathiot, J.-F.
2008-04-15
Within the framework of the covariant formulation of light-front dynamics, we develop a general nonperturbative renormalization scheme based on the Fock decomposition of the state vector and its truncation. The counterterms and bare parameters needed to renormalize the theory depend on the Fock sectors. We present a general strategy in order to calculate these quantities, as well as state vectors of physical systems, in a truncated Fock space. The explicit dependence of our formalism on the orientation of the light-front plane is essential in order to analyze the structure of the counterterms. We apply our formalism to the two-body (one fermion and one boson) truncation in the Yukawa model and in QED, and to the three-body truncation in a scalar model. In QED, we recover analytically, without any perturbative expansion, the renormalization of the electric charge, according to the requirements of the Ward identity.
NASA Technical Reports Server (NTRS)
Thomas-Keprta, Kathie L.; Clemett, Simon J.; Bazylinski, Dennis A.; Kirschvink, Joseph L.; McKay, David S.; Wentworth, Susan J.; Vali, H.; Gibson, Everett K.
2001-01-01
We suggest that the observation of truncated hexa-octahedral magnetites in ALH84001 are both consistent with, and in the absence of terrestrial inorganic analogs, likely formed by biogenic processes. Additional information is contained in the original extended abstract.
A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis
Rivas, Manuel A.; Graham, Daniel; Sulem, Patrick; Stevens, Christine; Desch, A. Nicole; Goyette, Philippe; Gudbjartsson, Daniel; Jonsdottir, Ingileif; Thorsteinsdottir, Unnur; Degenhardt, Frauke; Mucha, Sören; Kurki, Mitja I.; Li, Dalin; D'Amato, Mauro; Annese, Vito; Vermeire, Severine; Weersma, Rinse K.; Halfvarson, Jonas; Paavola-Sakki, Paulina; Lappalainen, Maarit; Lek, Monkol; Cummings, Beryl; Tukiainen, Taru; Haritunians, Talin; Halme, Leena; Koskinen, Lotta L. E.; Ananthakrishnan, Ashwin N.; Luo, Yang; Heap, Graham A.; Visschedijk, Marijn C.; Barrett, J; de Lange, K; Edwards, C; Hart, A; Hawkey, C; Jostins, L; Kennedy, N; Lamb, C; Lee, J; Lees, C; Mansfield, J; Mathew, C; Mowatt, C; Newman, W; Nimmo, E; Parkes, M; Pollard, M; Prescott, N; Randall, J; Rice, D; Satsangi, J; Simmons, A; Tremelling, M; Uhlig, H; Wilson, D; Abraham, C; Achkar, J.P; Bitton, A; Boucher, G; Croitoru, K; Fleshner, P; Glas, J; Kugathasan, S; Limbergen, J.V; Milgrom, R; Proctor, D; Regueiro, M; Schumm, P.L; Sharma, Y; Stempak, J.M; Targan, S.R; Wang, M.H; MacArthur, Daniel G.; Neale, Benjamin M.; Ahmad, Tariq; Anderson, Carl A.; Brant, Steven R.; Duerr, Richard H.; Silverberg, Mark S.; Cho, Judy H; Palotie, Aarno; Saavalainen, Päivi; Kontula, Kimmo; Färkkilä, Martti; McGovern, Dermot P. B.; Franke, Andre; Stefansson, Kari; Rioux, John D.; Xavier, Ramnik J.; Daly, Mark J.; Barrett, J.; de Lane, K.; Edwards, C.; Hart, A.; Hawkey, C.; Jostins, L.; Kennedy, N.; Lamb, C.; Lee, J.; Lees, C.; Mansfield, J.; Mathew, C.; Mowatt, C.; Newman, B.; Nimmo, E.; Parkes, M.; Pollard, M.; Prescott, N.; Randall, J.; Rice, D.; Satsangi, J.; Simmons, A.; Tremelling, M.; Uhlig, H.; Wilson, D.; Abraham, C.; Achkar, J. P.; Bitton, A.; Boucher, G.; Croitoru, K.; Fleshner, P.; Glas, J.; Kugathasan, S.; Limbergen, J. V.; Milgrom, R.; Proctor, D.; Regueiro, M.; Schumm, P. L.; Sharma, Y.; Stempak, J. M.; Targan, S. R.; Wang, M. H.
2016-01-01
Protein-truncating variants protective against human disease provide in vivo validation of therapeutic targets. Here we used targeted sequencing to conduct a search for protein-truncating variants conferring protection against inflammatory bowel disease exploiting knowledge of common variants associated with the same disease. Through replication genotyping and imputation we found that a predicted protein-truncating variant (rs36095412, p.R179X, genotyped in 11,148 ulcerative colitis patients and 295,446 controls, MAF=up to 0.78%) in RNF186, a single-exon ring finger E3 ligase with strong colonic expression, protects against ulcerative colitis (overall P=6.89 × 10−7, odds ratio=0.30). We further demonstrate that the truncated protein exhibits reduced expression and altered subcellular localization, suggesting the protective mechanism may reside in the loss of an interaction or function via mislocalization and/or loss of an essential transmembrane domain. PMID:27503255
A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis.
Rivas, Manuel A; Graham, Daniel; Sulem, Patrick; Stevens, Christine; Desch, A Nicole; Goyette, Philippe; Gudbjartsson, Daniel; Jonsdottir, Ingileif; Thorsteinsdottir, Unnur; Degenhardt, Frauke; Mucha, Sören; Kurki, Mitja I; Li, Dalin; D'Amato, Mauro; Annese, Vito; Vermeire, Severine; Weersma, Rinse K; Halfvarson, Jonas; Paavola-Sakki, Paulina; Lappalainen, Maarit; Lek, Monkol; Cummings, Beryl; Tukiainen, Taru; Haritunians, Talin; Halme, Leena; Koskinen, Lotta L E; Ananthakrishnan, Ashwin N; Luo, Yang; Heap, Graham A; Visschedijk, Marijn C; MacArthur, Daniel G; Neale, Benjamin M; Ahmad, Tariq; Anderson, Carl A; Brant, Steven R; Duerr, Richard H; Silverberg, Mark S; Cho, Judy H; Palotie, Aarno; Saavalainen, Päivi; Kontula, Kimmo; Färkkilä, Martti; McGovern, Dermot P B; Franke, Andre; Stefansson, Kari; Rioux, John D; Xavier, Ramnik J; Daly, Mark J; Barrett, J; de Lane, K; Edwards, C; Hart, A; Hawkey, C; Jostins, L; Kennedy, N; Lamb, C; Lee, J; Lees, C; Mansfield, J; Mathew, C; Mowatt, C; Newman, B; Nimmo, E; Parkes, M; Pollard, M; Prescott, N; Randall, J; Rice, D; Satsangi, J; Simmons, A; Tremelling, M; Uhlig, H; Wilson, D; Abraham, C; Achkar, J P; Bitton, A; Boucher, G; Croitoru, K; Fleshner, P; Glas, J; Kugathasan, S; Limbergen, J V; Milgrom, R; Proctor, D; Regueiro, M; Schumm, P L; Sharma, Y; Stempak, J M; Targan, S R; Wang, M H
2016-01-01
Protein-truncating variants protective against human disease provide in vivo validation of therapeutic targets. Here we used targeted sequencing to conduct a search for protein-truncating variants conferring protection against inflammatory bowel disease exploiting knowledge of common variants associated with the same disease. Through replication genotyping and imputation we found that a predicted protein-truncating variant (rs36095412, p.R179X, genotyped in 11,148 ulcerative colitis patients and 295,446 controls, MAF=up to 0.78%) in RNF186, a single-exon ring finger E3 ligase with strong colonic expression, protects against ulcerative colitis (overall P=6.89 × 10(-7), odds ratio=0.30). We further demonstrate that the truncated protein exhibits reduced expression and altered subcellular localization, suggesting the protective mechanism may reside in the loss of an interaction or function via mislocalization and/or loss of an essential transmembrane domain. PMID:27503255
Truncation of tau at E391 Promotes Early Pathological Changes in Transgenic Mice
McMillan, Pamela J.; Kraemer, Brian C.; Robinson, Linda; Leverenz, James B.; Raskind, Murray; Schellenberg, Gerard
2011-01-01
Proteolytic cleavage of tau at glutamic acid 391 (E391) is linked to the pathogenesis of Alzheimer disease (AD). This C-terminal truncated tau species exists in neurofibrillary tangles and abnormal neurites in the brains of AD patients and may potentiate tau polymerization. We generated a mouse model that expresses human tau truncated at E391 to begin to elucidate the role of this C-terminal truncated tau species in the development of tau pathology. Our results show that truncated but otherwise wild type human tau is sufficient to drive pre-tangle pathological changes in tau, including accumulation of insoluble tau, somatodendritic redistribution, formation of pathological conformations, and dual phosphorylation of tau at sites associated with AD pathology. In addition, these mice exhibit atypical neuritic tau immunoreactivity, including abnormal neuritic processes and dystrophic neurites. These results suggest that changes in tau proteolysis can initiate tauopathy. PMID:22002427
Cao, Youfang; Terebus, Anna; Liang, Jie
2016-04-01
The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEGs), we truncate the state space by limiting the total molecular copy numbers in each MEG. We further describe a theoretical framework for analysis of the truncation error in the steady-state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of (1) the birth and death model, (2) the single gene expression model, (3) the genetic toggle switch model, and (4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady-state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate our theories. Overall, the novel state space
Cao, Youfang; Terebus, Anna; Liang, Jie
2016-01-01
The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEG), we truncate the state space by limiting the total molecular copy numbers in each MEG. We further describe a theoretical framework for analysis of the truncation error in the steady state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of 1) the birth and death model, 2) the single gene expression model, 3) the genetic toggle switch model, and 4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate out theories. Overall, the novel state space
Bactericidal block copolymer micelles.
Vyhnalkova, Renata; Eisenberg, Adi; van de Ven, Theo
2011-05-12
Block copolymer micelles with bactericidal properties were designed to deactivate pathogens such as E. coli bacteria. The micelles of PS-b-PAA and PS-b-P4VP block copolymers were loaded with biocides TCMTB or TCN up to 20 or 30 wt.-%, depending on the type of antibacterial agent. Bacteria were exposed to loaded micelles and bacterial deactivation was evaluated. The micelles loaded with TCN are bactericidal; bacteria are killed in less than two minutes of exposure. The most likely interpretation of the data is that the biocide is transferred to the bacteria by repeated micelle/bacteria contacts, and not via the solution. PMID:21275041
Immature truncated O-glycophenotype of cancer directly induces oncogenic features
Radhakrishnan, Prakash; Dabelsteen, Sally; Madsen, Frey Brus; Francavilla, Chiara; Kopp, Katharina L.; Steentoft, Catharina; Vakhrushev, Sergey Y.; Olsen, Jesper V.; Hansen, Lars; Bennett, Eric P.; Woetmann, Anders; Yin, Guangliang; Chen, Longyun; Song, Haiyan; Bak, Mads; Hlady, Ryan A.; Peters, Staci L.; Opavsky, Rene; Thode, Christenze; Qvortrup, Klaus; Schjoldager, Katrine T.-B. G.; Clausen, Henrik; Hollingsworth, Michael A.; Wandall, Hans H.
2014-01-01
Aberrant expression of immature truncated O-glycans is a characteristic feature observed on virtually all epithelial cancer cells, and a very high frequency is observed in early epithelial premalignant lesions that precede the development of adenocarcinomas. Expression of the truncated O-glycan structures Tn and sialyl-Tn is strongly associated with poor prognosis and overall low survival. The genetic and biosynthetic mechanisms leading to accumulation of truncated O-glycans are not fully understood and include mutation or dysregulation of glycosyltransferases involved in elongation of O-glycans, as well as relocation of glycosyltransferases controlling initiation of O-glycosylation from Golgi to endoplasmic reticulum. Truncated O-glycans have been proposed to play functional roles for cancer-cell invasiveness, but our understanding of the biological functions of aberrant glycosylation in cancer is still highly limited. Here, we used exome sequencing of most glycosyltransferases in a large series of primary and metastatic pancreatic cancers to rule out somatic mutations as a cause of expression of truncated O-glycans. Instead, we found hypermethylation of core 1 β3-Gal-T-specific molecular chaperone, a key chaperone for O-glycan elongation, as the most prevalent cause. We next used gene editing to produce isogenic cell systems with and without homogenous truncated O-glycans that enabled, to our knowledge, the first polyomic and side-by-side evaluation of the cancer O-glycophenotype in an organotypic tissue model and in xenografts. The results strongly suggest that truncation of O-glycans directly induces oncogenic features of cell growth and invasion. The study provides support for targeting cancer-specific truncated O-glycans with immunotherapeutic measures. PMID:25118277
Quark-hadron duality and truncated moments of nucleon structure functions
Psaker, A.; Melnitchouk, W.; Christy, M. E.; Keppel, C.
2008-08-15
We employ a novel new approach to study local quark-hadron duality using 'truncated' moments, or integrals of structure functions over restricted regions of x, to determine the degree to which individual resonance regions are dominated by leading twist. Because truncated moments obey the same Q{sup 2} evolution equations as the leading twist parton distributions, this approach makes possible for the first time a description of resonance region data and the phenomenon of quark-hadron duality directly from QCD.
The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome.
Bartha, István; Rausell, Antonio; McLaren, Paul J; Mohammadi, Pejman; Tardaguila, Manuel; Chaturvedi, Nimisha; Fellay, Jacques; Telenti, Amalio
2015-12-01
Sequencing projects have identified large numbers of rare stop-gain and frameshift variants in the human genome. As most of these are observed in the heterozygous state, they test a gene's tolerance to haploinsufficiency and dominant loss of function. We analyzed the distribution of truncating variants across 16,260 autosomal protein coding genes in 11,546 individuals. We observed 39,893 truncating variants affecting 12,062 genes, which significantly differed from an expectation of 12,916 genes under a model of neutral de novo mutation (p<10-4). Extrapolating this to increasing numbers of sequenced individuals, we estimate that 10.8% of human genes do not tolerate heterozygous truncating variants. An additional 10 to 15% of truncated genes may be rescued by incomplete penetrance or compensatory mutations, or because the truncating variants are of limited functional impact. The study of protein truncating variants delineates the essential genome and, more generally, identifies rare heterozygous variants as an unexplored source of diversity of phenotypic traits and diseases. PMID:26642228
Truncation model in the triple-degenerate derivative nonlinear Schroedinger equation
Sanchez-Arriaga, G.; Hada, T.; Nariyuki, Y.
2009-04-15
The triple-degenerate derivative nonlinear Schroedinger (TDNLS) system modified with resistive wave damping and growth is truncated to study the coherent coupling of four waves, three Alfven and one acoustic, near resonance. In the conservative case, the truncation equations derive from a time independent Hamiltonian function with two degrees of freedom. Using a Poincare map analysis, two parameters regimes are explored. In the first regime we check how the modulational instability of the TDNLS system affects to the dynamics of the truncation model, while in the second one the exact triple degenerated case is discussed. In the dissipative case, the truncation model gives rise to a six dimensional flow with five free parameters. Computing some bifurcation diagrams the dependence with the sound to Alfven velocity ratio as well as the Alfven modes involved in the truncation is analyzed. The system exhibits a wealth of dynamics including chaotic attractor, several kinds of bifurcations, and crises. The truncation model was compared to numerical integrations of the TDNLS system.
Truncated tau deregulates synaptic markers in rat model for human tauopathy
Jadhav, Santosh; Katina, Stanislav; Kovac, Andrej; Kazmerova, Zuzana; Novak, Michal; Zilka, Norbert
2015-01-01
Synaptic failure and neurofibrillary degeneration are two major neuropathological substrates of cognitive dysfunction in Alzheimer’s disease (AD). Only a few studies have demonstrated a direct relationship between these two AD hallmarks. To investigate tau mediated synaptic injury we used rat model of tauopathy that develops extensive neurofibrillary pathology in the cortex. Using fractionation of cortical synapses, we identified an increase in endogenous rat tau isoforms in presynaptic compartment, and their mis-sorting to the postsynaptic density (PSD). Truncated transgenic tau was distributed in both compartments exhibiting specific phospho-pattern that was characteristic for each synaptic compartment. In the presynaptic compartment, truncated tau was associated with impairment of dynamic stability of microtubules which could be responsible for reduction of synaptic vesicles. In the PSD, truncated tau lowered the levels of neurofilaments. Truncated tau also significantly decreased the synaptic levels of Aβ40 but not Aβ42. These data show that truncated tau differentially deregulates synaptic proteome in pre- and postsynaptic compartments. Importantly, we show that alteration of Aβ can arise downstream of truncated tau pathology. PMID:25755633
Volume-of-interest reconstruction from severely truncated data in dental cone-beam CT
NASA Astrophysics Data System (ADS)
Zhang, Zheng; Kusnoto, Budi; Han, Xiao; Sidky, E. Y.; Pan, Xiaochuan
2015-03-01
As cone-beam computed tomography (CBCT) has gained popularity rapidly in dental imaging applications in the past two decades, radiation dose in CBCT imaging remains a potential, health concern to the patients. It is a common practice in dental CBCT imaging that only a small volume of interest (VOI) containing the teeth of interest is illuminated, thus substantially lowering imaging radiation dose. However, this would yield data with severe truncations along both transverse and longitudinal directions. Although images within the VOI reconstructed from truncated data can be of some practical utility, they often are compromised significantly by truncation artifacts. In this work, we investigate optimization-based reconstruction algorithms for VOI image reconstruction from CBCT data of dental patients containing severe truncations. In an attempt to further reduce imaging dose, we also investigate optimization-based image reconstruction from severely truncated data collected at projection views substantially fewer than those used in clinical dental applications. Results of our study show that appropriately designed optimization-based reconstruction can yield VOI images with reduced truncation artifacts, and that, when reconstructing from only one half, or even one quarter, of clinical data, it can also produce VOI images comparable to that of clinical images.
The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome
McLaren, Paul J.; Mohammadi, Pejman; Tardaguila, Manuel; Chaturvedi, Nimisha; Fellay, Jacques; Telenti, Amalio
2015-01-01
Sequencing projects have identified large numbers of rare stop-gain and frameshift variants in the human genome. As most of these are observed in the heterozygous state, they test a gene’s tolerance to haploinsufficiency and dominant loss of function. We analyzed the distribution of truncating variants across 16,260 autosomal protein coding genes in 11,546 individuals. We observed 39,893 truncating variants affecting 12,062 genes, which significantly differed from an expectation of 12,916 genes under a model of neutral de novo mutation (p<10−4). Extrapolating this to increasing numbers of sequenced individuals, we estimate that 10.8% of human genes do not tolerate heterozygous truncating variants. An additional 10 to 15% of truncated genes may be rescued by incomplete penetrance or compensatory mutations, or because the truncating variants are of limited functional impact. The study of protein truncating variants delineates the essential genome and, more generally, identifies rare heterozygous variants as an unexplored source of diversity of phenotypic traits and diseases. PMID:26642228
Semiparametric likelihood inference for left-truncated and right-censored data.
Huang, Chiung-Yu; Ning, Jing; Qin, Jing
2015-10-01
This paper proposes a new estimation procedure for the survival time distribution with left-truncated and right-censored data, where the distribution of the truncation time is known up to a finite-dimensional parameter vector. The paper expands on the Vardis multiplicative censoring model (Vardi, 1989. Multiplicative censoring, renewal processes, deconvolution and decreasing density: non-parametric estimation. Biometrika 76: , 751-761), establishes the connection between the likelihood under a generalized multiplicative censoring model and that for left-truncated and right-censored survival time data, and derives an Expectation-Maximization algorithm for model estimation. A formal test for checking the truncation time distribution is constructed based on the semiparametric likelihood ratio test statistic. In particular, testing the stationarity assumption that the underlying truncation time is uniformly distributed is performed by embedding the null uniform truncation time distribution in a smooth alternative (Neyman, 1937. Smooth test for goodness of fit. Skandinavisk Aktuarietidskrift 20: , 150-199). Asymptotic properties of the proposed estimator are established. Simulations are performed to evaluate the finite-sample performance of the proposed methods. The methods and theories are illustrated by analyzing the Canadian Study of Health and Aging and the Channing House data, where the stationarity assumption with respect to disease incidence holds for the former but not the latter. PMID:25796430
ERIC Educational Resources Information Center
Moore, Gary T.
1997-01-01
Discusses the importance of block play--including its contributions to perceptual, fine motor, and cognitive development--and components of a good preschool block play area. Recommends unit blocks complemented by stacking blocks, toys, beads, cubes, and Brio wooden toys. Makes recommendations for space, size, locations and connections to other…